From marci... at gmail.com Wed Feb 1 06:55:21 2017 From: marci... at gmail.com (Marcella Iannuzzi) Date: Tue, 31 Jan 2017 22:55:21 -0800 (PST) Subject: Distance colvar using Centre-of-Mass In-Reply-To: <4427a1b3-4696-4533-acc0-d5619d8fa8ef@googlegroups.com> References: <4427a1b3-4696-4533-acc0-d5619d8fa8ef@googlegroups.com> Message-ID: <2fd227c2-ef77-46f2-a810-c68bc41f826b@googlegroups.com> Hi, you can define a point as geometric center of a subset of atoms. regards Marcella On Tuesday, January 31, 2017 at 5:08:02 PM UTC+1, cjor wrote: > > Hello, > > Is there a way to code a centre-of-mass point in CP2K. > > > I want to use a distance colvar, *not *a distance to a plane etc. > > > ? > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mariella... at gmail.com Wed Feb 1 08:40:21 2017 From: mariella... at gmail.com (Mariella Ippolito) Date: Wed, 1 Feb 2017 00:40:21 -0800 (PST) Subject: proplem with cp2k built with intelmpi Message-ID: <3e159718-be6e-49c9-bc64-6d52bf879292@googlegroups.com> Dear all, I find some problems in running qs calculations with cp2K 4.1 compiled with intelmpi-2017 (the same run goes fine with the executable obtained with openmpi-gnu compiler). In particular in output I obtain ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ Trace(PS): 1200.0000000051 Electronic density on regular grids: NaN NaN Core density on regular grids: 1200.0000000000 -0.0000000000 Total charge density on r-space grids: NaN Total charge density g-space grids: -5.8357006210 Unlike the code compiled with openmpi-gnu gives: ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ Trace(PS): 1199.9999998902 Electronic density on regular grids: -1199.9999998901 0.0000001099 Core density on regular grids: 1199.9999999999 -0.0000000001 Total charge density on r-space grids: 0.0000001098 Total charge density g-space grids: 0.0000001099 Clearly there is something wrong with the quantities Electronic density on regular grids Total charge density on r-space grids Looking at the source code I find that the problem may come from the quantities tot_tho_r and tot_rho_r_arr, in qs_ks_utils.F Line 855 in qs_ks_utils.F CALL qs_rho_get(rho, tot_rho_r=tot_rho_r_arr, rho_ao_kp=rho_ao) If I print tot_rho_r_arr after this call I obtain NaN for both its components and as consequences also tot_rho_r = accurate_sum(tot_rho_r_arr) is NaN while if I run the executable gnu it gives the right value tot_rho_r = accurate_sum(tot_rho_r_arr) =- 1199.99999989 I attach the restart file used for the calculations. Can you help me to fix this problem? Best regards, Mariella -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: md.restart Type: application/octet-stream Size: 17530 bytes Desc: not available URL: From i.be... at epcc.ed.ac.uk Wed Feb 1 08:47:06 2017 From: i.be... at epcc.ed.ac.uk (Iain Bethune) Date: Wed, 1 Feb 2017 08:47:06 +0000 Subject: [CP2K:8615] proplem with cp2k built with intelmpi In-Reply-To: <3e159718-be6e-49c9-bc64-6d52bf879292@googlegroups.com> References: <3e159718-be6e-49c9-bc64-6d52bf879292@googlegroups.com> Message-ID: <81616B0E-F075-42E0-92A9-AAC08642467F@epcc.ed.ac.uk> Dear Mariella, As per some recent discussions about Intel 2017 on this discussion forum, it looks like some bug(s) existing in MKL 2017.1.143. The compiler and MPI library in this release appear to be OK, but you will need to use a previous MKL version. I don?t know if you have had successful Intel builds before, but there are several files which need to be compiled a lower optimisation to work around compiler. There are a set of arch files which are known to be working with the CP2K trunk available via the CP2K dashboard - see e.g. http://cp2k-www.epcc.ed.ac.uk/phi/psmp/regtest-arch (linked from http://dashboard.cp2k.org Cheers - Iain -- Iain Bethune Project Manager, EPCC Email: i.be... at epcc.ed.ac.uk Twitter: @IainBethune @PrimeGrid @CP2Kproject Web: http://www2.epcc.ed.ac.uk/~ibethune Tel/Fax: +44 (0)131 651 7183/6555 Mob: +44 (0)7598317015 Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD > On 1 Feb 2017, at 08:40, Mariella Ippolito wrote: > > Dear all, > I find some problems in running qs calculations with cp2K 4.1 compiled with intelmpi-2017 (the same run goes fine with the executable obtained with openmpi-gnu compiler). > In particular in output I obtain > > ----------------------------------- OT --------------------------------------- > > Step Update method Time Convergence Total energy Change > ------------------------------------------------------------------------------ > > Trace(PS): 1200.0000000051 > Electronic density on regular grids: NaN NaN > Core density on regular grids: 1200.0000000000 -0.0000000000 > Total charge density on r-space grids: NaN > Total charge density g-space grids: -5.8357006210 > > Unlike the code compiled with openmpi-gnu gives: > > ----------------------------------- OT --------------------------------------- > > Step Update method Time Convergence Total energy Change > ------------------------------------------------------------------------------ > > Trace(PS): 1199.9999998902 > Electronic density on regular grids: -1199.9999998901 0.0000001099 > Core density on regular grids: 1199.9999999999 -0.0000000001 > Total charge density on r-space grids: 0.0000001098 > Total charge density g-space grids: 0.0000001099 > > Clearly there is something wrong with the quantities > Electronic density on regular grids > Total charge density on r-space grids > > Looking at the source code I find that the problem may come from the quantities tot_tho_r and tot_rho_r_arr, in qs_ks_utils.F > > Line 855 in qs_ks_utils.F > CALL qs_rho_get(rho, tot_rho_r=tot_rho_r_arr, rho_ao_kp=rho_ao) > > If I print tot_rho_r_arr after this call I obtain NaN for both its components > and as consequences also > tot_rho_r = accurate_sum(tot_rho_r_arr) > is NaN > while if I run the executable gnu it gives the right value > tot_rho_r = accurate_sum(tot_rho_r_arr) =- 1199.99999989 > > I attach the restart file used for the calculations. > > Can you help me to fix this problem? > > Best regards, > Mariella > > -- > You received this message because you are subscribed to the Google Groups "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From i.be... at epcc.ed.ac.uk Wed Feb 1 09:51:44 2017 From: i.be... at epcc.ed.ac.uk (Iain Bethune) Date: Wed, 1 Feb 2017 09:51:44 +0000 Subject: [CP2K:8603] error in qs_ks_methods.F depending on number of cores (intel compiler) In-Reply-To: References: <8BEC3126-9A5F-4368-A114-B46A939ABA4C@epcc.ed.ac.uk> <6C993206-9797-493D-BA6B-0331BBF58BA7@epcc.ed.ac.uk> Message-ID: <6FA71BB7-20E6-47B6-A0ED-BBAD3E93CF52@epcc.ed.ac.uk> Hi Laurent, I can confirm that the problem with the energy going to NaN that you observed is indeed specific to the Intel compiler (at least it works for me with a local gfortran run). I think however there is also that there some issue (or at least numerical difficulty) with your input, since I observe that the total energy actually increases in the second SCF step, when it should be strictly decreasing when using OT. Maybe someone else can spot the problem? - Iain -- Iain Bethune Project Manager, EPCC Email: i.be... at epcc.ed.ac.uk Twitter: @IainBethune @PrimeGrid @CP2Kproject Web: http://www2.epcc.ed.ac.uk/~ibethune Tel/Fax: +44 (0)131 651 7183/6555 Mob: +44 (0)7598317015 Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD > On 29 Jan 2017, at 16:41, Laurent Joly wrote: > > Hi Iain, > > Thank you again for your help. > >> Further to what I reported this morning, I found that the MKL release 2017.1.132 is buggy. I was able to get a successful build using the compiler from the 2017.1.132 release and MKL from the previous (2017.0.098) release. > > I asked our local administrator if it was possible to install the > previous version of the intel compiler, or at least of the MKL > libraries. > >>> I got hold of the 2017.1.132 release and ran a regtest of the latest trunk code. Barring one regtest with numerical problems, it ran fine, so I don?t think there is something fundamentally broken with that version. Could you send your input file, and try running with the GLOBAL%PRINT_LEVEL HIGH so some more information is printed out before the error occurs? Maybe someone can spot the problem. Did you have any success running this input with previous builds of CP2K? > > Please find enclosed the input and ouput files obtained with > GLOBAL%PRINT_LEVEL HIGH. I tried with CP2K version 4.1 and 3.0 and got > similar results... > > Hopefully I will soon have access to the previous MKL release, and > keep you informed. In the meantime, I'm using a gfortran+acml > compilation, which runs fine (although more slowly)... > > Best regards, > Laurent > > >>>> On 19 Jan 2017, at 17:56, Laurent Joly wrote: >>>> >>>> Hi Iain, >>>> >>>> Thank you very much for your fast answer. >>>> >>>> I tried a simplified version of the arch file you sent (enclosed >>>> raptor2.psmp), but I keep getting the same behavior. I also tried to >>>> compile all the files with -O1 (enclosed raptor1.psmp and >>>> Linux-x86-64-intel-mic.psmp), or even -O0 (enclosed raptor3.psmp), but >>>> here again it makes no difference. >>>> >>>> When I try to run the regtests, the system hangs after printing >>>> "Copying tests into working directory ... done!"... But possibly this >>>> is another problem... >>>> >>>> Best regards, >>>> Laurent >>>> >>>> >>>> 2017-01-19 14:57 GMT+00:00 Iain Bethune : >>>>> Hi Laurent, >>>>> >>>>> We don?t have experience yet with exactly that version (ifort 17.0.1), but with the 17.0.0 compiler we find that a couple of files need to be built at reduced optimisation level - see https://dashboard.cp2k.org/archive/epcc-phi-psmp/rev_17693.txt for an example arch file which is working. >>>>> >>>>> Were you able to run the CP2K regression tests with success? >>>>> >>>>> Cheers >>>>> >>>>> - Iain >>>>> >>>>> -- >>>>> >>>>> Iain Bethune >>>>> Project Manager, EPCC >>>>> >>>>> Email: i.be... at epcc.ed.ac.uk >>>>> Twitter: @IainBethune @PrimeGrid @CP2Kproject >>>>> Web: http://www2.epcc.ed.ac.uk/~ibethune >>>>> Tel/Fax: +44 (0)131 651 7183/6555 >>>>> Mob: +44 (0)7598317015 >>>>> Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD >>>>> >>>>>> On 19 Jan 2017, at 14:51, Laurent Joly wrote: >>>>>> >>>>>> Dear all, >>>>>> >>>>>> I've been trying to compile CP2K 4.1 (I also tried with the 3.0 version) using the intel compiler version 2017.1.132. >>>>>> >>>>>> I used the Linux-x86-64-intel-host.popt and Linux-x86-64-intel-host.psmp arch files, and I had to modify the Linux-x86-64-intel-mic.psmp file following the instructions of the intel mkl link line advisor: https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor to make it work: >>>>>> >>>>>> $ diff Linux-x86-64-intel-mic.psmp.backup Linux-x86-64-intel-mic.psmp >>>>>> 231d230 >>>>>> < $(MKLROOT)/lib/intel64/libmkl_core.a \ >>>>>> 233,234c232,234 >>>>>> < -Wl,--end-group \ >>>>>> < $(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a >>>>>> --- >>>>>>> $(MKLROOT)/lib/intel64/libmkl_core.a \ >>>>>>> $(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a \ >>>>>>> -Wl,--end-group >>>>>> >>>>>> Then I had to run: ulimit -s unlimited in order to get rid of segmentation faults, and finally it worked... on 16 cores, but as soon as I tried to increase the number of cores I got this error message: >>>>>> >>>>>> KS energy is an abnormal value (NaN/Inf). >>>>>> qs_ks_methods.F:785 >>>>>> >>>>>> I enclose the complete output. Do you have some ideas on what could be the problem? >>>>>> >>>>>> Best regards, >>>>>> Laurent >>>>>> >>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google Groups "cp2k" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. >>>>>> To post to this group, send email to cp... at googlegroups.com. >>>>>> Visit this group at https://groups.google.com/group/cp2k. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> >>>>> >>>>> -- >>>>> The University of Edinburgh is a charitable body, registered in >>>>> Scotland, with registration number SC005336. >>>>> >>>>> -- >>>>> You received this message because you are subscribed to a topic in the Google Groups "cp2k" group. >>>>> To unsubscribe from this topic, visit https://groups.google.com/d/topic/cp2k/C2FO7VAUZEg/unsubscribe. >>>>> To unsubscribe from this group and all its topics, send an email to cp2k+uns... at googlegroups.com. >>>>> To post to this group, send email to cp... at googlegroups.com. >>>>> Visit this group at https://groups.google.com/group/cp2k. >>>>> For more options, visit https://groups.google.com/d/optout. >>>> >>>> >>>> >>>> -- >>>> Laurent JOLY >>>> >>>> Institut Lumi?re Mati?re - Universit? Lyon 1 >>>> Campus de la Doua, b?timent Brillouin >>>> 43 bd du 11 novembre 1918 >>>> 69622 Villeurbanne Cedex, France >>>> >>>> T?l: 04 724 326 11 - Fax: 04 724 326 48 >>>> Web: http://ilm-perso.univ-lyon1.fr/~ljoly/ >>>> >>>> -- >>>> You received this message because you are subscribed to the Google Groups "cp2k" group. >>>> To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. >>>> To post to this group, send email to cp... at googlegroups.com. >>>> Visit this group at https://groups.google.com/group/cp2k. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> -- >> You received this message because you are subscribed to a topic in the Google Groups "cp2k" group. >> To unsubscribe from this topic, visit https://groups.google.com/d/topic/cp2k/C2FO7VAUZEg/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to cp2k+uns... at googlegroups.com. >> To post to this group, send email to cp... at googlegroups.com. >> Visit this group at https://groups.google.com/group/cp2k. >> For more options, visit https://groups.google.com/d/optout. > > > > -- > Laurent JOLY > > Institut Lumi?re Mati?re - Universit? Lyon 1 > Campus de la Doua, b?timent Brillouin > 43 bd du 11 novembre 1918 > 69622 Villeurbanne Cedex, France > > T?l: 04 724 326 11 - Fax: 04 724 326 48 > Web: http://ilm-perso.univ-lyon1.fr/~ljoly/ > > -- > You received this message because you are subscribed to the Google Groups "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From mariella... at gmail.com Wed Feb 1 10:53:14 2017 From: mariella... at gmail.com (Mariella Ippolito) Date: Wed, 1 Feb 2017 02:53:14 -0800 (PST) Subject: [CP2K:8615] proplem with cp2k built with intelmpi In-Reply-To: <81616B0E-F075-42E0-92A9-AAC08642467F@epcc.ed.ac.uk> References: <3e159718-be6e-49c9-bc64-6d52bf879292@googlegroups.com> <81616B0E-F075-42E0-92A9-AAC08642467F@epcc.ed.ac.uk> Message-ID: <15afa4fa-6b54-448f-96c9-981ece7bffd0@googlegroups.com> Dear Iain, Thank you for your quick answer! I also thought that the problem was related to the mkl library, so I have tried to build cp2k using Scalapack, lapack and blas libraries, and I also reduced the optimization trying both O1 O0, but that job continues to give problems. I try again using the previous version of mkl and your arch file. At the moment I'm using the branch version of cp2k, do you suggest to use the trunk? Thank you, Mariella On Wednesday, February 1, 2017 at 9:47:09 AM UTC+1, IBethune wrote: > > Dear Mariella, > > As per some recent discussions about Intel 2017 on this discussion forum, > it looks like some bug(s) existing in MKL 2017.1.143. The compiler and MPI > library in this release appear to be OK, but you will need to use a > previous MKL version. I don?t know if you have had successful Intel builds > before, but there are several files which need to be compiled a lower > optimisation to work around compiler. There are a set of arch files which > are known to be working with the CP2K trunk available via the CP2K > dashboard - see e.g. http://cp2k-www.epcc.ed.ac.uk/phi/psmp/regtest-arch > (linked from http://dashboard.cp2k.org > > Cheers > > - Iain > > -- > > Iain Bethune > Project Manager, EPCC > > Email: i.b... at epcc.ed.ac.uk > Twitter: @IainBethune @PrimeGrid @CP2Kproject > Web: http://www2.epcc.ed.ac.uk/~ibethune > Tel/Fax > : > +44 (0)131 651 7183/6555 > Mob: +44 (0)7598317015 > Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, > EH9 3FD > > > On 1 Feb 2017, at 08:40, Mariella Ippolito > wrote: > > > > Dear all, > > I find some problems in running qs calculations with cp2K 4.1 compiled > with intelmpi-2017 (the same run goes fine with the executable obtained > with openmpi-gnu compiler). > > In particular in output I obtain > > > > ----------------------------------- OT > --------------------------------------- > > > > Step Update method Time Convergence Total energy > Change > > > ------------------------------------------------------------------------------ > > > > > Trace(PS): 1200.0000000051 > > Electronic density on regular grids: NaN > NaN > > Core density on regular grids: 1200.0000000000 > -0.0000000000 > > Total charge density on r-space grids: NaN > > Total charge density g-space grids: -5.8357006210 > > > > Unlike the code compiled with openmpi-gnu gives: > > > > ----------------------------------- OT > --------------------------------------- > > > > Step Update method Time Convergence Total energy > Change > > > ------------------------------------------------------------------------------ > > > > > Trace(PS): 1199.9999998902 > > Electronic density on regular grids: -1199.9999998901 > 0.0000001099 > > Core density on regular grids: 1199.9999999999 > -0.0000000001 > > Total charge density on r-space grids: 0.0000001098 > > Total charge density g-space grids: 0.0000001099 > > > > Clearly there is something wrong with the quantities > > Electronic density on regular grids > > Total charge density on r-space grids > > > > Looking at the source code I find that the problem may come from the > quantities tot_tho_r and tot_rho_r_arr, in qs_ks_utils.F > > > > Line 855 in qs_ks_utils.F > > CALL qs_rho_get(rho, tot_rho_r=tot_rho_r_arr, rho_ao_kp=rho_ao) > > > > If I print tot_rho_r_arr after this call I obtain NaN for both its > components > > and as consequences also > > tot_rho_r = accurate_sum(tot_rho_r_arr) > > is NaN > > while if I run the executable gnu it gives the right value > > tot_rho_r = accurate_sum(tot_rho_r_arr) =- 1199.99999989 > > > > I attach the restart file used for the calculations. > > > > Can you help me to fix this problem? > > > > Best regards, > > Mariella > > > > -- > > You received this message because you are subscribed to the Google > Groups "cp2k" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to cp2k+... at googlegroups.com . > > To post to this group, send email to cp... at googlegroups.com > . > > Visit this group at https://groups.google.com/group/cp2k. > > For more options, visit https://groups.google.com/d/optout. > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From chri... at gmail.com Wed Feb 1 11:27:19 2017 From: chri... at gmail.com (cjor) Date: Wed, 1 Feb 2017 03:27:19 -0800 (PST) Subject: Distance colvar using Centre-of-Mass In-Reply-To: <4427a1b3-4696-4533-acc0-d5619d8fa8ef@googlegroups.com> References: <4427a1b3-4696-4533-acc0-d5619d8fa8ef@googlegroups.com> Message-ID: Hi, thanks. Where is the point feature in the DISTANCE colvar? I can't find this option. I do NOT want a plane defined. &COLVAR &DISTANCE_POINT_PLANE &POINT TYPE GEO_CENTER ATOMS 1 &END &POINT TYPE GEO_CENTER ATOMS 48 &END &POINT TYPE GEO_CENTER ATOMS 60 &END &POINT TYPE GEO_CENTER ATOMS 69 70 &END ATOMS_PLANE 1 2 3 ATOM_POINT 4 &END DISTANCE_POINT_PLANE On Tuesday, 31 January 2017 16:08:02 UTC, cjor wrote: > > Hello, > > Is there a way to code a centre-of-mass point in CP2K. > > > I want to use a distance colvar, *not *a distance to a plane etc. > > > ? > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ljoly... at gmail.com Wed Feb 1 12:37:26 2017 From: ljoly... at gmail.com (Laurent Joly) Date: Wed, 1 Feb 2017 13:37:26 +0100 Subject: [CP2K:8618] error in qs_ks_methods.F depending on number of cores (intel compiler) In-Reply-To: <6FA71BB7-20E6-47B6-A0ED-BBAD3E93CF52@epcc.ed.ac.uk> References: <8BEC3126-9A5F-4368-A114-B46A939ABA4C@epcc.ed.ac.uk> <6C993206-9797-493D-BA6B-0331BBF58BA7@epcc.ed.ac.uk> <6FA71BB7-20E6-47B6-A0ED-BBAD3E93CF52@epcc.ed.ac.uk> Message-ID: Hi Iain, Our administrator installed the 2017.0 version of intel compiler and librairies. I compiled CP2K 4.1 with it and, although I still have to make more tests, it seems to be working. Regarding the behavior of the SCF, I'm using the DIIS minimizer. I'm not an expert on the OT method, but when I read in the manual: MINIMIZER MINIMIZER {Keyword} Minimizer to be used with the OT method This keyword cannot be repeated and it expects precisely one keyword. Default value: CG List of valid keywords: BROYDENBroyden mixing approximating the inverse Hessian CGConjugate Gradients: most reliable, use for difficult systems. The total energy should decrease at every OT CG step if the line search is appropriate. DIISDirect inversion in the iterative subspace: less reliable than CG, but sometimes about 50% faster SDSteepest descent: not recommended I understand that only with a CG minimizer and appropriate linesearch one should expect that the energy decreases at every timestep. Is it a generally expected property of the OT method? In any case, only the first SCF starting from an atomic density guess is slow to converge, and as soon as the MD is started, the SCF converges in roughly 10 iterations, which seems okay to me. Best regards, Laurent 2017-02-01 10:51 GMT+01:00 Iain Bethune : > Hi Laurent, > > I can confirm that the problem with the energy going to NaN that you observed is indeed specific to the Intel compiler (at least it works for me with a local gfortran run). I think however there is also that there some issue (or at least numerical difficulty) with your input, since I observe that the total energy actually increases in the second SCF step, when it should be strictly decreasing when using OT. Maybe someone else can spot the problem? > > - Iain > > -- > > Iain Bethune > Project Manager, EPCC > > Email: i.be... at epcc.ed.ac.uk > Twitter: @IainBethune @PrimeGrid @CP2Kproject > Web: http://www2.epcc.ed.ac.uk/~ibethune > Tel/Fax: +44 (0)131 651 7183/6555 > Mob: +44 (0)7598317015 > Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD > >> On 29 Jan 2017, at 16:41, Laurent Joly wrote: >> >> Hi Iain, >> >> Thank you again for your help. >> >>> Further to what I reported this morning, I found that the MKL release 2017.1.132 is buggy. I was able to get a successful build using the compiler from the 2017.1.132 release and MKL from the previous (2017.0.098) release. >> >> I asked our local administrator if it was possible to install the >> previous version of the intel compiler, or at least of the MKL >> libraries. >> >>>> I got hold of the 2017.1.132 release and ran a regtest of the latest trunk code. Barring one regtest with numerical problems, it ran fine, so I don?t think there is something fundamentally broken with that version. Could you send your input file, and try running with the GLOBAL%PRINT_LEVEL HIGH so some more information is printed out before the error occurs? Maybe someone can spot the problem. Did you have any success running this input with previous builds of CP2K? >> >> Please find enclosed the input and ouput files obtained with >> GLOBAL%PRINT_LEVEL HIGH. I tried with CP2K version 4.1 and 3.0 and got >> similar results... >> >> Hopefully I will soon have access to the previous MKL release, and >> keep you informed. In the meantime, I'm using a gfortran+acml >> compilation, which runs fine (although more slowly)... >> >> Best regards, >> Laurent >> >> >>>>> On 19 Jan 2017, at 17:56, Laurent Joly wrote: >>>>> >>>>> Hi Iain, >>>>> >>>>> Thank you very much for your fast answer. >>>>> >>>>> I tried a simplified version of the arch file you sent (enclosed >>>>> raptor2.psmp), but I keep getting the same behavior. I also tried to >>>>> compile all the files with -O1 (enclosed raptor1.psmp and >>>>> Linux-x86-64-intel-mic.psmp), or even -O0 (enclosed raptor3.psmp), but >>>>> here again it makes no difference. >>>>> >>>>> When I try to run the regtests, the system hangs after printing >>>>> "Copying tests into working directory ... done!"... But possibly this >>>>> is another problem... >>>>> >>>>> Best regards, >>>>> Laurent >>>>> >>>>> >>>>> 2017-01-19 14:57 GMT+00:00 Iain Bethune : >>>>>> Hi Laurent, >>>>>> >>>>>> We don?t have experience yet with exactly that version (ifort 17.0.1), but with the 17.0.0 compiler we find that a couple of files need to be built at reduced optimisation level - see https://dashboard.cp2k.org/archive/epcc-phi-psmp/rev_17693.txt for an example arch file which is working. >>>>>> >>>>>> Were you able to run the CP2K regression tests with success? >>>>>> >>>>>> Cheers >>>>>> >>>>>> - Iain >>>>>> >>>>>> -- >>>>>> >>>>>> Iain Bethune >>>>>> Project Manager, EPCC >>>>>> >>>>>> Email: i.be... at epcc.ed.ac.uk >>>>>> Twitter: @IainBethune @PrimeGrid @CP2Kproject >>>>>> Web: http://www2.epcc.ed.ac.uk/~ibethune >>>>>> Tel/Fax: +44 (0)131 651 7183/6555 >>>>>> Mob: +44 (0)7598317015 >>>>>> Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD >>>>>> >>>>>>> On 19 Jan 2017, at 14:51, Laurent Joly wrote: >>>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>> I've been trying to compile CP2K 4.1 (I also tried with the 3.0 version) using the intel compiler version 2017.1.132. >>>>>>> >>>>>>> I used the Linux-x86-64-intel-host.popt and Linux-x86-64-intel-host.psmp arch files, and I had to modify the Linux-x86-64-intel-mic.psmp file following the instructions of the intel mkl link line advisor: https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor to make it work: >>>>>>> >>>>>>> $ diff Linux-x86-64-intel-mic.psmp.backup Linux-x86-64-intel-mic.psmp >>>>>>> 231d230 >>>>>>> < $(MKLROOT)/lib/intel64/libmkl_core.a \ >>>>>>> 233,234c232,234 >>>>>>> < -Wl,--end-group \ >>>>>>> < $(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a >>>>>>> --- >>>>>>>> $(MKLROOT)/lib/intel64/libmkl_core.a \ >>>>>>>> $(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a \ >>>>>>>> -Wl,--end-group >>>>>>> >>>>>>> Then I had to run: ulimit -s unlimited in order to get rid of segmentation faults, and finally it worked... on 16 cores, but as soon as I tried to increase the number of cores I got this error message: >>>>>>> >>>>>>> KS energy is an abnormal value (NaN/Inf). >>>>>>> qs_ks_methods.F:785 >>>>>>> >>>>>>> I enclose the complete output. Do you have some ideas on what could be the problem? >>>>>>> >>>>>>> Best regards, >>>>>>> Laurent >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> You received this message because you are subscribed to the Google Groups "cp2k" group. >>>>>>> To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. >>>>>>> To post to this group, send email to cp... at googlegroups.com. >>>>>>> Visit this group at https://groups.google.com/group/cp2k. >>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> The University of Edinburgh is a charitable body, registered in >>>>>> Scotland, with registration number SC005336. >>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to a topic in the Google Groups "cp2k" group. >>>>>> To unsubscribe from this topic, visit https://groups.google.com/d/topic/cp2k/C2FO7VAUZEg/unsubscribe. >>>>>> To unsubscribe from this group and all its topics, send an email to cp2k+uns... at googlegroups.com. >>>>>> To post to this group, send email to cp... at googlegroups.com. >>>>>> Visit this group at https://groups.google.com/group/cp2k. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>>> >>>>> >>>>> -- >>>>> Laurent JOLY >>>>> >>>>> Institut Lumi?re Mati?re - Universit? Lyon 1 >>>>> Campus de la Doua, b?timent Brillouin >>>>> 43 bd du 11 novembre 1918 >>>>> 69622 Villeurbanne Cedex, France >>>>> >>>>> T?l: 04 724 326 11 - Fax: 04 724 326 48 >>>>> Web: http://ilm-perso.univ-lyon1.fr/~ljoly/ >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google Groups "cp2k" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. >>>>> To post to this group, send email to cp... at googlegroups.com. >>>>> Visit this group at https://groups.google.com/group/cp2k. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>> >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> -- >>> You received this message because you are subscribed to a topic in the Google Groups "cp2k" group. >>> To unsubscribe from this topic, visit https://groups.google.com/d/topic/cp2k/C2FO7VAUZEg/unsubscribe. >>> To unsubscribe from this group and all its topics, send an email to cp2k+uns... at googlegroups.com. >>> To post to this group, send email to cp... at googlegroups.com. >>> Visit this group at https://groups.google.com/group/cp2k. >>> For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Laurent JOLY >> >> Institut Lumi?re Mati?re - Universit? Lyon 1 >> Campus de la Doua, b?timent Brillouin >> 43 bd du 11 novembre 1918 >> 69622 Villeurbanne Cedex, France >> >> T?l: 04 724 326 11 - Fax: 04 724 326 48 >> Web: http://ilm-perso.univ-lyon1.fr/~ljoly/ >> >> -- >> You received this message because you are subscribed to the Google Groups "cp2k" group. >> To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. >> To post to this group, send email to cp... at googlegroups.com. >> Visit this group at https://groups.google.com/group/cp2k. >> For more options, visit https://groups.google.com/d/optout. >> > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -- > You received this message because you are subscribed to a topic in the Google Groups "cp2k" group. > To unsubscribe from this topic, visit https://groups.google.com/d/topic/cp2k/C2FO7VAUZEg/unsubscribe. > To unsubscribe from this group and all its topics, send an email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. -- Laurent JOLY Institut Lumi?re Mati?re - Universit? Lyon 1 Campus de la Doua, b?timent Brillouin 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex, France T?l: 04 724 326 11 - Fax: 04 724 326 48 Web: http://ilm-perso.univ-lyon1.fr/~ljoly/ From marci... at gmail.com Wed Feb 1 12:51:41 2017 From: marci... at gmail.com (Marcella Iannuzzi) Date: Wed, 1 Feb 2017 04:51:41 -0800 (PST) Subject: Distance colvar using Centre-of-Mass In-Reply-To: References: <4427a1b3-4696-4533-acc0-d5619d8fa8ef@googlegroups.com> Message-ID: <7117af52-14e7-4c41-8342-b20a832a2d73@googlegroups.com> CP2K_INPUT / FORCE_EVAL / SUBSYS / COLVAR / DISTANCE / POINT On Wednesday, February 1, 2017 at 12:27:20 PM UTC+1, cjor wrote: > > Hi, thanks. > > Where is the point feature in the DISTANCE colvar? I can't find this > option. > I do NOT want a plane defined. > > &COLVAR > &DISTANCE_POINT_PLANE > &POINT > TYPE GEO_CENTER > ATOMS 1 > &END > &POINT > TYPE GEO_CENTER > ATOMS 48 > &END > &POINT > TYPE GEO_CENTER > ATOMS 60 > &END > &POINT > TYPE GEO_CENTER > ATOMS 69 70 > &END > ATOMS_PLANE 1 2 3 > ATOM_POINT 4 > &END DISTANCE_POINT_PLANE > > > On Tuesday, 31 January 2017 16:08:02 UTC, cjor wrote: >> >> Hello, >> >> Is there a way to code a centre-of-mass point in CP2K. >> >> >> I want to use a distance colvar, *not *a distance to a plane etc. >> >> >> ? >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From mariella... at gmail.com Wed Feb 1 13:31:37 2017 From: mariella... at gmail.com (Mariella Ippolito) Date: Wed, 1 Feb 2017 05:31:37 -0800 (PST) Subject: [CP2K:8615] proplem with cp2k built with intelmpi In-Reply-To: <15afa4fa-6b54-448f-96c9-981ece7bffd0@googlegroups.com> References: <3e159718-be6e-49c9-bc64-6d52bf879292@googlegroups.com> <81616B0E-F075-42E0-92A9-AAC08642467F@epcc.ed.ac.uk> <15afa4fa-6b54-448f-96c9-981ece7bffd0@googlegroups.com> Message-ID: Dear Iain, I built again the code (trunk version) using MKL 2017.0.098 and your arch file: unfortunately I obtain the same results (Electronic density on regular grids = NaN). I read that some other users experienced similar problem but in their case the use MKL 2017.0.098 seem to solve the problem. Some other suggestion? Thank you, Mariella On Wednesday, February 1, 2017 at 11:53:15 AM UTC+1, Mariella Ippolito wrote: > > Dear Iain, > Thank you for your quick answer! > I also thought that the problem was related to the mkl library, so I have > tried to build cp2k using Scalapack, lapack and blas libraries, and I also > reduced the optimization trying both O1 O0, but that job continues to give > problems. > I try again using the previous version of mkl and your arch file. > At the moment I'm using the branch version of cp2k, do you suggest to use > the trunk? > > Thank you, > Mariella > > > On Wednesday, February 1, 2017 at 9:47:09 AM UTC+1, IBethune wrote: >> >> Dear Mariella, >> >> As per some recent discussions about Intel 2017 on this discussion forum, >> it looks like some bug(s) existing in MKL 2017.1.143. The compiler and MPI >> library in this release appear to be OK, but you will need to use a >> previous MKL version. I don?t know if you have had successful Intel builds >> before, but there are several files which need to be compiled a lower >> optimisation to work around compiler. There are a set of arch files which >> are known to be working with the CP2K trunk available via the CP2K >> dashboard - see e.g. http://cp2k-www.epcc.ed.ac.uk/phi/psmp/regtest-arch >> (linked from http://dashboard.cp2k.org >> >> Cheers >> >> - Iain >> >> -- >> >> Iain Bethune >> Project Manager, EPCC >> >> Email: i.b... at epcc.ed.ac.uk >> Twitter: @IainBethune @PrimeGrid @CP2Kproject >> Web: http://www2.epcc.ed.ac.uk/~ibethune >> Tel/Fax >> : >> +44 (0)131 651 7183/6555 >> Mob: +44 (0)7598317015 >> Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, >> Edinburgh, EH9 3FD >> >> > On 1 Feb 2017, at 08:40, Mariella Ippolito >> wrote: >> > >> > Dear all, >> > I find some problems in running qs calculations with cp2K 4.1 compiled >> with intelmpi-2017 (the same run goes fine with the executable obtained >> with openmpi-gnu compiler). >> > In particular in output I obtain >> > >> > ----------------------------------- OT >> --------------------------------------- >> > >> > Step Update method Time Convergence Total energy >> Change >> > >> ------------------------------------------------------------------------------ >> >> > >> > Trace(PS): 1200.0000000051 >> > Electronic density on regular grids: NaN >> NaN >> > Core density on regular grids: 1200.0000000000 >> -0.0000000000 >> > Total charge density on r-space grids: NaN >> > Total charge density g-space grids: -5.8357006210 >> > >> > Unlike the code compiled with openmpi-gnu gives: >> > >> > ----------------------------------- OT >> --------------------------------------- >> > >> > Step Update method Time Convergence Total energy >> Change >> > >> ------------------------------------------------------------------------------ >> >> > >> > Trace(PS): 1199.9999998902 >> > Electronic density on regular grids: -1199.9999998901 >> 0.0000001099 >> > Core density on regular grids: 1199.9999999999 >> -0.0000000001 >> > Total charge density on r-space grids: 0.0000001098 >> > Total charge density g-space grids: 0.0000001099 >> > >> > Clearly there is something wrong with the quantities >> > Electronic density on regular grids >> > Total charge density on r-space grids >> > >> > Looking at the source code I find that the problem may come from the >> quantities tot_tho_r and tot_rho_r_arr, in qs_ks_utils.F >> > >> > Line 855 in qs_ks_utils.F >> > CALL qs_rho_get(rho, tot_rho_r=tot_rho_r_arr, rho_ao_kp=rho_ao) >> > >> > If I print tot_rho_r_arr after this call I obtain NaN for both its >> components >> > and as consequences also >> > tot_rho_r = accurate_sum(tot_rho_r_arr) >> > is NaN >> > while if I run the executable gnu it gives the right value >> > tot_rho_r = accurate_sum(tot_rho_r_arr) =- 1199.99999989 >> > >> > I attach the restart file used for the calculations. >> > >> > Can you help me to fix this problem? >> > >> > Best regards, >> > Mariella >> > >> > -- >> > You received this message because you are subscribed to the Google >> Groups "cp2k" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> an email to cp2k+... at googlegroups.com. >> > To post to this group, send email to cp... at googlegroups.com. >> > Visit this group at https://groups.google.com/group/cp2k. >> > For more options, visit https://groups.google.com/d/optout. >> > >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjknig... at gmail.com Wed Feb 1 14:11:32 2017 From: cjknig... at gmail.com (Christopher Knight) Date: Wed, 1 Feb 2017 08:11:32 -0600 Subject: [CP2K:8622] proplem with cp2k built with intelmpi In-Reply-To: References: <3e159718-be6e-49c9-bc64-6d52bf879292@googlegroups.com> <81616B0E-F075-42E0-92A9-AAC08642467F@epcc.ed.ac.uk> <15afa4fa-6b54-448f-96c9-981ece7bffd0@googlegroups.com> Message-ID: <2F7831DF-75A5-414B-BD47-40BCBCC3520A@gmail.com> Have you already checked whether the issue goes away using "PREFERRED_FFT_LIBRARY FFTSG?? I?ve noticed this issue as well on KNL with cp2k-4.1 and Intel 2017.1.132. Using FFTSG appeared to fix the issue for me, but I haven?t debugged further yet (deadlines?). chris > On Feb 1, 2017, at 7:31 AM, Mariella Ippolito wrote: > > Dear Iain, > I built again the code (trunk version) using MKL 2017.0.098 and your arch file: unfortunately I obtain the same results (Electronic density on regular grids = NaN). > I read that some other users experienced similar problem but in their case the use MKL 2017.0.098 seem to solve the problem. > Some other suggestion? > > Thank you, > Mariella > > > On Wednesday, February 1, 2017 at 11:53:15 AM UTC+1, Mariella Ippolito wrote: > Dear Iain, > Thank you for your quick answer! > I also thought that the problem was related to the mkl library, so I have tried to build cp2k using Scalapack, lapack and blas libraries, and I also reduced the optimization trying both O1 O0, but that job continues to give problems. > I try again using the previous version of mkl and your arch file. > At the moment I'm using the branch version of cp2k, do you suggest to use the trunk? > > Thank you, > Mariella > > > On Wednesday, February 1, 2017 at 9:47:09 AM UTC+1, IBethune wrote: > Dear Mariella, > > As per some recent discussions about Intel 2017 on this discussion forum, it looks like some bug(s) existing in MKL 2017.1.143. The compiler and MPI library in this release appear to be OK, but you will need to use a previous MKL version. I don?t know if you have had successful Intel builds before, but there are several files which need to be compiled a lower optimisation to work around compiler. There are a set of arch files which are known to be working with the CP2K trunk available via the CP2K dashboard - see e.g. http://cp2k-www.epcc.ed.ac.uk/phi/psmp/regtest-arch (linked from http://dashboard.cp2k.org > > Cheers > > - Iain > > -- > > Iain Bethune > Project Manager, EPCC > > Email: i.b... at epcc.ed.ac.uk <> > Twitter: @IainBethune @PrimeGrid @CP2Kproject > Web: http://www2.epcc.ed.ac.uk/~ibethune > Tel/Fax : +44 (0)131 651 7183/6555 > Mob: +44 (0)7598317015 > Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD > > > On 1 Feb 2017, at 08:40, Mariella Ippolito > wrote: > > > > Dear all, > > I find some problems in running qs calculations with cp2K 4.1 compiled with intelmpi-2017 (the same run goes fine with the executable obtained with openmpi-gnu compiler). > > In particular in output I obtain > > > > ----------------------------------- OT --------------------------------------- > > > > Step Update method Time Convergence Total energy Change > > ------------------------------------------------------------------------------ > > > > Trace(PS): 1200.0000000051 > > Electronic density on regular grids: NaN NaN > > Core density on regular grids: 1200.0000000000 -0.0000000000 > > Total charge density on r-space grids: NaN > > Total charge density g-space grids: -5.8357006210 > > > > Unlike the code compiled with openmpi-gnu gives: > > > > ----------------------------------- OT --------------------------------------- > > > > Step Update method Time Convergence Total energy Change > > ------------------------------------------------------------------------------ > > > > Trace(PS): 1199.9999998902 > > Electronic density on regular grids: -1199.9999998901 0.0000001099 > > Core density on regular grids: 1199.9999999999 -0.0000000001 > > Total charge density on r-space grids: 0.0000001098 > > Total charge density g-space grids: 0.0000001099 > > > > Clearly there is something wrong with the quantities > > Electronic density on regular grids > > Total charge density on r-space grids > > > > Looking at the source code I find that the problem may come from the quantities tot_tho_r and tot_rho_r_arr, in qs_ks_utils.F > > > > Line 855 in qs_ks_utils.F > > CALL qs_rho_get(rho, tot_rho_r=tot_rho_r_arr, rho_ao_kp=rho_ao) > > > > If I print tot_rho_r_arr after this call I obtain NaN for both its components > > and as consequences also > > tot_rho_r = accurate_sum(tot_rho_r_arr) > > is NaN > > while if I run the executable gnu it gives the right value > > tot_rho_r = accurate_sum(tot_rho_r_arr) =- 1199.99999989 > > > > I attach the restart file used for the calculations. > > > > Can you help me to fix this problem? > > > > Best regards, > > Mariella > > > > -- > > You received this message because you are subscribed to the Google Groups "cp2k" group. > > To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+... at googlegroups.com <>. > > To post to this group, send email to cp... at googlegroups.com <>. > > Visit this group at https://groups.google.com/group/cp2k . > > For more options, visit https://groups.google.com/d/optout . > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > -- > You received this message because you are subscribed to the Google Groups "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com . > To post to this group, send email to cp... at googlegroups.com . > Visit this group at https://groups.google.com/group/cp2k . > For more options, visit https://groups.google.com/d/optout . -------------- next part -------------- An HTML attachment was scrubbed... URL: From i.be... at epcc.ed.ac.uk Wed Feb 1 22:58:07 2017 From: i.be... at epcc.ed.ac.uk (Iain Bethune) Date: Wed, 1 Feb 2017 22:58:07 +0000 Subject: [CP2K:8623] proplem with cp2k built with intelmpi In-Reply-To: <2F7831DF-75A5-414B-BD47-40BCBCC3520A@gmail.com> References: <3e159718-be6e-49c9-bc64-6d52bf879292@googlegroups.com> <81616B0E-F075-42E0-92A9-AAC08642467F@epcc.ed.ac.uk> <15afa4fa-6b54-448f-96c9-981ece7bffd0@googlegroups.com> <2F7831DF-75A5-414B-BD47-40BCBCC3520A@gmail.com> Message-ID: <31CED9C7-7034-4C54-9E83-F439FFB13757@epcc.ed.ac.uk> On my intel build (same as used for the dashboard testing), the input runs fine, at least until the first SCF step when I stopped it. The fact that it also works for you with a gfortran build also points to some local build configuration issue. One thing to try is a serial build with -O0 and reference BLAS/LAPACK as this essentially rules out any problems with the compiler/MKL. Obviously it will be very slow, but if you can get the calculation up to the point where it prints the first "Electronic density on regular grids? that is enough. Assuming this works you can then start increasing the optimisation and adding in MKL, MPI etc. and see what causes the failure. - Iain -- Iain Bethune Project Manager, EPCC Email: i.be... at epcc.ed.ac.uk Twitter: @IainBethune @PrimeGrid @CP2Kproject Web: http://www2.epcc.ed.ac.uk/~ibethune Tel/Fax: +44 (0)131 651 7183/6555 Mob: +44 (0)7598317015 Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD > On 1 Feb 2017, at 14:11, Christopher Knight wrote: > > Have you already checked whether the issue goes away using "PREFERRED_FFT_LIBRARY FFTSG?? > > I?ve noticed this issue as well on KNL with cp2k-4.1 and Intel 2017.1.132. Using FFTSG appeared to fix the issue for me, but I haven?t debugged further yet (deadlines?). > > chris > > > >> On Feb 1, 2017, at 7:31 AM, Mariella Ippolito wrote: >> >> Dear Iain, >> I built again the code (trunk version) using MKL 2017.0.098 and your arch file: unfortunately I obtain the same results (Electronic density on regular grids = NaN). >> I read that some other users experienced similar problem but in their case the use MKL 2017.0.098 seem to solve the problem. >> Some other suggestion? >> >> Thank you, >> Mariella >> >> >> On Wednesday, February 1, 2017 at 11:53:15 AM UTC+1, Mariella Ippolito wrote: >> Dear Iain, >> Thank you for your quick answer! >> I also thought that the problem was related to the mkl library, so I have tried to build cp2k using Scalapack, lapack and blas libraries, and I also reduced the optimization trying both O1 O0, but that job continues to give problems. >> I try again using the previous version of mkl and your arch file. >> At the moment I'm using the branch version of cp2k, do you suggest to use the trunk? >> >> Thank you, >> Mariella >> >> >> On Wednesday, February 1, 2017 at 9:47:09 AM UTC+1, IBethune wrote: >> Dear Mariella, >> >> As per some recent discussions about Intel 2017 on this discussion forum, it looks like some bug(s) existing in MKL 2017.1.143. The compiler and MPI library in this release appear to be OK, but you will need to use a previous MKL version. I don?t know if you have had successful Intel builds before, but there are several files which need to be compiled a lower optimisation to work around compiler. There are a set of arch files which are known to be working with the CP2K trunk available via the CP2K dashboard - see e.g. http://cp2k-www.epcc.ed.ac.uk/phi/psmp/regtest-arch (linked from http://dashboard.cp2k.org >> >> Cheers >> >> - Iain >> >> -- >> >> Iain Bethune >> Project Manager, EPCC >> >> Email: i.b... at epcc.ed.ac.uk >> Twitter: @IainBethune @PrimeGrid @CP2Kproject >> Web: http://www2.epcc.ed.ac.uk/~ibethune >> Tel/Fax: +44 (0)131 651 7183/6555 >> Mob: +44 (0)7598317015 >> Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD >> >> > On 1 Feb 2017, at 08:40, Mariella Ippolito wrote: >> > >> > Dear all, >> > I find some problems in running qs calculations with cp2K 4.1 compiled with intelmpi-2017 (the same run goes fine with the executable obtained with openmpi-gnu compiler). >> > In particular in output I obtain >> > >> > ----------------------------------- OT --------------------------------------- >> > >> > Step Update method Time Convergence Total energy Change >> > ------------------------------------------------------------------------------ >> > >> > Trace(PS): 1200.0000000051 >> > Electronic density on regular grids: NaN NaN >> > Core density on regular grids: 1200.0000000000 -0.0000000000 >> > Total charge density on r-space grids: NaN >> > Total charge density g-space grids: -5.8357006210 >> > >> > Unlike the code compiled with openmpi-gnu gives: >> > >> > ----------------------------------- OT --------------------------------------- >> > >> > Step Update method Time Convergence Total energy Change >> > ------------------------------------------------------------------------------ >> > >> > Trace(PS): 1199.9999998902 >> > Electronic density on regular grids: -1199.9999998901 0.0000001099 >> > Core density on regular grids: 1199.9999999999 -0.0000000001 >> > Total charge density on r-space grids: 0.0000001098 >> > Total charge density g-space grids: 0.0000001099 >> > >> > Clearly there is something wrong with the quantities >> > Electronic density on regular grids >> > Total charge density on r-space grids >> > >> > Looking at the source code I find that the problem may come from the quantities tot_tho_r and tot_rho_r_arr, in qs_ks_utils.F >> > >> > Line 855 in qs_ks_utils.F >> > CALL qs_rho_get(rho, tot_rho_r=tot_rho_r_arr, rho_ao_kp=rho_ao) >> > >> > If I print tot_rho_r_arr after this call I obtain NaN for both its components >> > and as consequences also >> > tot_rho_r = accurate_sum(tot_rho_r_arr) >> > is NaN >> > while if I run the executable gnu it gives the right value >> > tot_rho_r = accurate_sum(tot_rho_r_arr) =- 1199.99999989 >> > >> > I attach the restart file used for the calculations. >> > >> > Can you help me to fix this problem? >> > >> > Best regards, >> > Mariella >> > >> > -- >> > You received this message because you are subscribed to the Google Groups "cp2k" group. >> > To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+... at googlegroups.com. >> > To post to this group, send email to cp... at googlegroups.com. >> > Visit this group at https://groups.google.com/group/cp2k. >> > For more options, visit https://groups.google.com/d/optout. >> > >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> >> -- >> You received this message because you are subscribed to the Google Groups "cp2k" group. >> To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. >> To post to this group, send email to cp... at googlegroups.com. >> Visit this group at https://groups.google.com/group/cp2k. >> For more options, visit https://groups.google.com/d/optout. > > > -- > You received this message because you are subscribed to the Google Groups "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From i.be... at epcc.ed.ac.uk Wed Feb 1 23:02:09 2017 From: i.be... at epcc.ed.ac.uk (Iain Bethune) Date: Wed, 1 Feb 2017 23:02:09 +0000 Subject: [CP2K:8620] error in qs_ks_methods.F depending on number of cores (intel compiler) In-Reply-To: References: <8BEC3126-9A5F-4368-A114-B46A939ABA4C@epcc.ed.ac.uk> <6C993206-9797-493D-BA6B-0331BBF58BA7@epcc.ed.ac.uk> <6FA71BB7-20E6-47B6-A0ED-BBAD3E93CF52@epcc.ed.ac.uk> Message-ID: Glad you have it working. I?m not 100% sure on the minimizer, maybe someone else with more knowledge in this area can answer. I didn?t spot that you had chaged from CG to DIIS. Certainly with CG you do expect the energy to be strictly decreasing. - Iain -- Iain Bethune Project Manager, EPCC Email: i.be... at epcc.ed.ac.uk Twitter: @IainBethune @PrimeGrid @CP2Kproject Web: http://www2.epcc.ed.ac.uk/~ibethune Tel/Fax: +44 (0)131 651 7183/6555 Mob: +44 (0)7598317015 Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD > On 1 Feb 2017, at 12:37, Laurent Joly wrote: > > Hi Iain, > > Our administrator installed the 2017.0 version of intel compiler and > librairies. I compiled CP2K 4.1 with it and, although I still have to > make more tests, it seems to be working. > > Regarding the behavior of the SCF, I'm using the DIIS minimizer. I'm > not an expert on the OT method, but when I read in the manual: > > MINIMIZER MINIMIZER {Keyword} Minimizer to be used with the OT method > This keyword cannot be repeated and it expects precisely one keyword. > Default value: CG List of valid keywords: > BROYDENBroyden mixing approximating the inverse Hessian > CGConjugate Gradients: most reliable, use for difficult systems. The > total energy should decrease at every OT CG step if the line search is > appropriate. > DIISDirect inversion in the iterative subspace: less reliable than CG, > but sometimes about 50% faster > SDSteepest descent: not recommended > > I understand that only with a CG minimizer and appropriate linesearch > one should expect that the energy decreases at every timestep. Is it a > generally expected property of the OT method? In any case, only the > first SCF starting from an atomic density guess is slow to converge, > and as soon as the MD is started, the SCF converges in roughly 10 > iterations, which seems okay to me. > > Best regards, > Laurent > > > > > 2017-02-01 10:51 GMT+01:00 Iain Bethune : >> Hi Laurent, >> >> I can confirm that the problem with the energy going to NaN that you observed is indeed specific to the Intel compiler (at least it works for me with a local gfortran run). I think however there is also that there some issue (or at least numerical difficulty) with your input, since I observe that the total energy actually increases in the second SCF step, when it should be strictly decreasing when using OT. Maybe someone else can spot the problem? >> >> - Iain >> >> -- >> >> Iain Bethune >> Project Manager, EPCC >> >> Email: i.be... at epcc.ed.ac.uk >> Twitter: @IainBethune @PrimeGrid @CP2Kproject >> Web: http://www2.epcc.ed.ac.uk/~ibethune >> Tel/Fax: +44 (0)131 651 7183/6555 >> Mob: +44 (0)7598317015 >> Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD >> >>> On 29 Jan 2017, at 16:41, Laurent Joly wrote: >>> >>> Hi Iain, >>> >>> Thank you again for your help. >>> >>>> Further to what I reported this morning, I found that the MKL release 2017.1.132 is buggy. I was able to get a successful build using the compiler from the 2017.1.132 release and MKL from the previous (2017.0.098) release. >>> >>> I asked our local administrator if it was possible to install the >>> previous version of the intel compiler, or at least of the MKL >>> libraries. >>> >>>>> I got hold of the 2017.1.132 release and ran a regtest of the latest trunk code. Barring one regtest with numerical problems, it ran fine, so I don?t think there is something fundamentally broken with that version. Could you send your input file, and try running with the GLOBAL%PRINT_LEVEL HIGH so some more information is printed out before the error occurs? Maybe someone can spot the problem. Did you have any success running this input with previous builds of CP2K? >>> >>> Please find enclosed the input and ouput files obtained with >>> GLOBAL%PRINT_LEVEL HIGH. I tried with CP2K version 4.1 and 3.0 and got >>> similar results... >>> >>> Hopefully I will soon have access to the previous MKL release, and >>> keep you informed. In the meantime, I'm using a gfortran+acml >>> compilation, which runs fine (although more slowly)... >>> >>> Best regards, >>> Laurent >>> >>> >>>>>> On 19 Jan 2017, at 17:56, Laurent Joly wrote: >>>>>> >>>>>> Hi Iain, >>>>>> >>>>>> Thank you very much for your fast answer. >>>>>> >>>>>> I tried a simplified version of the arch file you sent (enclosed >>>>>> raptor2.psmp), but I keep getting the same behavior. I also tried to >>>>>> compile all the files with -O1 (enclosed raptor1.psmp and >>>>>> Linux-x86-64-intel-mic.psmp), or even -O0 (enclosed raptor3.psmp), but >>>>>> here again it makes no difference. >>>>>> >>>>>> When I try to run the regtests, the system hangs after printing >>>>>> "Copying tests into working directory ... done!"... But possibly this >>>>>> is another problem... >>>>>> >>>>>> Best regards, >>>>>> Laurent >>>>>> >>>>>> >>>>>> 2017-01-19 14:57 GMT+00:00 Iain Bethune : >>>>>>> Hi Laurent, >>>>>>> >>>>>>> We don?t have experience yet with exactly that version (ifort 17.0.1), but with the 17.0.0 compiler we find that a couple of files need to be built at reduced optimisation level - see https://dashboard.cp2k.org/archive/epcc-phi-psmp/rev_17693.txt for an example arch file which is working. >>>>>>> >>>>>>> Were you able to run the CP2K regression tests with success? >>>>>>> >>>>>>> Cheers >>>>>>> >>>>>>> - Iain >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> Iain Bethune >>>>>>> Project Manager, EPCC >>>>>>> >>>>>>> Email: i.be... at epcc.ed.ac.uk >>>>>>> Twitter: @IainBethune @PrimeGrid @CP2Kproject >>>>>>> Web: http://www2.epcc.ed.ac.uk/~ibethune >>>>>>> Tel/Fax: +44 (0)131 651 7183/6555 >>>>>>> Mob: +44 (0)7598317015 >>>>>>> Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD >>>>>>> >>>>>>>> On 19 Jan 2017, at 14:51, Laurent Joly wrote: >>>>>>>> >>>>>>>> Dear all, >>>>>>>> >>>>>>>> I've been trying to compile CP2K 4.1 (I also tried with the 3.0 version) using the intel compiler version 2017.1.132. >>>>>>>> >>>>>>>> I used the Linux-x86-64-intel-host.popt and Linux-x86-64-intel-host.psmp arch files, and I had to modify the Linux-x86-64-intel-mic.psmp file following the instructions of the intel mkl link line advisor: https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor to make it work: >>>>>>>> >>>>>>>> $ diff Linux-x86-64-intel-mic.psmp.backup Linux-x86-64-intel-mic.psmp >>>>>>>> 231d230 >>>>>>>> < $(MKLROOT)/lib/intel64/libmkl_core.a \ >>>>>>>> 233,234c232,234 >>>>>>>> < -Wl,--end-group \ >>>>>>>> < $(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a >>>>>>>> --- >>>>>>>>> $(MKLROOT)/lib/intel64/libmkl_core.a \ >>>>>>>>> $(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a \ >>>>>>>>> -Wl,--end-group >>>>>>>> >>>>>>>> Then I had to run: ulimit -s unlimited in order to get rid of segmentation faults, and finally it worked... on 16 cores, but as soon as I tried to increase the number of cores I got this error message: >>>>>>>> >>>>>>>> KS energy is an abnormal value (NaN/Inf). >>>>>>>> qs_ks_methods.F:785 >>>>>>>> >>>>>>>> I enclose the complete output. Do you have some ideas on what could be the problem? >>>>>>>> >>>>>>>> Best regards, >>>>>>>> Laurent >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> You received this message because you are subscribed to the Google Groups "cp2k" group. >>>>>>>> To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. >>>>>>>> To post to this group, send email to cp... at googlegroups.com. >>>>>>>> Visit this group at https://groups.google.com/group/cp2k. >>>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> The University of Edinburgh is a charitable body, registered in >>>>>>> Scotland, with registration number SC005336. >>>>>>> >>>>>>> -- >>>>>>> You received this message because you are subscribed to a topic in the Google Groups "cp2k" group. >>>>>>> To unsubscribe from this topic, visit https://groups.google.com/d/topic/cp2k/C2FO7VAUZEg/unsubscribe. >>>>>>> To unsubscribe from this group and all its topics, send an email to cp2k+uns... at googlegroups.com. >>>>>>> To post to this group, send email to cp... at googlegroups.com. >>>>>>> Visit this group at https://groups.google.com/group/cp2k. >>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Laurent JOLY >>>>>> >>>>>> Institut Lumi?re Mati?re - Universit? Lyon 1 >>>>>> Campus de la Doua, b?timent Brillouin >>>>>> 43 bd du 11 novembre 1918 >>>>>> 69622 Villeurbanne Cedex, France >>>>>> >>>>>> T?l: 04 724 326 11 - Fax: 04 724 326 48 >>>>>> Web: http://ilm-perso.univ-lyon1.fr/~ljoly/ >>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google Groups "cp2k" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. >>>>>> To post to this group, send email to cp... at googlegroups.com. >>>>>> Visit this group at https://groups.google.com/group/cp2k. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> >>>> >>>> >>>> -- >>>> The University of Edinburgh is a charitable body, registered in >>>> Scotland, with registration number SC005336. >>>> >>>> -- >>>> You received this message because you are subscribed to a topic in the Google Groups "cp2k" group. >>>> To unsubscribe from this topic, visit https://groups.google.com/d/topic/cp2k/C2FO7VAUZEg/unsubscribe. >>>> To unsubscribe from this group and all its topics, send an email to cp2k+uns... at googlegroups.com. >>>> To post to this group, send email to cp... at googlegroups.com. >>>> Visit this group at https://groups.google.com/group/cp2k. >>>> For more options, visit https://groups.google.com/d/optout. >>> >>> >>> >>> -- >>> Laurent JOLY >>> >>> Institut Lumi?re Mati?re - Universit? Lyon 1 >>> Campus de la Doua, b?timent Brillouin >>> 43 bd du 11 novembre 1918 >>> 69622 Villeurbanne Cedex, France >>> >>> T?l: 04 724 326 11 - Fax: 04 724 326 48 >>> Web: http://ilm-perso.univ-lyon1.fr/~ljoly/ >>> >>> -- >>> You received this message because you are subscribed to the Google Groups "cp2k" group. >>> To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. >>> To post to this group, send email to cp... at googlegroups.com. >>> Visit this group at https://groups.google.com/group/cp2k. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> -- >> You received this message because you are subscribed to a topic in the Google Groups "cp2k" group. >> To unsubscribe from this topic, visit https://groups.google.com/d/topic/cp2k/C2FO7VAUZEg/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to cp2k+uns... at googlegroups.com. >> To post to this group, send email to cp... at googlegroups.com. >> Visit this group at https://groups.google.com/group/cp2k. >> For more options, visit https://groups.google.com/d/optout. > > > > -- > Laurent JOLY > > Institut Lumi?re Mati?re - Universit? Lyon 1 > Campus de la Doua, b?timent Brillouin > 43 bd du 11 novembre 1918 > 69622 Villeurbanne Cedex, France > > T?l: 04 724 326 11 - Fax: 04 724 326 48 > Web: http://ilm-perso.univ-lyon1.fr/~ljoly/ > > -- > You received this message because you are subscribed to the Google Groups "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From igla... at gmail.com Thu Feb 2 05:59:23 2017 From: igla... at gmail.com (Ivan Gladich) Date: Wed, 1 Feb 2017 21:59:23 -0800 (PST) Subject: Questions about AdBF-QM/MM in cp2k Message-ID: Dear Cp2K users, I am a newbie of CP2K and I am trying to use Adaptive Buffered force QM-MM (AdBF-QM/MM) in cp2k https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351341/ to study a radical specie in water I have a couple of questions. 1) Using ... &QMMM &QM_KIND Br MM_INDEX 1 &END QM_KIND &QM_KIND O1 MM_INDEX 2 &END QM_KIND &FORCE_MIXING MAX_N_QM 500 R_CORE 0.0 0.1 #dimension of the core region for the reduced QM/MM calculation. Could be 0 if you have the force field R_QM 3.0 3.5 #Dimension of the dynamical core region R_BUF 3.0 3.5 #dimensione of the buffere region QM_KIND_ELEMENT_MAPPING Br Br #atoms that can be adaptively selectefor the QM region QM_KIND_ELEMENT_MAPPING O O #atoms that can be adaptively selected for the QM region QM_KIND_ELEMENT_MAPPING H H #atoms that can be adaptively selectedfor the QM region EXTENDED_DELTA_CHARGE 0 # this is the charge of the QM_dynamical + buffer region. MOMENTUM_CONSERVATION_REGION QM #only to dynamical core, you can also choose BUFFER for QM+BUFFER MOMENTUM_CONSERVATION_TYPE EQUAL_A #equal acceleration on each atom, or EQUAL_F, equal force &END FORCE_MIXING .... And I got in my output QMMM FORCE MIXING final count (not including links): N_QM core_list 2 N_QM core 0 N_QM extended 12 N_QM buffered 63 QMMM FORCE MIXING final count (not including links): N_QM core_list 2 N_QM core 0 N_QM extended 12 N_QM buffered 63 QMMM FORCE MIXING final count (not including links): N_QM core_list 2 N_QM core 0 N_QM extended 12 N_QM buffered 63 QMMM FORCE MIXING final count (not including links): N_QM core_list 2 N_QM core 0 N_QM extended 12 N_QM buffered 63 QMMM FORCE MIXING final count (not including links): N_QM core_list 2 N_QM core 0 N_QM extended 12 N_QM buffered 63 ... Is N_QM core = 0 the number of atoms in my dynamical QM region? Moreover, reading the paper N_QM extended "is constructed adding a buffer region around the QM dynamical core" But N_QM extended =12 and N_QM buffered is 63, so it cannot be (N_QM should be the same of the buffer plus the dynamical core)... 2) How does the R_BUF and R_QM works? R_BUF is a radius around each atoms belonging to the QM dynamical core region OR R_BUF is centered around the QM_CORE (in my case determined by Br and O position) and, thus, I should impose always R_QM =< R_BUF ? 3) Is it possible to write, at each time step of my run, a label or the indexes of the atoms in the dynamical and extended QM/MM region? I tried using &FORCE_MIXING_LABELS FORMAT XYZ &EACH MD 1 &END EACH COMMON_ITERATION_LEVELS 0 &END FORCE_MIXING_LABELS but it seems that it labels only the atoms in the QM CORE, i.e., *fmlabels-1_23.xyz 6482 i = 23, time = 11.500, E = -21.9207476721 BR 10.0000000000 10.0000000000 10.0000000000 O 10.0000000000 10.0000000000 10.0000000000 O 0.0000000000 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 ... Thank you for any possible help or comment Best Regards Ivan -------------- next part -------------- An HTML attachment was scrubbed... URL: From mariella... at gmail.com Thu Feb 2 09:21:02 2017 From: mariella... at gmail.com (Mariella Ippolito) Date: Thu, 2 Feb 2017 10:21:02 +0100 Subject: [CP2K:8625] proplem with cp2k built with intelmpi In-Reply-To: <31CED9C7-7034-4C54-9E83-F439FFB13757@epcc.ed.ac.uk> References: <3e159718-be6e-49c9-bc64-6d52bf879292@googlegroups.com> <81616B0E-F075-42E0-92A9-AAC08642467F@epcc.ed.ac.uk> <15afa4fa-6b54-448f-96c9-981ece7bffd0@googlegroups.com> <2F7831DF-75A5-414B-BD47-40BCBCC3520A@gmail.com> <31CED9C7-7034-4C54-9E83-F439FFB13757@epcc.ed.ac.uk> Message-ID: Using "PREFERRED_FFT_LIBRARY FFTSG? finally fix the issue. Thank you, Mariella On 1 February 2017 at 23:58, Iain Bethune wrote: > On my intel build (same as used for the dashboard testing), the input runs > fine, at least until the first SCF step when I stopped it. The fact that > it also works for you with a gfortran build also points to some local build > configuration issue. One thing to try is a serial build with -O0 and > reference BLAS/LAPACK as this essentially rules out any problems with the > compiler/MKL. Obviously it will be very slow, but if you can get the > calculation up to the point where it prints the first "Electronic density > on regular grids? that is enough. Assuming this works you can then start > increasing the optimisation and adding in MKL, MPI etc. and see what causes > the failure. > > - Iain > > > -- > > Iain Bethune > Project Manager, EPCC > > Email: i.be... at epcc.ed.ac.uk > Twitter: @IainBethune @PrimeGrid @CP2Kproject > Web: http://www2.epcc.ed.ac.uk/~ibethune > Tel/Fax: +44 (0)131 651 7183/6555 > Mob: +44 (0)7598317015 > Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, > EH9 3FD > > > On 1 Feb 2017, at 14:11, Christopher Knight > wrote: > > > > Have you already checked whether the issue goes away using > "PREFERRED_FFT_LIBRARY FFTSG?? > > > > I?ve noticed this issue as well on KNL with cp2k-4.1 and Intel > 2017.1.132. Using FFTSG appeared to fix the issue for me, but I haven?t > debugged further yet (deadlines?). > > > > chris > > > > > > > >> On Feb 1, 2017, at 7:31 AM, Mariella Ippolito < > mariella... at gmail.com> wrote: > >> > >> Dear Iain, > >> I built again the code (trunk version) using MKL 2017.0.098 and your > arch file: unfortunately I obtain the same results (Electronic density on > regular grids = NaN). > >> I read that some other users experienced similar problem but in their > case the use MKL 2017.0.098 seem to solve the problem. > >> Some other suggestion? > >> > >> Thank you, > >> Mariella > >> > >> > >> On Wednesday, February 1, 2017 at 11:53:15 AM UTC+1, Mariella Ippolito > wrote: > >> Dear Iain, > >> Thank you for your quick answer! > >> I also thought that the problem was related to the mkl library, so I > have tried to build cp2k using Scalapack, lapack and blas libraries, and I > also reduced the optimization trying both O1 O0, but that job continues to > give problems. > >> I try again using the previous version of mkl and your arch file. > >> At the moment I'm using the branch version of cp2k, do you suggest to > use the trunk? > >> > >> Thank you, > >> Mariella > >> > >> > >> On Wednesday, February 1, 2017 at 9:47:09 AM UTC+1, IBethune wrote: > >> Dear Mariella, > >> > >> As per some recent discussions about Intel 2017 on this discussion > forum, it looks like some bug(s) existing in MKL 2017.1.143. The compiler > and MPI library in this release appear to be OK, but you will need to use a > previous MKL version. I don?t know if you have had successful Intel builds > before, but there are several files which need to be compiled a lower > optimisation to work around compiler. There are a set of arch files which > are known to be working with the CP2K trunk available via the CP2K > dashboard - see e.g. http://cp2k-www.epcc.ed.ac.uk/phi/psmp/regtest-arch > (linked from http://dashboard.cp2k.org > >> > >> Cheers > >> > >> - Iain > >> > >> -- > >> > >> Iain Bethune > >> Project Manager, EPCC > >> > >> Email: i.b... at epcc.ed.ac.uk > >> Twitter: @IainBethune @PrimeGrid @CP2Kproject > >> Web: http://www2.epcc.ed.ac.uk/~ibethune > >> Tel/Fax: +44 (0)131 651 7183/6555 > >> Mob: +44 (0)7598317015 > >> Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, > Edinburgh, EH9 3FD > >> > >> > On 1 Feb 2017, at 08:40, Mariella Ippolito > wrote: > >> > > >> > Dear all, > >> > I find some problems in running qs calculations with cp2K 4.1 > compiled with intelmpi-2017 (the same run goes fine with the executable > obtained with openmpi-gnu compiler). > >> > In particular in output I obtain > >> > > >> > ----------------------------------- OT ------------------------------ > --------- > >> > > >> > Step Update method Time Convergence Total > energy Change > >> > ------------------------------------------------------------ > ------------------ > >> > > >> > Trace(PS): 1200.0000000051 > >> > Electronic density on regular grids: NaN > NaN > >> > Core density on regular grids: 1200.0000000000 > -0.0000000000 > >> > Total charge density on r-space grids: NaN > >> > Total charge density g-space grids: -5.8357006210 > >> > > >> > Unlike the code compiled with openmpi-gnu gives: > >> > > >> > ----------------------------------- OT > --------------------------------------- > >> > > >> > Step Update method Time Convergence Total > energy Change > >> > ------------------------------------------------------------ > ------------------ > >> > > >> > Trace(PS): 1199.9999998902 > >> > Electronic density on regular grids: -1199.9999998901 > 0.0000001099 > >> > Core density on regular grids: 1199.9999999999 > -0.0000000001 > >> > Total charge density on r-space grids: 0.0000001098 > >> > Total charge density g-space grids: 0.0000001099 > >> > > >> > Clearly there is something wrong with the quantities > >> > Electronic density on regular grids > >> > Total charge density on r-space grids > >> > > >> > Looking at the source code I find that the problem may come from the > quantities tot_tho_r and tot_rho_r_arr, in qs_ks_utils.F > >> > > >> > Line 855 in qs_ks_utils.F > >> > CALL qs_rho_get(rho, tot_rho_r=tot_rho_r_arr, rho_ao_kp=rho_ao) > >> > > >> > If I print tot_rho_r_arr after this call I obtain NaN for both its > components > >> > and as consequences also > >> > tot_rho_r = accurate_sum(tot_rho_r_arr) > >> > is NaN > >> > while if I run the executable gnu it gives the right value > >> > tot_rho_r = accurate_sum(tot_rho_r_arr) =- 1199.99999989 > >> > > >> > I attach the restart file used for the calculations. > >> > > >> > Can you help me to fix this problem? > >> > > >> > Best regards, > >> > Mariella > >> > > >> > -- > >> > You received this message because you are subscribed to the Google > Groups "cp2k" group. > >> > To unsubscribe from this group and stop receiving emails from it, > send an email to cp2k+... at googlegroups.com. > >> > To post to this group, send email to cp... at googlegroups.com. > >> > Visit this group at https://groups.google.com/group/cp2k. > >> > For more options, visit https://groups.google.com/d/optout. > >> > > >> > >> > >> -- > >> The University of Edinburgh is a charitable body, registered in > >> Scotland, with registration number SC005336. > >> > >> > >> -- > >> You received this message because you are subscribed to the Google > Groups "cp2k" group. > >> To unsubscribe from this group and stop receiving emails from it, send > an email to cp2k+uns... at googlegroups.com. > >> To post to this group, send email to cp... at googlegroups.com. > >> Visit this group at https://groups.google.com/group/cp2k. > >> For more options, visit https://groups.google.com/d/optout. > > > > > > -- > > You received this message because you are subscribed to the Google > Groups "cp2k" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to cp2k+uns... at googlegroups.com. > > To post to this group, send email to cp... at googlegroups.com. > > Visit this group at https://groups.google.com/group/cp2k. > > For more options, visit https://groups.google.com/d/optout. > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -- > You received this message because you are subscribed to a topic in the > Google Groups "cp2k" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/cp2k/ppBRwaQ6w-s/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dries.va... at gmail.com Thu Feb 2 09:56:07 2017 From: dries.va... at gmail.com (Dries Van Rompaey) Date: Thu, 2 Feb 2017 01:56:07 -0800 (PST) Subject: [CP2K:8557] Runtime fail during regtest In-Reply-To: <070CB24C-D2E1-4756-8F9C-73BC4C248380@epcc.ed.ac.uk> References: <7a3a5ad0-e92a-4e37-9533-a22ce13c782a@googlegroups.com> <070CB24C-D2E1-4756-8F9C-73BC4C248380@epcc.ed.ac.uk> Message-ID: Hi Iain, The updated build works like a charm. Thanks Dries Op vrijdag 27 januari 2017 10:13:27 UTC+1 schreef IBethune: > > Hi Dries, > > This issue is now fixed in r17712 on the SVN trunk. Please note that the > Mac arch files have also been updated, so please make sure you also update > those. > > Cheers > > - Iain > > -- > > Iain Bethune > Project Manager, EPCC > > Email: i.b... at epcc.ed.ac.uk > Twitter: @IainBethune @PrimeGrid @CP2Kproject > Web: http://www2.epcc.ed.ac.uk/~ibethune > Tel/Fax : +44 (0)131 651 > 7183/6555 > Mob: +44 (0)7598317015 > Addr: 2404 JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, > EH9 3FD > > > On 18 Jan 2017, at 12:20, Dries Van Rompaey > wrote: > > > > Hi everyone, > > I get the following error when I try to regtest my fresh install of cp2k > 4.1 on an iMac running OS X 10.12.2 Sierra: > > > > $make ARCH=Darwin-IntelMacintosh-gfortran VERSION=sopt test > > > > > > > > [...] > > > > > > > > > /Users/dvr/Downloads/cp2k-4.1/regtesting/Darwin-IntelMacintosh-gfortran/sopt/TEST-Darwin-IntelMacintosh-gfortran-sopt-2017-01-18_12-15-28/UNIT/dbcsr_unittest.out > > > > > > > > > Program received signal SIGABRT: Process abort signal. > > > > > > > > Backtrace for this error: > > > > #0 0x10e70cff6 > > > > #1 0x10e70c593 > > > > #2 0x7fffcb182bb9 > > > > EXIT CODE: 134 MEANING: RUNTIME FAIL > > > > > > Arch details: > > CC = cc > > CPP = > > FC = gfortran > > LD = gfortran > > AR = ar -r > > RANLIB = ranlib > > DFLAGS = -D__NO_STATM_ACCESS -D_FFTW3 > > FCFLAGS = -O2 -ffast-math -funroll-loops -ftree-vectorize -ffree-form > $(DFLAGS) > > LDFLAGS = $(FCFLAGS) > > LIBS = -Wl,-framework -Wl,Accelerate -Wl,-Y -Wl,10 > > > > Please let me know if I can provide any further details to narrow down > the problem. > > Thanks in advance for your time, > > > > Dries > > > > > > -- > > You received this message because you are subscribed to the Google > Groups "cp2k" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to cp2k+... at googlegroups.com . > > To post to this group, send email to cp... at googlegroups.com > . > > Visit this group at https://groups.google.com/group/cp2k. > > For more options, visit https://groups.google.com/d/optout. > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuri.a.... at gmail.com Thu Feb 2 12:37:21 2017 From: nuri.a.... at gmail.com (Nuri Yazdani) Date: Thu, 2 Feb 2017 04:37:21 -0800 (PST) Subject: Vacuum level for charged systems Message-ID: <87802206-33c2-4536-a66f-294d426ba3e1@googlegroups.com> Hi all, First to summarize the question: how/can one extract the vacuum level from a calculation done on a charged (non periodic!) system, such that the energies taken from two calculations with different amounts of charge can be compared on an absolute scale to one another? Also, if someone could provide a reference for where this or a similar situation has been looked at/addressed? Why I want to know this is explained in more detail below. I am doing calculations on charged molecules, including HF. I am trying to look into the reorganization energy associated with hopping of carrier from one charge molecule to another. To estimate this, I calculate the energies for a charged (+1e-) and neutral molecule: E0{A,n} = E{A,n}+E{F,ref}, where E{A,n} are the energy spectra I get from CP2k for the neutral molecule, and E{F,ref} is the reference level to vacuum E0{C,n} = E{C,n}+E{C,ref}, where E{C,n} are the energy spectra I get from CP2k for the charged molecule, and E{F,ref} is the reference level to vacuum for that calculation If there are N occupied molecular orbitals in the neutral molecule, than the reorganization energy can be approximated as: lambda = Sum{1:N}(E{C,n}+E{C,ref}) + Sum{1:N+1}(E{A,n}+E{A,ref}) - Sum{1:N+1}(E{C,n}+E{C,ref}) - Sum{1:N}(E{A,n}+E{A,ref}) lambda = Sum{1:N}(E{C,n}-E{A,n}) + Sum{1:N+1}(E{A,n}-E{C,n}) - E{C,ref} + E{A,ref} So the end product is directly proportional to the difference in reference energies. Cheers, Nuri -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuri.a.... at gmail.com Thu Feb 2 12:42:06 2017 From: nuri.a.... at gmail.com (Nuri Yazdani) Date: Thu, 2 Feb 2017 04:42:06 -0800 (PST) Subject: Vacuum level for charged systems In-Reply-To: <87802206-33c2-4536-a66f-294d426ba3e1@googlegroups.com> References: <87802206-33c2-4536-a66f-294d426ba3e1@googlegroups.com> Message-ID: A quick addition.. One thing I was thinking of doing was to use the energy of the deepest (lowest energy) states from the two calculations as an approximation to the difference in the reference levels. There are 543 occupied molecular orbitals in my system, and the difference in energy from the HOMO to the deepest is 16eV. Would this in general be a reasonable assumption? -------------- next part -------------- An HTML attachment was scrubbed... URL: From MattWa... at gmail.com Thu Feb 2 13:53:03 2017 From: MattWa... at gmail.com (Matt W) Date: Thu, 2 Feb 2017 05:53:03 -0800 (PST) Subject: Vacuum level for charged systems In-Reply-To: References: <87802206-33c2-4536-a66f-294d426ba3e1@googlegroups.com> Message-ID: <55f8a54c-ebcd-4d9f-bc8c-019128f33c6a@googlegroups.com> Hi, for non-periodic systems there should be no problem. The potential drops off as 1/r to a constant which you can define as your vacuum level. You might need a very large box or do some sort of extrapolation for accurate values. Matt On Thursday, February 2, 2017 at 12:42:06 PM UTC, Nuri Yazdani wrote: > > A quick addition.. One thing I was thinking of doing was to use the energy > of the deepest (lowest energy) states from the two calculations as an > approximation to the difference in the reference levels. There are 543 > occupied molecular orbitals in my system, and the difference in energy from > the HOMO to the deepest is 16eV. Would this in general be a reasonable > assumption? > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuri.a.... at gmail.com Thu Feb 2 18:07:01 2017 From: nuri.a.... at gmail.com (Nuri Yazdani) Date: Thu, 2 Feb 2017 10:07:01 -0800 (PST) Subject: Vacuum level for charged systems In-Reply-To: <55f8a54c-ebcd-4d9f-bc8c-019128f33c6a@googlegroups.com> References: <87802206-33c2-4536-a66f-294d426ba3e1@googlegroups.com> <55f8a54c-ebcd-4d9f-bc8c-019128f33c6a@googlegroups.com> Message-ID: Hi Matt, Thanks for the quick reply! I had done this first thing when the calculation had finished, but the problem was that the vacuum level I extracted depended on the direction of r!!! This confused me alot, and I thought there was some weird passivation going on... But thanks to your reply, I realized the error of my ways: I had set PERIODIC NONE in the cell section, and assumed the POISSON would then also be set to PERIODIC NONE, but indeed, one must set the periodicity in both the CELL and POISSON section... Cheers, NUri -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuri.a.... at gmail.com Thu Feb 2 18:08:42 2017 From: nuri.a.... at gmail.com (Nuri Yazdani) Date: Thu, 2 Feb 2017 10:08:42 -0800 (PST) Subject: Vacuum level for charged systems In-Reply-To: References: <87802206-33c2-4536-a66f-294d426ba3e1@googlegroups.com> <55f8a54c-ebcd-4d9f-bc8c-019128f33c6a@googlegroups.com> Message-ID: <8427ca8d-0238-452c-acd6-841de55a5695@googlegroups.com> Its presumably harmless to use a periodic poisson solver if you have a neutral system and a large enough cell size, but with the charge one would need quite a ginormous cell size for this to not matter.. -------------- next part -------------- An HTML attachment was scrubbed... URL: From no... at bollweevil.gdbg.org Thu Feb 2 20:11:55 2017 From: no... at bollweevil.gdbg.org (Noam Bernstein) Date: Thu, 2 Feb 2017 15:11:55 -0500 Subject: [CP2K:8626] Questions about AdBF-QM/MM in cp2k In-Reply-To: References: Message-ID: On Thu, Feb 2, 2017 at 12:59 AM, Ivan Gladich wrote: > Dear Cp2K users, > > I am a newbie of CP2K and I am trying to use Adaptive Buffered force QM-MM > (AdBF-QM/MM) in cp2k > > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351341/ > > to study a radical specie in water > I have a couple of questions. > > 1) Using > > ... > > &QMMM > > > &QM_KIND Br > > MM_INDEX 1 > > &END QM_KIND > > > > &QM_KIND O1 > > MM_INDEX 2 > > &END QM_KIND > > > &FORCE_MIXING > > MAX_N_QM 500 > > R_CORE 0.0 0.1 #dimension of the core region for the reduced QM/MM > calculation. Could be 0 if you have the force field > > R_QM 3.0 3.5 #Dimension of the dynamical core region > > R_BUF 3.0 3.5 #dimensione of the buffere region > > QM_KIND_ELEMENT_MAPPING Br Br #atoms that can be adaptively > selectefor the QM region > > QM_KIND_ELEMENT_MAPPING O O #atoms that can be adaptively selected > for the QM region > > QM_KIND_ELEMENT_MAPPING H H #atoms that can be adaptively > selectedfor the QM region > > EXTENDED_DELTA_CHARGE 0 # this is the charge of the QM_dynamical + > buffer region. > > MOMENTUM_CONSERVATION_REGION QM #only to dynamical core, you can > also choose BUFFER for QM+BUFFER > > MOMENTUM_CONSERVATION_TYPE EQUAL_A #equal acceleration on each > atom, or EQUAL_F, equal force > > &END FORCE_MIXING > > .... > > And I got in my output > > QMMM FORCE MIXING final count (not including links): N_QM core_list 2 > N_QM core 0 N_QM extended 12 N_QM buffered 63 > > QMMM FORCE MIXING final count (not including links): N_QM core_list 2 > N_QM core 0 N_QM extended 12 N_QM buffered 63 > > QMMM FORCE MIXING final count (not including links): N_QM core_list 2 > N_QM core 0 N_QM extended 12 N_QM buffered 63 > > QMMM FORCE MIXING final count (not including links): N_QM core_list 2 > N_QM core 0 N_QM extended 12 N_QM buffered 63 > > QMMM FORCE MIXING final count (not including links): N_QM core_list 2 > N_QM core 0 N_QM extended 12 N_QM buffered 63 > > > ... > > > Is N_QM core = 0 the number of atoms in my dynamical QM region? No, I apologize for the somewhat confusing output. "N_QM core" is the number added to the core list by the action of R_CORE. I.e. The core region consists of a fixed list (the atoms specified by the conventional QM/MM directives) + an additional region, which is every atom within R_CORE of the fixed list. The core region (combining those two, the list and the R_CORE based additions) is QM in both reduced and extended calculations whose forces will be mixed. The QM dynamics region includes all those core atoms, plus whatever is included by R_QM (based on distance from core atoms). > > Moreover, reading the paper N_QM extended "is constructed adding a buffer > region around the QM dynamical core" > > But N_QM extended =12 and N_QM buffered is 63, so it cannot be (N_QM should > be the same of the buffer plus the dynamical core)... I think here the notation of the code and the paper are unfortunately not quite consistent. N_QM extended refers to what the paper calls the dynamical QM region (I'm pretty sure it's actually just the part that's in addition to the core). It doesn't help that there are dynamically selected atoms in the core region (as well as in the QM dynamics region and buffer region), but that shouldn't be confused with the region that follows QM force dynamics. > > > 2) How does the R_BUF and R_QM works? > > > R_BUF is a radius around each atoms belonging to the QM dynamical core > region > > > OR > > > R_BUF is centered around the QM_CORE (in my case determined by Br and O > position) and, thus, I should impose always R_QM =< R_BUF ? More like the former, but not exactly, at least not if you're using the terminology of either the paper or the code. As the code documentation says, it's applied around every atom that should follow QM forces, i.e. the core list + the core distance (R_CORE) based + the QM dynamical region distance (R_QM) based. > > > 3) Is it possible to write, at each time step of my run, a label or the > indexes of the atoms in the dynamical and extended QM/MM region? > > > I tried using > > > &FORCE_MIXING_LABELS > > FORMAT XYZ > > &EACH > > MD 1 > > &END EACH > > COMMON_ITERATION_LEVELS 0 > > &END FORCE_MIXING_LABELS > > > but it seems that it labels only the atoms in the QM CORE, i.e., > *fmlabels-1_23.xyz > > > 6482 > > i = 23, time = 11.500, E = -21.9207476721 > > BR 10.0000000000 10.0000000000 10.0000000000 > > O 10.0000000000 10.0000000000 10.0000000000 > > O 0.0000000000 0.0000000000 0.0000000000 > > H 0.0000000000 0.0000000000 0.0000000000 > > H 0.0000000000 0.0000000000 0.0000000000 > Good question. I'll take a look at the source and remind myself what kind of functionality is available. Noam From MattWa... at gmail.com Thu Feb 2 20:37:44 2017 From: MattWa... at gmail.com (Matt W) Date: Thu, 2 Feb 2017 12:37:44 -0800 (PST) Subject: Vacuum level for charged systems In-Reply-To: References: <87802206-33c2-4536-a66f-294d426ba3e1@googlegroups.com> <55f8a54c-ebcd-4d9f-bc8c-019128f33c6a@googlegroups.com> Message-ID: Yes. It is a 'feature' that both the cell and Poisson sections need to be set. As you say, for a neutral system it is not too important. Matt On Thursday, February 2, 2017 at 6:07:02 PM UTC, Nuri Yazdani wrote: > > Hi Matt, > Thanks for the quick reply! > I had done this first thing when the calculation had finished, but the > problem was that the vacuum level I extracted depended on the direction of > r!!! This confused me alot, and I thought there was some weird passivation > going on... But thanks to your reply, I realized the error of my ways: > I had set PERIODIC NONE in the cell section, and assumed the POISSON would > then also be set to PERIODIC NONE, but indeed, one must set the periodicity > in both the CELL and POISSON section... > Cheers, > NUri > -------------- next part -------------- An HTML attachment was scrubbed... URL: From no... at bollweevil.gdbg.org Thu Feb 2 20:40:29 2017 From: no... at bollweevil.gdbg.org (Noam Bernstein) Date: Thu, 2 Feb 2017 15:40:29 -0500 Subject: [CP2K:8626] Questions about AdBF-QM/MM in cp2k In-Reply-To: References: Message-ID: On Thu, Feb 2, 2017 at 3:11 PM, Noam Bernstein wrote: > On Thu, Feb 2, 2017 at 12:59 AM, Ivan Gladich wrote: >> >> >> 3) Is it possible to write, at each time step of my run, a label or the >> indexes of the atoms in the dynamical and extended QM/MM region? >> >> >> I tried using >> >> >> &FORCE_MIXING_LABELS >> >> FORMAT XYZ >> >> &EACH >> >> MD 1 >> >> &END EACH >> >> COMMON_ITERATION_LEVELS 0 >> >> &END FORCE_MIXING_LABELS >> >> >> but it seems that it labels only the atoms in the QM CORE, i.e., >> *fmlabels-1_23.xyz >> >> >> 6482 >> >> i = 23, time = 11.500, E = -21.9207476721 >> >> BR 10.0000000000 10.0000000000 10.0000000000 >> >> O 10.0000000000 10.0000000000 10.0000000000 >> >> O 0.0000000000 0.0000000000 0.0000000000 >> >> H 0.0000000000 0.0000000000 0.0000000000 >> >> H 0.0000000000 0.0000000000 0.0000000000 >> > > Good question. I'll take a look at the source and remind myself what > kind of functionality is available. I looked at the source, and I see no reason why this should be the case. As far as I can tell it should write all the labels, values 4-10. How sure are you that there aren't some atoms with other label settings (> 0)? I think I'd need a full example (all the input files) that shows this problem to usefully investigate further. Ideally one that runs quickly. Noam From hardika... at gmail.com Fri Feb 3 10:24:08 2017 From: hardika... at gmail.com (Rahul Hardikar) Date: Fri, 3 Feb 2017 02:24:08 -0800 (PST) Subject: NAN output in in the *.LagrangeMultiplier file Message-ID: <9170b7d7-c176-4267-ac1c-1b2dac57163f@googlegroups.com> Dear Users/Experts, While running a QM/MM calculation for water molecules the output in the LagrangeMultiplier file is as follows Shake Lagrangian Multipliers: 24.425314277 -94.890187502 2.406631412 61.005724254 -78.361868824 28.428915483 66.118473470 -30.425607216 25.519130389 145.847761190 223.368208924 -92.946040717 159.908841030 33.340424280 -31.070636815 11.309165895 213.800221359 -63.757398799 -183.370302683 -118.382437816 . . . . . . . . . . . . Shake Lagrangian Multipliers: NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN . . . . . . . . . . . . However in a MM (NVT) simulation it does not happen this way. There are numbers in place of NAN. Can someone help me to understand this behavior in cp2k. Regards, Rahul -------------- next part -------------- An HTML attachment was scrubbed... URL: From rolf.d... at gmail.com Fri Feb 3 10:41:34 2017 From: rolf.d... at gmail.com (Rolf David) Date: Fri, 3 Feb 2017 02:41:34 -0800 (PST) Subject: Questions about AdBF-QM/MM in cp2k In-Reply-To: References: Message-ID: <070cc4e4-fded-429a-8975-bed3e2c420eb@googlegroups.com> For the force-mixing labels, for me it works I have 10.0 for list/core, 7.0 for extended and 5.0 for buffered. (for CP2K version 3.0) I have a parell question if I may: How can we restart a ad-qmmm calculations ?: I run a first dynamics, at the last step at the end i got: QMMM FORCE MIXING final count (not including links): N_QM core_list 11 N_QM core 0 N_QM extended 42 N_QM buffered 111 And restarting it, the very first step : QMMM FORCE MIXING final count (not including links): N_QM core_list 11 N_QM core 0 N_QM extended 33 N_QM buffered 87 + the WFN: READ RESTART : WARNING : DIFFERENT natom, returning 131 164 So for the minimal QM region, I got only core_list, so it doesen't change and it can read the WFN restart files But for the extended, since it is buffer in buffer out related, it varies. Is there a way to let CP2K now which atoms where in the extended/buffered ? (Except putting the min/max the same for R_*** distances) For info, these test were run on the 2.x (rev 16205) and i used: R_CORE [angstrom] 0.0 0.0 R_QM [angstrom] 2.5 3.0 R_BUF [angstrom] 2.5 3.0 A part for the restart issues, which can be penalising when using national/eu clusters where there is a wall time, it runs smoothly Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From michel... at enea.it Fri Feb 3 13:17:39 2017 From: michel... at enea.it (Michele Gusso) Date: Fri, 3 Feb 2017 05:17:39 -0800 (PST) Subject: Tersoff potentials with many elements Message-ID: Dear developers, it seems that there is a bug when using tersoff potentials with more than one element. The SUBROUTINE read_tersoff_section in file force_fields_input.F fills the cp2k variables of the various potentials pairs, always with the same (i.e. the first) data set of tersoff potentials read from the input file. I think that the lines of the kind: CALL section_vals_val_get(tersoff_section, "A", r_val=nonbonded%pot(start+isec)%pot%set(1)%tersoff%A) should be changed in CALL section_vals_val_get(tersoff_section, "A", i_rep_section=isec, r_val=nonbonded%pot(start+isec)%pot%set(1)%tersoff%A) Could you please check if I am correct ? (note that if this is correct the same should be done also for siepmann potentials). I have attached the input file I have used for this test. Thank you for your kind help. Best regards, Michele Gusso -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: SiH_tersoff.inp Type: chemical/x-gamess-input Size: 2529 bytes Desc: not available URL: From nuri.a.... at gmail.com Fri Feb 3 14:31:12 2017 From: nuri.a.... at gmail.com (Nuri Yazdani) Date: Fri, 3 Feb 2017 06:31:12 -0800 (PST) Subject: Computing total energy with -RESTART.wfn and no SCF iterations Message-ID: Hi All, I would like to calculate the total energy and hartree_potential for a system using HF, where I give a -RESTART.wfn file. The thing is, I want it to do the calculation using the wavefunctions from the -RESTART.wfn file without doing any SCF optimization steps (I want to calculate the total energy of a molecule which is *instantaneously* charged, i.e. use the wavefunctions found for the uncharged molecule to calculate the total energy of the charged molecule). I set in Section DFT (see attached file): &SCF SCF_GUESS RESTART MAX_SCF 0 EPS_SCF ${EPS_SCF} &OT PRECONDITIONER FULL_SINGLE_INVERSE &END &OUTER_SCF MAX_SCF 0 EPS_SCF ${EPS_SCF} &END &END SCF along with &PRINT &V_HARTREE_CUBE FILENAME ${FILE}_V.cube &END V_HARTREE_CUBE &MO_CUBES FILENAME ${FILE}.cube NLUMO 6 NHOMO 6 STRIDE 8 8 8 WRITE_CUBE .TRUE. &END MO_CUBES &PDOS FILENAME ${FILE}.pdos NLUMO 1000 &END PDOS &END PRINT However, it seems with no SCF iterations, none of the files I ask for are printed, and the calculations output file has only the standard start and end text: ** Copyright (C) by CP2K developers group (2000 - 2017) ** ** ** ******************************************************************************* ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): 0.000000000000000 ------------------------------------------------------------------------------- - - - DBCSR STATISTICS - Does anyone know how I can get this to work?? Also, I havent been able to test if this works yet or not, but is it possible to do this using a -RESTART.wfn file from the same system but with different charged state, or will this flag an error? cheers, Nuri -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthia... at psi.ch Fri Feb 3 15:00:37 2017 From: matthia... at psi.ch (Matthias Krack) Date: Fri, 3 Feb 2017 07:00:37 -0800 (PST) Subject: Computing total energy with -RESTART.wfn and no SCF iterations In-Reply-To: References: Message-ID: <0724744d-bae1-4e9c-925e-d99fa4404d5e@googlegroups.com> Hi Nuri MAX_SCF=0 will suppress any SCF iteration. You may try to set EPS_SCF to a large value like 1E6 to enforce an immediate SCF convergence, but you will probably run into new trouble, since the number of MOs on the restart file might not match. Best Matthias On Friday, 3 February 2017 15:31:12 UTC+1, Nuri Yazdani wrote: > > Hi All, > I would like to calculate the total energy and hartree_potential for a > system using HF, where I give a -RESTART.wfn file. The thing is, I want it > to do the calculation using the wavefunctions from the -RESTART.wfn file > without doing any SCF optimization steps (I want to calculate the total > energy of a molecule which is *instantaneously* charged, i.e. use the > wavefunctions found for the uncharged molecule to calculate the total > energy of the charged molecule). > > I set in Section DFT (see attached file): > &SCF > SCF_GUESS RESTART > MAX_SCF 0 > EPS_SCF ${EPS_SCF} > &OT > PRECONDITIONER FULL_SINGLE_INVERSE > &END > &OUTER_SCF > MAX_SCF 0 > EPS_SCF ${EPS_SCF} > &END > &END SCF > > along with > > &PRINT > &V_HARTREE_CUBE > FILENAME ${FILE}_V.cube > &END V_HARTREE_CUBE > &MO_CUBES > FILENAME ${FILE}.cube > NLUMO 6 > NHOMO 6 > STRIDE 8 8 8 > WRITE_CUBE .TRUE. > &END MO_CUBES > &PDOS > FILENAME ${FILE}.pdos > NLUMO 1000 > &END PDOS > &END PRINT > > However, it seems with no SCF iterations, none of the files I ask for are > printed, and the calculations output file has only the standard start and > end text: > > ** Copyright (C) by CP2K developers group (2000 - 2017) > ** > ** > ** > > ******************************************************************************* > > ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): > 0.000000000000000 > > > > ------------------------------------------------------------------------------- > - > - > - DBCSR STATISTICS > - > > Does anyone know how I can get this to work?? Also, I havent been able to > test if this works yet or not, but is it possible to do this using a > -RESTART.wfn file from the same system but with different charged state, or > will this flag an error? > cheers, > Nuri > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuri.a.... at gmail.com Fri Feb 3 15:59:14 2017 From: nuri.a.... at gmail.com (Nuri Yazdani) Date: Fri, 3 Feb 2017 07:59:14 -0800 (PST) Subject: Computing total energy with -RESTART.wfn and no SCF iterations In-Reply-To: <0724744d-bae1-4e9c-925e-d99fa4404d5e@googlegroups.com> References: <0724744d-bae1-4e9c-925e-d99fa4404d5e@googlegroups.com> Message-ID: <580f0869-4a6a-467d-b4c3-1492debae924@googlegroups.com> HI Matthias, Thanks for the quick reply. The problem with setting the EPS to something high is that it will still perform one optimization step. I want to get the total energy from the supplied wavefunction as is without any modification. -------------- next part -------------- An HTML attachment was scrubbed... URL: From brehmin... at googlemail.com Fri Feb 3 20:45:45 2017 From: brehmin... at googlemail.com (M. Brehm) Date: Fri, 3 Feb 2017 12:45:45 -0800 (PST) Subject: Computing total energy with -RESTART.wfn and no SCF iterations In-Reply-To: References: Message-ID: <135a37a6-588d-4977-b338-1901e3385a80@googlegroups.com> Just a quick idea: Maybe setting the mixing parameter "Alpha" to zero will do it. Then CP2k will perform one or more SCF steps, but the wave function should not change at all. Best regards, Martin -------------- next part -------------- An HTML attachment was scrubbed... URL: From igla... at gmail.com Sun Feb 5 06:00:11 2017 From: igla... at gmail.com (Ivan Gladich) Date: Sun, 5 Feb 2017 09:00:11 +0300 Subject: [CP2K:8638] Re: Questions about AdBF-QM/MM in cp2k In-Reply-To: <070cc4e4-fded-429a-8975-bed3e2c420eb@googlegroups.com> References: <070cc4e4-fded-429a-8975-bed3e2c420eb@googlegroups.com> Message-ID: Dear Noam, Dear Rolf, thank you for your reply, they helped me to better understand the meaning of R_QM, R_CORE and EXTENDED and the differences with to the paper. Concerning the labels I still have some unclear point. For example, I got for the last step > QMMM FORCE MIXING final count (not including links): N_QM core_list 2 N_QM core 0 N_QM extended 12 N_QM buffered 66 but, if I look at my non-zero labels I see 6482 i = 50, time = 25.000, E = -108.8420993135 BR 10.0000000000 10.0000000000 10.0000000000 O 10.0000000000 10.0000000000 10.0000000000 O 5.0000000000 5.0000000000 5.0000000000 H 5.0000000000 5.0000000000 5.0000000000 H 5.0000000000 5.0000000000 5.0000000000 O 7.0000000000 7.0000000000 7.0000000000 H 7.0000000000 7.0000000000 7.0000000000 H 7.0000000000 7.0000000000 7.0000000000 O 5.0000000000 5.0000000000 5.0000000000 H 5.0000000000 5.0000000000 5.0000000000 H 5.0000000000 5.0000000000 5.0000000000 O 5.0000000000 5.0000000000 5.0000000000 H 5.0000000000 5.0000000000 5.0000000000 H 5.0000000000 5.0000000000 5.0000000000 O 5.0000000000 5.0000000000 5.0000000000 H 5.0000000000 5.0000000000 5.0000000000 H 5.0000000000 5.0000000000 5.0000000000 So, two questions a) 10 should be the core list atoms but which is the meaning of labels 7 and 5? b) I cannot match the numbers because the labels tells me that I have 17 QM atoms in the extended or extended plus buffer. The Output points toward much higher number (66) You can find my inputs at the following link goo.gl/C15cBY Thank you again for your help, it was extremely useful. Ivan On Fri, Feb 3, 2017 at 1:41 PM, Rolf David wrote: > > > For the force-mixing labels, for me it works > I have 10.0 for list/core, 7.0 for extended and 5.0 for buffered. (for > CP2K version 3.0) > > I have a parell question if I may: > > How can we restart a ad-qmmm calculations ?: > > I run a first dynamics, at the last step at the end i got: > > QMMM FORCE MIXING final count (not including links): N_QM core_list > 11 N_QM core 0 N_QM extended 42 N_QM buffered 111 > > > > And restarting it, the very first step : > > QMMM FORCE MIXING final count (not including links): N_QM core_list > 11 N_QM core 0 N_QM extended 33 N_QM buffered 87 > > > + the WFN: READ RESTART : WARNING : DIFFERENT natom, returning > 131 164 > > > So for the minimal QM region, I got only core_list, so it doesen't change > and it can read the WFN restart files > > But for the extended, since it is buffer in buffer out related, it varies. > > > Is there a way to let CP2K now which atoms where in the extended/buffered > ? (Except putting the min/max the same for R_*** distances) > > > For info, these test were run on the 2.x (rev 16205) and i used: > > > R_CORE [angstrom] 0.0 0.0 > > R_QM [angstrom] 2.5 3.0 > > R_BUF [angstrom] 2.5 3.0 > > > > > > A part for the restart issues, which can be penalising when using > national/eu clusters where there is a wall time, it runs smoothly > > > Thanks > > > -- > You received this message because you are subscribed to a topic in the > Google Groups "cp2k" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/cp2k/u4xcztECsE0/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tfran... at gmail.com Sun Feb 5 19:06:36 2017 From: tfran... at gmail.com (tfran... at gmail.com) Date: Sun, 5 Feb 2017 11:06:36 -0800 (PST) Subject: Comparison between CP2K and Quantum Espresso Message-ID: <0ffff976-c924-4c83-ad18-1b2fe2ecbe91@googlegroups.com> Dear all, I am currently testing my new machine, which is a cluster 2 Supermicro 2048U RT4 nodes with 4x2.6GHZ Intel Broadwell 10Core CPUs. The point is that in order to check the scalability and the performances of the machine with 40 processors, I run several single point calculations of the same structure both with CP2K version 4.1 ssmp and Quantum Espresso 5.1.1 It turns out that for the time spent by CP2K to converge a single point calculation with 40 processors, for a system of 256 atoms, was of the order of 13316.63 seconds (taken from the output in the TIMING BLOCK in the end of the output file [TOTAL TIME AVERAGE); whereas for the QE, the same calculation, with the same system ect. took just 1845.76 seconds. So, because we strongly want to work with CP2K, also for running some dynamics and exploit its scalability, may i ask you to kindly check if the input file of the CP2K I used is properly set? I am more expert in QE rather than CP2K, so I might have miss something essential. For matter of comparison I attached the two input files used, one for the CP2K and the other of the QE. Thanks in advance for the kind help! Best Regards, Tommaso -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cp2k.inp Type: chemical/x-gamess-input Size: 3283 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: qe.inp Type: chemical/x-gamess-input Size: 1650 bytes Desc: not available URL: From chenh... at gmail.com Sun Feb 5 20:50:49 2017 From: chenh... at gmail.com (NUCP2K) Date: Sun, 5 Feb 2017 12:50:49 -0800 (PST) Subject: questions about TDDFPT2 Message-ID: <2d496684-08e2-408d-a645-b8fbf2c0d11c@googlegroups.com> Dear CP2K Developers and Users, I just tried out the latest implementation of time-dependent density functional perturbation theory (TDDFPT) in CP2K, and found some serious inconsistencies on the calculated excitation energy. I tested the TDDFPT2 on an isolated water (H2O) molecule using the attached input file. Interestingly, the calculated excitation energy of 10.075 eV is much much greater than the HOMO-LUMO gap of 9.137 eV, even though the transition is dominated (>99.9%) by the electron transfer from HOMO to LUMO. It seems to me that the diagonal terms of the TDDFPT response matrix are not appropriately assigned, leading to the apparent inconsistency. Perhaps, the subroutine "tddfpt_init_by_energy_diff" in qs_tddfpt2_methods.F should be fixed to yield correct orbital energy gap. Please correct me if my understanding is wrong. Thanks. Hanning &FORCE_EVAL METHOD QS &PROPERTIES &TDDFPT NSTATES 1 MAX_ITER 100 MAX_KV 10 CONVERGENCE [eV] 1.0E-3 &DIPOLE_MOMENTS DIPOLE_FORM LENGTH &END DIPOLE_MOMENTS &MGRID COMMENSURATE CUTOFF 50 &END MGRID &END TDDFPT &END PROPERTIES &DFT BASIS_SET_FILE_NAME BASIS_SET POTENTIAL_FILE_NAME POTENTIAL &MGRID COMMENSURATE CUTOFF 50 &END MGRID &POISSON PERIODIC NONE POISSON WAVELET &END POISSON &SCF SCF_GUESS ATOMIC &END SCF &XC &XC_FUNCTIONAL PBE &END XC_FUNCTIONAL &XC_GRID XC_DERIV SPLINE2_SMOOTH &END XC_GRID &END XC &END DFT &SUBSYS &CELL ABC 6.0 6.0 6.0 PERIODIC NONE &END CELL &COORD O 3.000000 3.000000 3.000000 H2O1 H 3.000000 3.000000 4.000000 H2O1 H 3.942809 3.000000 2.666667 H2O1 &END COORD &KIND H BASIS_SET SZV-GTH POTENTIAL GTH-PADE-q1 &END KIND &KIND O BASIS_SET SZV-GTH POTENTIAL GTH-PADE-q6 &END KIND &TOPOLOGY &END TOPOLOGY &END SUBSYS &END FORCE_EVAL &GLOBAL PROJECT WATER PRINT_LEVEL MEDIUM RUN_TYPE ENERGY &END GLOBAL -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Mon Feb 6 14:34:49 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Mon, 6 Feb 2017 15:34:49 +0100 Subject: [CP2K:8640] Tersoff potentials with many elements In-Reply-To: References: Message-ID: Thank you. I have fixed this bug in the Trunk SVN version. regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Michele Gusso Sent by: cp... at googlegroups.com Date: 02/03/2017 02:17PM Subject: [CP2K:8640] Tersoff potentials with many elements Dear developers, it seems ?that there is a bug when using tersoff potentials with more than one element.The SUBROUTINE read_tersoff_section in file ?force_fields_input.F fills the cp2k variables of the various potentials pairs,always with the same (i.e. the first) data set of tersoff potentials read from the input file.I think that the lines of the kind:CALL section_vals_val_get(tersoff_section, "A", r_val=nonbonded%pot(start+isec)%pot%set(1)%tersoff%A)should be changed in?CALL section_vals_val_get(tersoff_section, "A", i_rep_section=isec,r_val=nonbonded%pot(start+isec)%pot%set(1)%tersoff%A) Could you please check if I am correct ? (note that if this is correct the same should be done also for siepmann potentials).I have attached the input file I have used for this test.Thank you for your kind help. Best regards,Michele Gusso -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. [attachment "SiH_tersoff.inp" removed by J?rg Hutter/at/UZH] From hut... at chem.uzh.ch Mon Feb 6 15:04:36 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Mon, 6 Feb 2017 16:04:36 +0100 Subject: [CP2K:8645] Comparison between CP2K and Quantum Espresso In-Reply-To: <0ffff976-c924-4c83-ad18-1b2fe2ecbe91@googlegroups.com> References: <0ffff976-c924-4c83-ad18-1b2fe2ecbe91@googlegroups.com> Message-ID: Hi without additional information (e.g. output files or complete input) I will have to do guessing. There are two parts to this calculation - time per SCF step - number of SCF steps needed for convergence SCF convergence: you start from an atomic guess (CP2K) and a random wfn (QE). Although the convergence asked for is the same (1.e-7) this means different things in the two codes (check change in energy for the last step). For CP2K you can optimize the settings for the convergence, but as you do start from scratch only once the more important part is what is the timing per step. (You probably also don't need CHOLESKY OFF?, you use the most expensive PRECONDITIONER, DIIS might not be good to start with ...) Your settings are ok, but rather tight in many respect, e.g. large and diffuse basis set, high cutoff. Non orthorhombic cell is also not optimal for CP2K. So this is a very expensive calculation in CP2K standards. regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: tfran... at gmail.com Sent by: cp... at googlegroups.com Date: 02/05/2017 08:06PM Subject: [CP2K:8645] Comparison between CP2K and Quantum Espresso Dear all,I am currently testing my new machine, which is a cluster?2 Supermicro 2048U RT4 nodes with?4x2.6GHZ Intel Broadwell 10Core CPUs.The point is that in order to check the scalability and the performances of the machine with 40 processors, I run several single point calculations of the same structure both with CP2K version 4.1?ssmp and Quantum Espresso 5.1.1?It turns out that for the time spent by CP2K to converge a single point calculation with 40 processors, for a system of 256 atoms, was of the order of 13316.63 seconds (taken from the output in the TIMING BLOCK in the end of the output file [TOTAL TIME AVERAGE); whereas for the QE, the same calculation, with the same system ect. took just 1845.76 seconds.?So, because we strongly want to work with CP2K, also for running some dynamics and exploit its scalability, may i ask you to?kindly check if the input file of the CP2K I used is properly set? I am more expert in QE rather than CP2K, so I might have miss something essential. For matter of comparison I attached the two input files used, one for the CP2K and the other of the QE. Thanks in advance for the kind help! Best Regards,Tommaso? -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. [attachment "cp2k.inp" removed by J?rg Hutter/at/UZH] [attachment "qe.inp" removed by J?rg Hutter/at/UZH] From MattWa... at gmail.com Mon Feb 6 15:22:45 2017 From: MattWa... at gmail.com (Matt W) Date: Mon, 6 Feb 2017 07:22:45 -0800 (PST) Subject: questions about TDDFPT2 In-Reply-To: <2d496684-08e2-408d-a645-b8fbf2c0d11c@googlegroups.com> References: <2d496684-08e2-408d-a645-b8fbf2c0d11c@googlegroups.com> Message-ID: <5b81aee5-7b1a-41fe-b1bd-03ed6715d94e@googlegroups.com> Hi Hanning, I've not had a chance to look at your particular calculation. Such a small basis set, and small box could lead to strange results in any case. More generally, there is no reason, even if the transition is a pure single determinant HOMO to LUMO, for the energy to be that of the HOMO_LUMO gap. There are still additional terms in the TDDFT kernel that will shift the transition energy. For GGAs the shifts can be in either direction, there is no general rule. We have checked small molecule transition energies vs gamess-us and were pretty happy with the comparison. HTH, Matt On Sunday, February 5, 2017 at 8:50:49 PM UTC, NUCP2K wrote: > > Dear CP2K Developers and Users, > > I just tried out the latest implementation of time-dependent density > functional perturbation theory (TDDFPT) in CP2K, and found some serious > inconsistencies on the calculated excitation energy. > > I tested the TDDFPT2 on an isolated water (H2O) molecule using the > attached input file. Interestingly, the calculated excitation energy of > 10.075 eV is much much greater than the HOMO-LUMO gap of 9.137 eV, even > though the transition is dominated (>99.9%) by the electron transfer from > HOMO to LUMO. > > It seems to me that the diagonal terms of the TDDFPT response matrix are > not appropriately assigned, leading to the apparent inconsistency. Perhaps, > the subroutine "tddfpt_init_by_energy_diff" in qs_tddfpt2_methods.F should > be fixed to yield correct orbital energy gap. > > Please correct me if my understanding is wrong. > > Thanks. > > Hanning > > > &FORCE_EVAL > METHOD QS > &PROPERTIES > &TDDFPT > NSTATES 1 > MAX_ITER 100 > MAX_KV 10 > CONVERGENCE [eV] 1.0E-3 > &DIPOLE_MOMENTS > DIPOLE_FORM LENGTH > &END DIPOLE_MOMENTS > &MGRID > COMMENSURATE > CUTOFF 50 > &END MGRID > &END TDDFPT > &END PROPERTIES > &DFT > BASIS_SET_FILE_NAME BASIS_SET > POTENTIAL_FILE_NAME POTENTIAL > &MGRID > COMMENSURATE > CUTOFF 50 > &END MGRID > &POISSON > PERIODIC NONE > POISSON WAVELET > &END POISSON > &SCF > SCF_GUESS ATOMIC > &END SCF > &XC > &XC_FUNCTIONAL PBE > &END XC_FUNCTIONAL > &XC_GRID > XC_DERIV SPLINE2_SMOOTH > &END XC_GRID > &END XC > &END DFT > &SUBSYS > &CELL > ABC 6.0 6.0 6.0 > PERIODIC NONE > &END CELL > &COORD > O 3.000000 3.000000 3.000000 H2O1 > H 3.000000 3.000000 4.000000 H2O1 > H 3.942809 3.000000 2.666667 H2O1 > &END COORD > &KIND H > BASIS_SET SZV-GTH > POTENTIAL GTH-PADE-q1 > &END KIND > &KIND O > BASIS_SET SZV-GTH > POTENTIAL GTH-PADE-q6 > &END KIND > &TOPOLOGY > &END TOPOLOGY > &END SUBSYS > &END FORCE_EVAL > &GLOBAL > PROJECT WATER > PRINT_LEVEL MEDIUM > RUN_TYPE ENERGY > &END GLOBAL > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tfran... at gmail.com Mon Feb 6 17:17:49 2017 From: tfran... at gmail.com (tfran... at gmail.com) Date: Mon, 6 Feb 2017 09:17:49 -0800 (PST) Subject: [CP2K:8645] Comparison between CP2K and Quantum Espresso In-Reply-To: References: <0ffff976-c924-4c83-ad18-1b2fe2ecbe91@googlegroups.com> Message-ID: <168a13df-678c-419b-b5f1-56e5645edcf7@googlegroups.com> Dear Prof. Hutter, first of all, thanks a lot for your kind reply. Il giorno luned? 6 febbraio 2017 16:04:41 UTC+1, jgh ha scritto: > > Hi > > without additional information (e.g. output files or complete input) > I will have to do guessing. > > There are two parts to this calculation > - time per SCF step > - number of SCF steps needed for convergence > > SCF convergence: you start from an atomic guess (CP2K) and a random > wfn (QE). Although the convergence asked for is the same (1.e-7) > this means different things in the two codes (check change in energy > for the last step). For CP2K you can optimize the settings for the convergence, but as you do start from scratch only once the more > important part is what is the timing per step. > (You probably also don't need CHOLESKY OFF?, > you use the most expensive PRECONDITIONER, > DIIS might not be good to start with ...) Ok, i will check this part in detail in order to better tune the input to my and to get rid of the "most" expensive part as much as I can. > > Your settings are ok, but rather tight in many respect, e.g. large and > diffuse basis set, high cutoff. Non orthorhombic cell is also not > optimal for CP2K. > Ok, I will decrease the settings parameters in order to allow a better flexibility in terms of the cutoff eat. Unfortunately all the systems I am dealing with are or monoclinic or triclinic. Now that I am aware of this pitfall, I will reset all the parameters in order to enhance the jobs as much as they can. > So this is a very expensive calculation in CP2K standards. > > regards > > Juerg > > Thanks a lot again for clarifying me these crucial points! Best Regards, Tommaso > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: hut... at chem.uzh.ch > > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----cp... at googlegroups.com wrote: -----To: cp2k < > cp... at googlegroups.com > > From: tfra... at gmail.com > Sent by: cp... at googlegroups.com > Date: 02/05/2017 08:06PM > Subject: [CP2K:8645] Comparison between CP2K and Quantum Espresso > > Dear all,I am currently testing my new machine, which is a cluster 2 > Supermicro 2048U RT4 nodes with 4x2.6GHZ Intel Broadwell 10Core CPUs.The > point is that in order to check the scalability and the performances of the > machine with 40 processors, I run several single point calculations of the > same structure both with CP2K version 4.1 ssmp and Quantum Espresso > 5.1.1 It turns out that for the time spent by CP2K to converge a single > point calculation with 40 processors, for a system of 256 atoms, was of the > order of 13316.63 seconds (taken from the output in the TIMING BLOCK in the > end of the output file [TOTAL TIME AVERAGE); whereas for the QE, the same > calculation, with the same system ect. took just 1845.76 seconds. So, > because we strongly want to work with CP2K, also for running some dynamics > and exploit its scalability, may i ask you to kindly check if the input > file of the CP2K I used is properly set? I am more expert in QE rather than > CP2K, so I might have miss something essential. > For matter of comparison I attached the two input files used, one for the > CP2K and the other of the QE. > Thanks in advance for the kind help! > > > > > > > > > > > > > > > > > > > Best Regards,Tommaso > > > > > > > > > > -- > > You received this message because you are subscribed to the Google Groups > "cp2k" group. > > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+... at googlegroups.com . > > To post to this group, send email to cp... at googlegroups.com . > > > Visit this group at https://groups.google.com/group/cp2k. > > For more options, visit https://groups.google.com/d/optout. > > > > [attachment "cp2k.inp" removed by J?rg Hutter/at/UZH] > [attachment "qe.inp" removed by J?rg Hutter/at/UZH] > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shun3... at gmail.com Mon Feb 6 17:24:11 2017 From: shun3... at gmail.com (Shun) Date: Mon, 6 Feb 2017 09:24:11 -0800 (PST) Subject: Geometry optimization of SiO2 Message-ID: Hi I am a beginner of cp2k and trying to optimize the structure of SiO2 to make sure that cp2k works for zeolite I want to calculate. The following input file was submitted and the BFGS Optimization was fine first. But, the SCF of the 3rd optimization cycle was not converged and I saw the structure made big change. What is the problem of this? I attempted also other structures of SiO2 but same problem happened again. If you have a advice, suggestion or solution, let me know please. ************************** &GLOBAL PROJECT_NAME sio2 RUN_TYPE GEO_OPT &END GLOBAL &MOTION &GEO_OPT OPTIMIZER BFGS MAX_ITER 5000 MAX_DR 1.0000000000000000E-4 MAX_FORCE 1E-6 &END GEO_OPT &END MOTION &FORCE_EVAL METHOD QS &DFT BASIS_SET_FILE_~/cp2k-3.0/data/GTH_BASIS_SETS POTENTIAL_FILE_NAME ~/cp2k-3.0/data/POTENTIAL &SCF EPS_SCF 1.0E-6 MAX_SCF 200 &MIXING T ALPHA 0.1 &END MIXING &END SCF &QS METHOD GPW &END QS &MGRID CUTOFF 300 &END MGRID &XC &XC_FUNCTIONAL &END XC_FUNCTIONAL &END XC &END DFT &SUBSYS &CELL PERIODIC XYZ A 4.916000000000000 0.000000000000000 0.000000000000000 B -2.458000000000000 4.257380885004300 0.000000000000000 C 0.000000000000000 0.000000000000000 5.407000000000000 &END CELL &COORD Si -1.529859200000000 3.118957236354151 4.758700699999999 Si -0.080622400000000 1.117988220402129 1.154394500000000 Si 2.379098200000000 0.860416676859369 2.956006900000000 O 0.000000000000000 0.000000000000000 0.000000000000000 O -0.594098600000000 2.495250936701020 0.517990600000000 O -0.600489400000000 3.740960583653279 3.594573599999999 O 1.372301400000000 1.357678764227871 1.798908900000000 O 2.451363400000000 1.978404897261498 4.123918900000000 O 3.828826600000000 0.623706299653130 2.314736700000000 &END COORD &KIND Si BASIS_SET DZVP-GTH POTENTIAL GTH-PBE-q4 &END KIND &KIND O BASIS_SET DZVP-GTH POTENTIAL GTH-PBE-q6 &END KIND &END SUBSYS &END FORCE_EVAL ********************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From donaldduc... at gmail.com Mon Feb 6 17:27:17 2017 From: donaldduc... at gmail.com (donaldducksdaughter) Date: Mon, 6 Feb 2017 09:27:17 -0800 (PST) Subject: Aluminium TZV2P-MOLOPT BASIS SET Message-ID: Dear all, I'm interested in obtaining a MOLOPT basis set for use with GTH pseudo potentials (which cannot be found in the cp2k/data or on the github website). I'm specifically interested in a TZV2P MOLOPT basis set for Aluminium (Al). The highest order MOLOPT Al basis set for use with the GTH pseudo potential, which I could find, is the DZVP-MOLOPT-SR-GTH. For consistency with respect to the other atoms in my system, I would like to use this for Aluminium unusual basis set. How would I be able to generate this or has this basis set already been generated? However, for a non-MOLOPT basis set the Al TZV2P-GTH Al basis set is available. Hence, would you recommend moving all my atoms to non-molopt basis sets instead? Thanks for taking the time to read this request. Many thanks in advance. Best wishes, Julia -------------- next part -------------- An HTML attachment was scrubbed... URL: From lingsa... at gmail.com Mon Feb 6 17:35:42 2017 From: lingsa... at gmail.com (S Ling) Date: Mon, 6 Feb 2017 17:35:42 +0000 Subject: [CP2K:8651] Aluminium TZV2P-MOLOPT BASIS SET In-Reply-To: References: Message-ID: Dear Julia, Please have a look at the basis sets included in the BASIS_MOLOPT_UCL file which we recently uploaded to trunk version of the code. The file is in the $CP2K/co2k/data directory if you download the trunk version of the code, or you can download it directly from here: https://sourceforge.net/p/cp2k/code/17747/tree/trunk/cp2k/data/BASIS_MOLOPT_UCL We have generated TZVP/TZV2P quality for majority of the heavy elements in the periodic table to be used together with GTH pseudopotential. These basis sets should be more complete than the SZV/DZVP-MOLOPT basis sets included in the original BASIS_MOLOPT file. SL On 6 February 2017 at 17:15, donaldducksdaughter < donaldduc... at gmail.com> wrote: > Dear all, > > I'm interested in obtaining a MOLOPT basis set for use with GTH pseudo > potentials (which cannot be found in the cp2k/data or on the github > website). I'm specifically interested in a TZV2P MOLOPT basis set for > Aluminium (Al). The highest order MOLOPT Al basis set for use with the GTH > pseudo potential, which I could find, is the DZVP-MOLOPT-SR-GTH. For > consistency with respect to the other atoms in my system, I would like to > use this for Aluminium unusual basis set. How would I be able to generate > this or has this basis set already been generated? However, for a > non-MOLOPT basis set the Al TZV2P-GTH Al basis set is available. Hence, would > you recommend moving all my atoms to non-molopt basis sets instead? > > Thanks for taking the time to read this request. > > Many thanks in advance. > > Best wishes, > > Julia > > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From donaldduc... at gmail.com Mon Feb 6 18:11:36 2017 From: donaldduc... at gmail.com (donaldducksdaughter) Date: Mon, 6 Feb 2017 10:11:36 -0800 (PST) Subject: [CP2K:8651] Aluminium TZV2P-MOLOPT BASIS SET In-Reply-To: References: Message-ID: <2c8a4b76-c852-485d-b6cd-8f5db780cde9@googlegroups.com> Thank you so much! It was not included in my cp2k/data directory. Best, Julia Am Montag, 6. Februar 2017 18:35:43 UTC+1 schrieb S Ling: > > Dear Julia, > > Please have a look at the basis sets included in the BASIS_MOLOPT_UCL file > which we recently uploaded to trunk version of the code. The file is in the > $CP2K/co2k/data directory if you download the trunk version of the code, or > you can download it directly from here: > > > https://sourceforge.net/p/cp2k/code/17747/tree/trunk/cp2k/data/BASIS_MOLOPT_UCL > > > We have generated TZVP/TZV2P quality for majority of the heavy elements in > the periodic table to be used together with GTH pseudopotential. These > basis sets should be more complete than the SZV/DZVP-MOLOPT basis sets > included in the original BASIS_MOLOPT file. > > SL > > > On 6 February 2017 at 17:15, donaldducksdaughter > wrote: > >> Dear all, >> >> I'm interested in obtaining a MOLOPT basis set for use with GTH pseudo >> potentials (which cannot be found in the cp2k/data or on the github >> website). I'm specifically interested in a TZV2P MOLOPT basis set for >> Aluminium (Al). The highest order MOLOPT Al basis set for use with the GTH >> pseudo potential, which I could find, is the DZVP-MOLOPT-SR-GTH. For >> consistency with respect to the other atoms in my system, I would like to >> use this for Aluminium unusual basis set. How would I be able to generate >> this or has this basis set already been generated? However, for a >> non-MOLOPT basis set the Al TZV2P-GTH Al basis set is available. Hence, would >> you recommend moving all my atoms to non-molopt basis sets instead? >> >> Thanks for taking the time to read this request. >> >> Many thanks in advance. >> >> Best wishes, >> >> Julia >> >> -- >> You received this message because you are subscribed to the Google Groups >> "cp2k" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to cp2k+... at googlegroups.com . >> To post to this group, send email to cp... at googlegroups.com >> . >> Visit this group at https://groups.google.com/group/cp2k. >> For more options, visit https://groups.google.com/d/optout. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From no... at bollweevil.gdbg.org Mon Feb 6 21:17:52 2017 From: no... at bollweevil.gdbg.org (Noam Bernstein) Date: Mon, 6 Feb 2017 16:17:52 -0500 Subject: [CP2K:8644] Re: Questions about AdBF-QM/MM in cp2k In-Reply-To: References: <070cc4e4-fded-429a-8975-bed3e2c420eb@googlegroups.com> Message-ID: On Sun, Feb 5, 2017 at 1:00 AM, Ivan Gladich wrote: > Dear Noam, > > > So, two questions > > a) 10 should be the core list atoms but which is the meaning of labels 7 and > 5? 10.0 is core list 7.0 is QM dynamics (what's called, misleadingly, "N_QM extended" above), 5.0 is buffer > b) I cannot match the numbers because the labels tells me that I have 17 QM > atoms in the extended or extended plus buffer. > The Output points toward much higher number (66) If those lines are the only ones that are non-zero, then I agree there's a mismatch, but it's hard for me to imagine how that happens, since the files are written from the same internal data structures that are used to generate the counts that are printed above. I'll try to run with your input files. Noam From nuri.a.... at gmail.com Tue Feb 7 10:47:24 2017 From: nuri.a.... at gmail.com (Nuri Yazdani) Date: Tue, 7 Feb 2017 02:47:24 -0800 (PST) Subject: Computing total energy with -RESTART.wfn and no SCF iterations In-Reply-To: References: Message-ID: Thanks for the feedback Martin and Matthias! Your trick worked Martin, I set the alpha to 0 and then checked the energies and wavefunctions output form the calculation and they were identical to those in the restart file. However, you were right Matthias, I was not able to use a restart file for a calculation with a different charge, as the number of MOs did not match up. I will have to think of another way to calculate this.... Anyways, just wanted to close the thread in case someone else may find it helpful in the future. Cheers, Nuri -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthia... at psi.ch Tue Feb 7 11:30:58 2017 From: matthia... at psi.ch (Matthias Krack) Date: Tue, 7 Feb 2017 03:30:58 -0800 (PST) Subject: Computing total energy with -RESTART.wfn and no SCF iterations In-Reply-To: References: Message-ID: Hi Nuri you could try the ADDED_MOS keyword (works with diagonalization) for the initial run with the uncharged system before you give up and close this thread.It should work if there are more MOs on the restart file than needed. Best Matthias On Tuesday, 7 February 2017 11:47:24 UTC+1, Nuri Yazdani wrote: > > > Thanks for the feedback Martin and Matthias! > Your trick worked Martin, I set the alpha to 0 and then checked the > energies and wavefunctions output form the calculation and they were > identical to those in the restart file. > However, you were right Matthias, I was not able to use a restart file for > a calculation with a different charge, as the number of MOs did not match > up. I will have to think of another way to calculate this.... > Anyways, just wanted to close the thread in case someone else may find it > helpful in the future. > Cheers, > Nuri > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Tue Feb 7 14:19:08 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Tue, 7 Feb 2017 15:19:08 +0100 Subject: [CP2K:8652] Geometry optimization of SiO2 In-Reply-To: References: Message-ID: Hi Please specify a XC functional ???? &XC ?????? &XC_FUNCTIONAL <--- here <--- or here ?????? &END XC_FUNCTIONAL ???? &END XC you can also optimize your SCF section for better convergence, see examples regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Shun Sent by: cp... at googlegroups.com Date: 02/06/2017 06:19PM Subject: [CP2K:8652] Geometry optimization of SiO2 Hi I am a beginner of cp2k and trying to optimize the structure of SiO2 to make sure that cp2k works for zeolite I want to calculate. The following input file was submitted and the BFGS Optimization was fine first. But, 3rd and 4th SCF cycle of the optimization was not converged and I saw the structure made big change. What is the problem of this? I attempted also other structures of SiO2 but same problem happened again. If you have a advice, suggestion or solution, let me know please. ? ************************** &GLOBAL ?? PROJECT_NAME sio2 ?? RUN_TYPE? GEO_OPT ?&END GLOBAL ?&MOTION ?? &GEO_OPT ???? OPTIMIZER BFGS ???? MAX_ITER? 5000 ???? MAX_DR???? 1.0000000000000000E-4 ???? MAX_FORCE???? 1E-6 ?? &END GEO_OPT ?&END MOTION ?&FORCE_EVAL ?? METHOD? QS ?? &DFT ???? BASIS_SET_FILE_~/cp2k-3.0/data/GTH_BASIS_SETS ???? POTENTIAL_FILE_NAME ~/cp2k-3.0/data/POTENTIAL ??? &SCF ?????? EPS_SCF 1.0E-6 ?????? MAX_SCF 200 ?????? &MIXING T ????????? ALPHA 0.1 ?????? &END MIXING ???? &END SCF ???? &QS ?????? METHOD? GPW ???? &END QS ???? &MGRID ?????? CUTOFF??? 300 ???? &END MGRID ???? &XC ?????? &XC_FUNCTIONAL ?????? &END XC_FUNCTIONAL ???? &END XC ?? &END DFT ?? &SUBSYS &CELL ? PERIODIC XYZ ? A?? 4.916000000000000?? 0.000000000000000?? 0.000000000000000 ? B? -2.458000000000000?? 4.257380885004300?? 0.000000000000000 ? C?? 0.000000000000000?? 0.000000000000000?? 5.407000000000000 &END CELL &COORD Si -1.529859200000000?? 3.118957236354151?? 4.758700699999999 Si -0.080622400000000?? 1.117988220402129?? 1.154394500000000 Si? 2.379098200000000?? 0.860416676859369?? 2.956006900000000 O? 0.000000000000000?? 0.000000000000000?? 0.000000000000000 O -0.594098600000000?? 2.495250936701020?? 0.517990600000000 O -0.600489400000000?? 3.740960583653279?? 3.594573599999999 O? 1.372301400000000?? 1.357678764227871?? 1.798908900000000 O? 2.451363400000000?? 1.978404897261498?? 4.123918900000000 O? 3.828826600000000?? 0.623706299653130?? 2.314736700000000 &END COORD ???? &KIND Si ?????? BASIS_SET DZVP-GTH ?????? POTENTIAL GTH-PBE-q4 ???? &END KIND ???? &KIND O ?????? BASIS_SET DZVP-GTH ?????? POTENTIAL GTH-PBE-q6 ???? &END KIND ?? &END SUBSYS ?&END FORCE_EVAL ********************************************* -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. From no... at bollweevil.gdbg.org Tue Feb 7 16:06:11 2017 From: no... at bollweevil.gdbg.org (Noam Bernstein) Date: Tue, 7 Feb 2017 11:06:11 -0500 Subject: [CP2K:8644] Re: Questions about AdBF-QM/MM in cp2k In-Reply-To: References: <070cc4e4-fded-429a-8975-bed3e2c420eb@googlegroups.com> Message-ID: On Mon, Feb 6, 2017 at 4:17 PM, Noam Bernstein wrote: > > If those lines are the only ones that are non-zero, then I agree > there's a mismatch, but it's hard for me to imagine how that happens, > since the files are written from the same internal data structures > that are used to generate the counts that are printed above. I'll try > to run with your input files. I ran with the input files on google drive (except only 5 time steps), and do not see any problems. My output is entirely consistent: tin 1203 : fgrep N_QM stdout QMMM FORCE MIXING final count (not including links): N_QM core_list 2 N_QM core 0 N_QM extended 9 N_QM buffered 45 QMMM FORCE MIXING final count (not including links): N_QM core_list 2 N_QM core 0 N_QM extended 9 N_QM buffered 45 QMMM FORCE MIXING final count (not including links): N_QM core_list 2 N_QM core 0 N_QM extended 9 N_QM buffered 45 QMMM FORCE MIXING final count (not including links): N_QM core_list 2 N_QM core 0 N_QM extended 9 N_QM buffered 45 QMMM FORCE MIXING final count (not including links): N_QM core_list 2 N_QM core 0 N_QM extended 9 N_QM buffered 45 QMMM FORCE MIXING final count (not including links): N_QM core_list 2 N_QM core 0 N_QM extended 9 N_QM buffered 45 tin 1204 : fgrep -c ' 10.0' *fmlabel*xyz BrO_md-fmlabels-1_0.xyz:2 BrO_md-fmlabels-1_1.xyz:2 BrO_md-fmlabels-1_2.xyz:2 BrO_md-fmlabels-1_3.xyz:2 BrO_md-fmlabels-1_4.xyz:2 BrO_md-fmlabels-1_5.xyz:2 tin 1205 : fgrep -c ' 7.0' *fmlabel*xyz BrO_md-fmlabels-1_0.xyz:9 BrO_md-fmlabels-1_1.xyz:9 BrO_md-fmlabels-1_2.xyz:9 BrO_md-fmlabels-1_3.xyz:9 BrO_md-fmlabels-1_4.xyz:9 BrO_md-fmlabels-1_5.xyz:9 tin 1206 : fgrep -c ' 5.0' *fmlabel*xyz BrO_md-fmlabels-1_0.xyz:45 BrO_md-fmlabels-1_1.xyz:45 BrO_md-fmlabels-1_2.xyz:45 BrO_md-fmlabels-1_3.xyz:45 BrO_md-fmlabels-1_4.xyz:45 BrO_md-fmlabels-1_5.xyz:45 From chenh... at gmail.com Tue Feb 7 22:27:10 2017 From: chenh... at gmail.com (Hanning Chen) Date: Tue, 7 Feb 2017 17:27:10 -0500 Subject: [CP2K:8650] Re: questions about TDDFPT2 In-Reply-To: <5b81aee5-7b1a-41fe-b1bd-03ed6715d94e@googlegroups.com> References: <2d496684-08e2-408d-a645-b8fbf2c0d11c@googlegroups.com> <5b81aee5-7b1a-41fe-b1bd-03ed6715d94e@googlegroups.com> Message-ID: Matt, Thanks for your clarification. I agree with you that the coupling term between occupied-virtual orbital pairs may deviate the excitation energy from HOMO-LUMO gap. I was just surprised by the rather large deviation on an isolated molecule which may stem from its small basis set as well as its small box size, as your suggested. I will make the system bigger with a larger basis set. Best, Hanning On Mon, Feb 6, 2017 at 10:22 AM, Matt W wrote: > Hi Hanning, > > I've not had a chance to look at your particular calculation. Such a small > basis set, and small box could lead to strange results in any case. More > generally, there is no reason, even if the transition is a pure single > determinant HOMO to LUMO, for the energy to be that of the HOMO_LUMO gap. > There are still additional terms in the TDDFT kernel that will shift the > transition energy. > For GGAs the shifts can be in either direction, there is no general rule. > We have checked small molecule transition energies vs gamess-us and were > pretty happy with the comparison. > > HTH, > > Matt > > > On Sunday, February 5, 2017 at 8:50:49 PM UTC, NUCP2K wrote: >> >> Dear CP2K Developers and Users, >> >> I just tried out the latest implementation of time-dependent density >> functional perturbation theory (TDDFPT) in CP2K, and found some serious >> inconsistencies on the calculated excitation energy. >> >> I tested the TDDFPT2 on an isolated water (H2O) molecule using the >> attached input file. Interestingly, the calculated excitation energy of >> 10.075 eV is much much greater than the HOMO-LUMO gap of 9.137 eV, even >> though the transition is dominated (>99.9%) by the electron transfer from >> HOMO to LUMO. >> >> It seems to me that the diagonal terms of the TDDFPT response matrix >> are not appropriately assigned, leading to the apparent inconsistency. >> Perhaps, the subroutine "tddfpt_init_by_energy_diff" in >> qs_tddfpt2_methods.F should be fixed to yield correct orbital energy gap. >> >> Please correct me if my understanding is wrong. >> >> Thanks. >> >> Hanning >> >> >> &FORCE_EVAL >> METHOD QS >> &PROPERTIES >> &TDDFPT >> NSTATES 1 >> MAX_ITER 100 >> MAX_KV 10 >> CONVERGENCE [eV] 1.0E-3 >> &DIPOLE_MOMENTS >> DIPOLE_FORM LENGTH >> &END DIPOLE_MOMENTS >> &MGRID >> COMMENSURATE >> CUTOFF 50 >> &END MGRID >> &END TDDFPT >> &END PROPERTIES >> &DFT >> BASIS_SET_FILE_NAME BASIS_SET >> POTENTIAL_FILE_NAME POTENTIAL >> &MGRID >> COMMENSURATE >> CUTOFF 50 >> &END MGRID >> &POISSON >> PERIODIC NONE >> POISSON WAVELET >> &END POISSON >> &SCF >> SCF_GUESS ATOMIC >> &END SCF >> &XC >> &XC_FUNCTIONAL PBE >> &END XC_FUNCTIONAL >> &XC_GRID >> XC_DERIV SPLINE2_SMOOTH >> &END XC_GRID >> &END XC >> &END DFT >> &SUBSYS >> &CELL >> ABC 6.0 6.0 6.0 >> PERIODIC NONE >> &END CELL >> &COORD >> O 3.000000 3.000000 3.000000 H2O1 >> H 3.000000 3.000000 4.000000 H2O1 >> H 3.942809 3.000000 2.666667 H2O1 >> &END COORD >> &KIND H >> BASIS_SET SZV-GTH >> POTENTIAL GTH-PADE-q1 >> &END KIND >> &KIND O >> BASIS_SET SZV-GTH >> POTENTIAL GTH-PADE-q6 >> &END KIND >> &TOPOLOGY >> &END TOPOLOGY >> &END SUBSYS >> &END FORCE_EVAL >> &GLOBAL >> PROJECT WATER >> PRINT_LEVEL MEDIUM >> RUN_TYPE ENERGY >> &END GLOBAL >> > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amazing... at gmail.com Wed Feb 8 09:57:56 2017 From: amazing... at gmail.com (David T) Date: Wed, 8 Feb 2017 01:57:56 -0800 (PST) Subject: bond energy and BSSE in cp2k Message-ID: <30d382f9-6183-4f46-b6bc-833d9df5cd6e@googlegroups.com> Dear all Apologies if my question is silly but I prefer sound fool and doing things right than make a fool mistake. I need to calculate some MCO bond energy in a 3D periodic system. My question is related to the peculiarity of CP2K. I mean if I would do this using a pure plane-wave code I wouldn't have to care about BSSE while on contrary doing on a pure GTO code either I use a fully converged basis-set or I need to add it. My idea was that on CP2K I do not need to use BSSE but I've seen the key BSSE is present as sub-field of FORCE EVAL. So I am confused now :-) Do I need or do I need not to care about BSSE? any help or give an explanation will be really welcome -------------- next part -------------- An HTML attachment was scrubbed... URL: From amazing... at gmail.com Wed Feb 8 10:09:15 2017 From: amazing... at gmail.com (David T) Date: Wed, 8 Feb 2017 02:09:15 -0800 (PST) Subject: Comparison between CP2K and Quantum Espresso In-Reply-To: <0ffff976-c924-4c83-ad18-1b2fe2ecbe91@googlegroups.com> References: <0ffff976-c924-4c83-ad18-1b2fe2ecbe91@googlegroups.com> Message-ID: Hi Tommaso as you I am more expert on QE and only recently moved on CP2K. On my experience CP2K is much more quicker and allows to work with bigger systems that planewave code could not afford. On the other hand it is true that this is really system depended so the fact that for nano-porous material CP2K is more efficient could not be true for other systems. After having read the inputs a comment I can give to you is that you are probably not making a fair comparison. I've see you use ultrasoft pseudo which allows a very low cut-off and can be "though" as minimal basis-set. So you should probably use some corresponding low basis-set in CP2K (for instance a dobule zera instead of triple zeta). Probably more important another thing I can tell you is that I've seen that if CP2K is not properly compiled, its performance can be slow. For instance my own version with mpi, mkl, libxsmm and elpa is about 30% faster than the standard one I found on our cluster. Moreover the speediness of the code can be further boosted if you use also GPU and hybrid openMP-MPI. P.S. a curiosity, in QE why are you using a single point shifted from gamma? if there is not a major reason using the gamma algorithm on QE can accelerate you calc up to 30% -------------- next part -------------- An HTML attachment was scrubbed... URL: From tfran... at gmail.com Wed Feb 8 10:28:48 2017 From: tfran... at gmail.com (tfran... at gmail.com) Date: Wed, 8 Feb 2017 02:28:48 -0800 (PST) Subject: Comparison between CP2K and Quantum Espresso In-Reply-To: References: <0ffff976-c924-4c83-ad18-1b2fe2ecbe91@googlegroups.com> Message-ID: Dear David, first of all thanks a lot for your very useful comments. I will benchmark my system in CP2K with a lower basis sets, in order to test again the parameters and to have better reference with respect to QE. Regarding the compilation of the program in our cluster, I think that it is the pitfall and that our technician missed something. He told me ( because I am not allowed to install anything, but only the technician ) that he compiled the precompiled version of CP2K. But I am pretty sure he missed some of the libraries you listed above. Indeed I am insisting in a more "serious" compilation of the program, that we wanna massively exploit for our dynamics. Regarding the single point shift from the gamma point in QE, that was suggested by one of my old Professors. At that time ( almost three years ago) he told us that the shift is recommended. I always used that setting, without honestly taking care too much about the change in performances. By the way, thanks a lot for the really useful hints. Now I will re-benchemark the new machine testing several levels of theory as you suggested. Best Regards, Tommaso Francese Il giorno mercoled? 8 febbraio 2017 11:09:16 UTC+1, David T ha scritto: > > Hi Tommaso > > as you I am more expert on QE and only recently moved on CP2K. > On my experience CP2K is much more quicker and allows to work with bigger > systems that planewave code could not afford. On the other hand it is true > that this is really system depended so the fact that for nano-porous > material CP2K is more efficient could not be true for other systems. > After having read the inputs a comment I can give to you is that you are > probably not making a fair comparison. > I've see you use ultrasoft pseudo which allows a very low cut-off and can > be "though" as minimal basis-set. So you should probably use some > corresponding low basis-set in CP2K (for instance a dobule zera instead of > triple zeta). > > Probably more important another thing I can tell you is that I've seen > that if CP2K is not properly compiled, its performance can be slow. For > instance my own version with mpi, mkl, libxsmm and elpa is about 30% faster > than the standard one I found on our cluster. > Moreover the speediness of the code can be further boosted if you use also > GPU and hybrid openMP-MPI. > > P.S. a curiosity, in QE why are you using a single point shifted from > gamma? if there is not a major reason using the gamma algorithm on QE can > accelerate you calc up to 30% > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lingsa... at gmail.com Wed Feb 8 12:11:54 2017 From: lingsa... at gmail.com (S Ling) Date: Wed, 8 Feb 2017 12:11:54 +0000 Subject: [CP2K:8663] bond energy and BSSE in cp2k In-Reply-To: <30d382f9-6183-4f46-b6bc-833d9df5cd6e@googlegroups.com> References: <30d382f9-6183-4f46-b6bc-833d9df5cd6e@googlegroups.com> Message-ID: Hi It's not 100% true that you don't have to care about BSSE in plane-wave codes. If you perform a cell optimisation using plane-wave codes, the number of plane waves may change as your cell volume increases or decreases. I know there are plane wave codes (e.g. CASTEP) which provide option to do finite basis set corrections. For CP2K which uses localised basis sets, BSSE due to basis set incompleteness is always there, but depending on which basis sets you're using, what systems you're looking at (bulk or surface or isolated molecules), and which properties you are interested in, BSSE may be strong or can be neglected. BSSEs are usually non-negligible in binding energy calculations, especially if you use moderate basis sets like DZVP-MOLOPT-SR-GTH. SL On 8 February 2017 at 09:57, David T wrote: > Dear all > Apologies if my question is silly but I prefer sound fool and doing things > right than make a fool mistake. > > I need to calculate some MCO bond energy in a 3D periodic system. > > My question is related to the peculiarity of CP2K. > I mean if I would do this using a pure plane-wave code I wouldn't have to > care about BSSE while on contrary doing on a pure GTO code either I use a > fully converged basis-set or I need to add it. > > My idea was that on CP2K I do not need to use BSSE but I've seen the key > BSSE is present as sub-field of FORCE EVAL. > > So I am confused now :-) > > Do I need or do I need not to care about BSSE? > > any help or give an explanation will be really welcome > > > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amazing... at gmail.com Wed Feb 8 13:26:11 2017 From: amazing... at gmail.com (David T) Date: Wed, 8 Feb 2017 05:26:11 -0800 (PST) Subject: [CP2K:8663] bond energy and BSSE in cp2k In-Reply-To: References: <30d382f9-6183-4f46-b6bc-833d9df5cd6e@googlegroups.com> Message-ID: <969c2f50-6bf4-49ee-89b7-bab8e8e44ac6@googlegroups.com> Hi thanks for answering. Concerning about plane-wave I guess you are referring to the problem of pulay stress. It is a completely different problem. 1st of all, as you written it can appear on cases of volume optimisation, 2ndly it should not! appear if your cut-off was well converged and if you are optimising a ridiculous unit-cell or using bad functional like PW91 or neglecting vdW corrections in systems where it is required etc.. if it does something was not good in your starting choice of functional, cut-off, cell parameters etc.. That said and coming back to the BSSE thanks for answering. So basically it is the same of normal LCAO code. I simply didn't know CP2K use local basis-set but I thought it was combining local GTO with plane-waves. So I will now study a bit better what the plane-wave are supposed to be/do. Best Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From koche... at gmail.com Wed Feb 8 13:40:54 2017 From: koche... at gmail.com (Victor K) Date: Wed, 8 Feb 2017 05:40:54 -0800 (PST) Subject: H20-64 performance benchmark Message-ID: <5939cdd7-9555-41e5-a80f-a3c5f01e721a@googlegroups.com> Hi, I'm newbie to cp2k and I'm trying to get performance numbers from cp2k library. According to https://www.cp2k.org/performance page one of the usefull benchmarks for this should be H2O-64.inp, but I'm unalbe to run it even for 128 ranks without some evalation error. I use Intel MPI, cp2k 4.1, and run benchmark like this: mpirun -np 128 ../../../exe/Linux-x86-64-intel/cp2k.popt ./H2O-64.inp Could you please advice what I'm missing while launching? Example output: ... ******************************************************************************* * ___ * * / \ * * [ABORT] * * \___/ Cholesky decompose failed: the matrix is not positive definite or * * | ill-conditioned. * * O/| * * /| | * * / \ fm/cp_fm_cholesky.F:94 * ******************************************************************************* ===== Routine Calling Stack ===== 11 cp_fm_cholesky_decompose 10 make_basis_sm 9 reorthogonalize_vectors 8 wfi_extrapolate 7 scf_env_initial_rho_setup 6 init_scf_run 5 qs_energies 4 qs_forces 3 velocity_verlet 2 qs_mol_dyn_low 1 CP2K -------------- next part -------------- An HTML attachment was scrubbed... URL: From lingsa... at gmail.com Wed Feb 8 13:46:53 2017 From: lingsa... at gmail.com (S Ling) Date: Wed, 8 Feb 2017 13:46:53 +0000 Subject: [CP2K:8666] bond energy and BSSE in cp2k In-Reply-To: <969c2f50-6bf4-49ee-89b7-bab8e8e44ac6@googlegroups.com> References: <30d382f9-6183-4f46-b6bc-833d9df5cd6e@googlegroups.com> <969c2f50-6bf4-49ee-89b7-bab8e8e44ac6@googlegroups.com> Message-ID: Hi You're right. Apparently, my understanding was wrong and I mixed things up when I was referring to the BSSE vs plane-wave basis sets; BSSE is absent in plane wave codes. The GPW method in CP2K uses mixed Gaussian/plane-wave basis sets as you said, so there is always BSSE in the part of the calculation which is done using localised Gaussian basis sets. SL On 8 February 2017 at 13:26, David T wrote: > Hi > > thanks for answering. > > Concerning about plane-wave I guess you are referring to the problem of > pulay stress. It is a completely different problem. > 1st of all, as you written it can appear on cases of volume optimisation, > 2ndly it should not! appear if your cut-off was well converged and if you > are optimising a ridiculous unit-cell or using bad functional like PW91 or > neglecting vdW corrections in systems where it is required etc.. if it does > something was not good in your starting choice of functional, cut-off, cell > parameters etc.. > > That said and coming back to the BSSE thanks for answering. > > So basically it is the same of normal LCAO code. > > I simply didn't know CP2K use local basis-set but I thought it was > combining local GTO with plane-waves. So I will now study a bit better what > the plane-wave are supposed to be/do. > > > Best > > Davide > > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ari.p.s... at gmail.com Wed Feb 8 13:50:32 2017 From: ari.p.s... at gmail.com (Ari Paavo Seitsonen) Date: Wed, 8 Feb 2017 14:50:32 +0100 Subject: [CP2K:8668] H20-64 performance benchmark In-Reply-To: <5939cdd7-9555-41e5-a80f-a3c5f01e721a@googlegroups.com> References: <5939cdd7-9555-41e5-a80f-a3c5f01e721a@googlegroups.com> Message-ID: Dear Victor, My guess: Just yesterday I had the same problem; the "solution" for me was to switch to a different version, either in the compiler and/or the Intel MPI library (I did not try all the different combinations for figure out which one or ones were errorneous). 'gfortran' and OpenMPI usually works much more reliably, if you cannot try that, I would indeed recommend trying with different versions of Intel (compilers and/or MPI). Greetings from Paris, apsi PS The machine in question was 'Occigen' in Montpellier, the combination that worked was remove module impi/5.1.3.258 (intelmpi) remove module mkl/compilers_and_libraries_2016.4.258/linux (Intel MKL) remove module idb/compilers_and_libraries_2016.4.258/linux (Intel Debugger) remove module intel/16.4.258 (Intel Compiler Suite) The one that did not: load module mkl/compilers_and_libraries_2017.0.098/linux (Intel MKL) load module idb/compilers_and_libraries_2017.0.098/linux (Intel Debugger) load module intel/17.0 (Intel Compiler Suite) load module impi/2017.0.098 (intelmpi) #> ifort --version ifort (IFORT) 17.0.0 20160721 Copyright (C) 1985-2016 Intel Corporation. All rights reserved. 2017-02-08 14:40 GMT+01:00 Victor K : > Hi, > > I'm newbie to cp2k and I'm trying to get performance numbers from cp2k > library. According to https://www.cp2k.org/performance page one of the > usefull benchmarks for this should be H2O-64.inp, but I'm unalbe to run it > even for 128 ranks without some evalation error. > I use Intel MPI, cp2k 4.1, and run benchmark like this: > mpirun -np 128 ../../../exe/Linux-x86-64-intel/cp2k.popt ./H2O-64.inp > > Could you please advice what I'm missing while launching? > > > Example output: > > ... > > ************************************************************ > ******************* > * ___ * > * / \ * > * [ABORT] * > * \___/ Cholesky decompose failed: the matrix is not positive definite or * > * | ill-conditioned. * > * O/| * > * /| | * > * / \ fm/cp_fm_cholesky.F:94 * > ************************************************************ > ******************* > > > ===== Routine Calling Stack ===== > > 11 cp_fm_cholesky_decompose > 10 make_basis_sm > 9 reorthogonalize_vectors > 8 wfi_extrapolate > 7 scf_env_initial_rho_setup > 6 init_scf_run > 5 qs_energies > 4 qs_forces > 3 velocity_verlet > 2 qs_mol_dyn_low > 1 CP2K > > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.S... at iki.fi / http://www.iki.fi/~apsi/ Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935 -------------- next part -------------- An HTML attachment was scrubbed... URL: From amazing... at gmail.com Wed Feb 8 14:25:14 2017 From: amazing... at gmail.com (David T) Date: Wed, 8 Feb 2017 06:25:14 -0800 (PST) Subject: [CP2K:8666] bond energy and BSSE in cp2k In-Reply-To: References: <30d382f9-6183-4f46-b6bc-833d9df5cd6e@googlegroups.com> <969c2f50-6bf4-49ee-89b7-bab8e8e44ac6@googlegroups.com> Message-ID: <1c96f08e-9bb4-4136-98a4-d09a0fdd7525@googlegroups.com> thanks On Wednesday, 8 February 2017 14:46:56 UTC+1, S Ling wrote: > > Hi > > You're right. Apparently, my understanding was wrong and I mixed things up > when I was referring to the BSSE vs plane-wave basis sets; BSSE is absent > in plane wave codes. > > The GPW method in CP2K uses mixed Gaussian/plane-wave basis sets as you > said, so there is always BSSE in the part of the calculation which is done > using localised Gaussian basis sets. > > SL > > > On 8 February 2017 at 13:26, David T > > wrote: > >> Hi >> >> thanks for answering. >> >> Concerning about plane-wave I guess you are referring to the problem of >> pulay stress. It is a completely different problem. >> 1st of all, as you written it can appear on cases of volume optimisation, >> 2ndly it should not! appear if your cut-off was well converged and if you >> are optimising a ridiculous unit-cell or using bad functional like PW91 or >> neglecting vdW corrections in systems where it is required etc.. if it does >> something was not good in your starting choice of functional, cut-off, cell >> parameters etc.. >> >> That said and coming back to the BSSE thanks for answering. >> >> So basically it is the same of normal LCAO code. >> >> I simply didn't know CP2K use local basis-set but I thought it was >> combining local GTO with plane-waves. So I will now study a bit better what >> the plane-wave are supposed to be/do. >> >> >> Best >> >> Davide >> >> -- >> You received this message because you are subscribed to the Google Groups >> "cp2k" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to cp2k+... at googlegroups.com . >> To post to this group, send email to cp... at googlegroups.com >> . >> Visit this group at https://groups.google.com/group/cp2k. >> For more options, visit https://groups.google.com/d/optout. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ashishd... at gmail.com Wed Feb 8 16:24:30 2017 From: ashishd... at gmail.com (ashish dabral) Date: Wed, 8 Feb 2017 08:24:30 -0800 (PST) Subject: How to calculate Fermi energy of metals? Message-ID: Hi, I would like to know how to calculate the fermi energy of metals using cp2k. For example, Cu has a fermi energy of around 7.0eV, which can also be calculated using the general formula involving carrier concentration ( https://en.wikipedia.org/wiki/Fermi_energy, the three dimensional case.) I would like to know how can I obtain this value (approximate) from the bulk metal unit cell. I am interested in transition metals mostly. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From ari.p.s... at gmail.com Wed Feb 8 22:15:17 2017 From: ari.p.s... at gmail.com (Ari Paavo Seitsonen) Date: Wed, 8 Feb 2017 23:15:17 +0100 Subject: [CP2K:8672] How to calculate Fermi energy of metals? In-Reply-To: References: Message-ID: Dear Ashish Dabral, The only way _I_ know is to calculate a system with surface (well, two, slab model) and then align the Fermi energy via the potential in the middle of the slab - should be thick enough so that in the middle it is converged - and the potential in the middle of the vacuum. So the value of "Fermi energy" would be the work function. I guess that one would get the same value if one would then take the difference of the potential in the middle of the slab and potential in the vacuum, and then uses that after aliging the difference between the potential and the Fermi energy in a bulk system. With GGA one usually gets too small values of the work function if I remember correctly (self-interaction/asymptotics), by about 0.5-1 eV depending on the material. Greetings, apsi 2017-02-08 17:17 GMT+01:00 ashish dabral : > Hi, > > I would like to know how to calculate the fermi energy of metals using > cp2k. > For example, Cu has a fermi energy of around 7.0eV, which can also be > calculated using the general formula involving carrier concentration ( > https://en.wikipedia.org/wiki/Fermi_energy, the > three dimensional case.) I would like to know how can I obtain this value > (approximate) from the bulk metal unit cell. > > Thanks > > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.S... at iki.fi / http://www.iki.fi/~apsi/ Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935 -------------- next part -------------- An HTML attachment was scrubbed... URL: From MattWa... at gmail.com Wed Feb 8 22:59:57 2017 From: MattWa... at gmail.com (Matt W) Date: Wed, 8 Feb 2017 14:59:57 -0800 (PST) Subject: [CP2K:8672] How to calculate Fermi energy of metals? In-Reply-To: References: Message-ID: <084e105f-ae90-4155-bd17-de2a75323874@googlegroups.com> Hi, the OP might need to be a bit careful with the definition of the fermi energy and explain what they are after. I think there are different conventions around. I think the free-electron models he referred to, and that 7 eV for copper number, measure the chemical potential / fermi energy relative to the bottom of the band. So it corresponds to something like the energy from the lowest 4s copper states up to the highest occupied states. What you would use it for, I am not quite sure. So I think it is not the same thing as a physical measure relative to the vacuum, i.e. work function. Matt On Wednesday, February 8, 2017 at 10:15:19 PM UTC, Ari Paavo Seitsonen wrote: > > Dear Ashish Dabral, > > The only way _I_ know is to calculate a system with surface (well, two, > slab model) and then align the Fermi energy via the potential in the middle > of the slab - should be thick enough so that in the middle it is converged > - and the potential in the middle of the vacuum. So the value of "Fermi > energy" would be the work function. I guess that one would get the same > value if one would then take the difference of the potential in the middle > of the slab and potential in the vacuum, and then uses that after aliging > the difference between the potential and the Fermi energy in a bulk system. > > With GGA one usually gets too small values of the work function if I > remember correctly (self-interaction/asymptotics), by about 0.5-1 eV > depending on the material. > > Greetings, > > apsi > > 2017-02-08 17:17 GMT+01:00 ashish dabral >: > >> Hi, >> >> I would like to know how to calculate the fermi energy of metals using >> cp2k. >> For example, Cu has a fermi energy of around 7.0eV, which can also be >> calculated using the general formula involving carrier concentration ( >> https://en.wikipedia.org/wiki/Fermi_energy, the >> three dimensional case.) I would like to know how can I obtain this value >> (approximate) from the bulk metal unit cell. >> >> Thanks >> >> -- >> You received this message because you are subscribed to the Google Groups >> "cp2k" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to cp2k+... at googlegroups.com . >> To post to this group, send email to cp... at googlegroups.com >> . >> Visit this group at https://groups.google.com/group/cp2k. >> For more options, visit https://groups.google.com/d/optout. >> > > > > -- > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari Paavo Seitsonen / Ari.P... at iki.fi / > http://www.iki.fi/~apsi/ > Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris > Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ashishd... at gmail.com Wed Feb 8 23:09:25 2017 From: ashishd... at gmail.com (ashish dabral) Date: Wed, 8 Feb 2017 15:09:25 -0800 (PST) Subject: [CP2K:8672] How to calculate Fermi energy of metals? In-Reply-To: References: Message-ID: <9925ef8f-c4a2-4dae-8d84-96019d0269af@googlegroups.com> Thanks for your reply Ari. I am looking for the fermi energy from the bottom of the conduction band. I think what you are referring to is the work function. Matt has specified the same thing in the next reply. The information, nonetheless, is useful. Thanks. On Wednesday, 8 February 2017 23:15:19 UTC+1, Ari Paavo Seitsonen wrote: > > Dear Ashish Dabral, > > The only way _I_ know is to calculate a system with surface (well, two, > slab model) and then align the Fermi energy via the potential in the middle > of the slab - should be thick enough so that in the middle it is converged > - and the potential in the middle of the vacuum. So the value of "Fermi > energy" would be the work function. I guess that one would get the same > value if one would then take the difference of the potential in the middle > of the slab and potential in the vacuum, and then uses that after aliging > the difference between the potential and the Fermi energy in a bulk system. > > With GGA one usually gets too small values of the work function if I > remember correctly (self-interaction/asymptotics), by about 0.5-1 eV > depending on the material. > > Greetings, > > apsi > > 2017-02-08 17:17 GMT+01:00 ashish dabral >: > >> Hi, >> >> I would like to know how to calculate the fermi energy of metals using >> cp2k. >> For example, Cu has a fermi energy of around 7.0eV, which can also be >> calculated using the general formula involving carrier concentration ( >> https://en.wikipedia.org/wiki/Fermi_energy, the >> three dimensional case.) I would like to know how can I obtain this value >> (approximate) from the bulk metal unit cell. >> >> Thanks >> >> -- >> You received this message because you are subscribed to the Google Groups >> "cp2k" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to cp2k+... at googlegroups.com . >> To post to this group, send email to cp... at googlegroups.com >> . >> Visit this group at https://groups.google.com/group/cp2k. >> For more options, visit https://groups.google.com/d/optout. >> > > > > -- > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari Paavo Seitsonen / Ari.P... at iki.fi / > http://www.iki.fi/~apsi/ > Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris > Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ashishd... at gmail.com Wed Feb 8 23:15:53 2017 From: ashishd... at gmail.com (ashish dabral) Date: Wed, 8 Feb 2017 15:15:53 -0800 (PST) Subject: [CP2K:8672] How to calculate Fermi energy of metals? In-Reply-To: <084e105f-ae90-4155-bd17-de2a75323874@googlegroups.com> References: <084e105f-ae90-4155-bd17-de2a75323874@googlegroups.com> Message-ID: Hi Matt, Yes, indeed I am looking for the chemical potential/ fermi energy (at 0K or otherwise, assuming it doesn't change much with temperature). I need to find the the highest occupied states with respect to the bottom of conduction band for the metal. I would like to align semiconductors wrt to the fermi energy to evaluate metal-semiconductor junction properties. Thanks On Wednesday, 8 February 2017 23:59:58 UTC+1, Matt W wrote: > > Hi, > > the OP might need to be a bit careful with the definition of the fermi > energy and explain what they are after. I think there are different > conventions around. > > I think the free-electron models he referred to, and that 7 eV for copper > number, measure the chemical potential / fermi energy relative to the > bottom of the band. So it corresponds to something like the energy from the > lowest 4s copper states up to the highest occupied states. What you would > use it for, I am not quite sure. > > So I think it is not the same thing as a physical measure relative to the > vacuum, i.e. work function. > > Matt > > On Wednesday, February 8, 2017 at 10:15:19 PM UTC, Ari Paavo Seitsonen > wrote: >> >> Dear Ashish Dabral, >> >> The only way _I_ know is to calculate a system with surface (well, two, >> slab model) and then align the Fermi energy via the potential in the middle >> of the slab - should be thick enough so that in the middle it is converged >> - and the potential in the middle of the vacuum. So the value of "Fermi >> energy" would be the work function. I guess that one would get the same >> value if one would then take the difference of the potential in the middle >> of the slab and potential in the vacuum, and then uses that after aliging >> the difference between the potential and the Fermi energy in a bulk system. >> >> With GGA one usually gets too small values of the work function if I >> remember correctly (self-interaction/asymptotics), by about 0.5-1 eV >> depending on the material. >> >> Greetings, >> >> apsi >> >> 2017-02-08 17:17 GMT+01:00 ashish dabral : >> >>> Hi, >>> >>> I would like to know how to calculate the fermi energy of metals using >>> cp2k. >>> For example, Cu has a fermi energy of around 7.0eV, which can also be >>> calculated using the general formula involving carrier concentration ( >>> https://en.wikipedia.org/wiki/Fermi_energy, the >>> three dimensional case.) I would like to know how can I obtain this >>> value (approximate) from the bulk metal unit cell. >>> >>> Thanks >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "cp2k" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to cp2k+... at googlegroups.com. >>> To post to this group, send email to cp... at googlegroups.com. >>> Visit this group at https://groups.google.com/group/cp2k. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> >> >> -- >> >> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- >> Ari Paavo Seitsonen / Ari.P... at iki.fi / http://www.iki.fi/~apsi/ >> Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris >> Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935 >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From MattWa... at gmail.com Thu Feb 9 14:39:46 2017 From: MattWa... at gmail.com (Matt W) Date: Thu, 9 Feb 2017 06:39:46 -0800 (PST) Subject: [CP2K:8672] How to calculate Fermi energy of metals? In-Reply-To: References: <084e105f-ae90-4155-bd17-de2a75323874@googlegroups.com> Message-ID: <0e1abc1d-3ac3-416c-9234-4f63cf0a3ded@googlegroups.com> Hi, you are approximately trying to find states that fit the free-electron model it seems. Best I could suggest is to look at projected density of states and see if you can see a clear increase in copper (or whatever element) s functions in a sensible energy range. You could also look a band dispersion in k-space and try and find approximate parabolas leading up to the fermi level ... Whether these features will be easy to spot in a real transition metal calculation, I don't know. Matt On Wednesday, February 8, 2017 at 11:15:54 PM UTC, ashish dabral wrote: > > > Hi Matt, > > Yes, indeed I am looking for the chemical potential/ fermi energy (at 0K > or otherwise, assuming it doesn't change much with temperature). > I need to find the the highest occupied states with respect to the bottom > of conduction band for the metal. I would like to align semiconductors wrt > to the fermi energy to evaluate metal-semiconductor junction properties. > > Thanks > > On Wednesday, 8 February 2017 23:59:58 UTC+1, Matt W wrote: >> >> Hi, >> >> the OP might need to be a bit careful with the definition of the fermi >> energy and explain what they are after. I think there are different >> conventions around. >> >> I think the free-electron models he referred to, and that 7 eV for copper >> number, measure the chemical potential / fermi energy relative to the >> bottom of the band. So it corresponds to something like the energy from the >> lowest 4s copper states up to the highest occupied states. What you would >> use it for, I am not quite sure. >> >> So I think it is not the same thing as a physical measure relative to the >> vacuum, i.e. work function. >> >> Matt >> >> On Wednesday, February 8, 2017 at 10:15:19 PM UTC, Ari Paavo Seitsonen >> wrote: >>> >>> Dear Ashish Dabral, >>> >>> The only way _I_ know is to calculate a system with surface (well, >>> two, slab model) and then align the Fermi energy via the potential in the >>> middle of the slab - should be thick enough so that in the middle it is >>> converged - and the potential in the middle of the vacuum. So the value of >>> "Fermi energy" would be the work function. I guess that one would get the >>> same value if one would then take the difference of the potential in the >>> middle of the slab and potential in the vacuum, and then uses that after >>> aliging the difference between the potential and the Fermi energy in a bulk >>> system. >>> >>> With GGA one usually gets too small values of the work function if I >>> remember correctly (self-interaction/asymptotics), by about 0.5-1 eV >>> depending on the material. >>> >>> Greetings, >>> >>> apsi >>> >>> 2017-02-08 17:17 GMT+01:00 ashish dabral : >>> >>>> Hi, >>>> >>>> I would like to know how to calculate the fermi energy of metals using >>>> cp2k. >>>> For example, Cu has a fermi energy of around 7.0eV, which can also be >>>> calculated using the general formula involving carrier concentration ( >>>> https://en.wikipedia.org/wiki/Fermi_energy, the >>>> three dimensional case.) I would like to know how can I obtain this >>>> value (approximate) from the bulk metal unit cell. >>>> >>>> Thanks >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "cp2k" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to cp2k+... at googlegroups.com. >>>> To post to this group, send email to cp... at googlegroups.com. >>>> Visit this group at https://groups.google.com/group/cp2k. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> >>> >>> -- >>> >>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- >>> Ari Paavo Seitsonen / Ari.P... at iki.fi / http://www.iki.fi/~apsi/ >>> Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris >>> Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935 >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From ashishd... at gmail.com Thu Feb 9 16:44:49 2017 From: ashishd... at gmail.com (ashish dabral) Date: Thu, 9 Feb 2017 08:44:49 -0800 (PST) Subject: [CP2K:8672] How to calculate Fermi energy of metals? In-Reply-To: <0e1abc1d-3ac3-416c-9234-4f63cf0a3ded@googlegroups.com> References: <084e105f-ae90-4155-bd17-de2a75323874@googlegroups.com> <0e1abc1d-3ac3-416c-9234-4f63cf0a3ded@googlegroups.com> Message-ID: Thanks for the suggestion. If I could find a reference for expermental data for fermi energies for metals, my problem would be solved, but apparently that is not straightforward either. On Thursday, 9 February 2017 15:39:46 UTC+1, Matt W wrote: > > Hi, > > you are approximately trying to find states that fit the free-electron > model it seems. > > Best I could suggest is to look at projected density of states and see if > you can see a clear increase in copper (or whatever element) s functions in > a sensible energy range. > > You could also look a band dispersion in k-space and try and find > approximate parabolas leading up to the fermi level ... > > Whether these features will be easy to spot in a real transition metal > calculation, I don't know. > > Matt > > On Wednesday, February 8, 2017 at 11:15:54 PM UTC, ashish dabral wrote: >> >> >> Hi Matt, >> >> Yes, indeed I am looking for the chemical potential/ fermi energy (at 0K >> or otherwise, assuming it doesn't change much with temperature). >> I need to find the the highest occupied states with respect to the bottom >> of conduction band for the metal. I would like to align semiconductors wrt >> to the fermi energy to evaluate metal-semiconductor junction properties. >> >> Thanks >> >> On Wednesday, 8 February 2017 23:59:58 UTC+1, Matt W wrote: >>> >>> Hi, >>> >>> the OP might need to be a bit careful with the definition of the fermi >>> energy and explain what they are after. I think there are different >>> conventions around. >>> >>> I think the free-electron models he referred to, and that 7 eV for >>> copper number, measure the chemical potential / fermi energy relative to >>> the bottom of the band. So it corresponds to something like the energy from >>> the lowest 4s copper states up to the highest occupied states. What you >>> would use it for, I am not quite sure. >>> >>> So I think it is not the same thing as a physical measure relative to >>> the vacuum, i.e. work function. >>> >>> Matt >>> >>> On Wednesday, February 8, 2017 at 10:15:19 PM UTC, Ari Paavo Seitsonen >>> wrote: >>>> >>>> Dear Ashish Dabral, >>>> >>>> The only way _I_ know is to calculate a system with surface (well, >>>> two, slab model) and then align the Fermi energy via the potential in the >>>> middle of the slab - should be thick enough so that in the middle it is >>>> converged - and the potential in the middle of the vacuum. So the value of >>>> "Fermi energy" would be the work function. I guess that one would get the >>>> same value if one would then take the difference of the potential in the >>>> middle of the slab and potential in the vacuum, and then uses that after >>>> aliging the difference between the potential and the Fermi energy in a bulk >>>> system. >>>> >>>> With GGA one usually gets too small values of the work function if I >>>> remember correctly (self-interaction/asymptotics), by about 0.5-1 eV >>>> depending on the material. >>>> >>>> Greetings, >>>> >>>> apsi >>>> >>>> 2017-02-08 17:17 GMT+01:00 ashish dabral : >>>> >>>>> Hi, >>>>> >>>>> I would like to know how to calculate the fermi energy of metals using >>>>> cp2k. >>>>> For example, Cu has a fermi energy of around 7.0eV, which can also be >>>>> calculated using the general formula involving carrier concentration ( >>>>> https://en.wikipedia.org/wiki/Fermi_energy, the >>>>> three dimensional case.) I would like to know how can I obtain this >>>>> value (approximate) from the bulk metal unit cell. >>>>> >>>>> Thanks >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "cp2k" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to cp2k+... at googlegroups.com. >>>>> To post to this group, send email to cp... at googlegroups.com. >>>>> Visit this group at https://groups.google.com/group/cp2k. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> >>>> >>>> -- >>>> >>>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- >>>> Ari Paavo Seitsonen / Ari.P... at iki.fi / http://www.iki.fi/~apsi/ >>>> Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris >>>> Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935 >>>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From wei.w... at gmail.com Thu Feb 9 19:09:00 2017 From: wei.w... at gmail.com (Wei Lai) Date: Thu, 9 Feb 2017 11:09:00 -0800 (PST) Subject: collective variables in NPT metadynamics Message-ID: Dear cp2k users and developers, I am wondering if it is possible to employ lattice information (such as lattice vectors) as collective variables in NPT metadynamics. I looked through 3.0 and 4.1 versions but didn't find such options. Thanks, Wei -------------- next part -------------- An HTML attachment was scrubbed... URL: From olive... at gmail.com Thu Feb 9 20:05:57 2017 From: olive... at gmail.com (Luiz Fernando Lopes Oliveira) Date: Thu, 9 Feb 2017 12:05:57 -0800 (PST) Subject: PLUMED output files update Message-ID: <6bb70af6-2f02-4b6b-ae3a-5349fe4d3490@googlegroups.com> I'm using PLUMED for MetaD simulation and it seems that its output files (usually named COLVAR and HILLS) will only be updated at the end of the simulation. Did someone encounter a similar problem? Is it normal? Using other codes I don't have this issue. My CP2K files are getting update normally though -------------- next part -------------- An HTML attachment was scrubbed... URL: From elra... at gmail.com Fri Feb 10 02:59:03 2017 From: elra... at gmail.com (E R) Date: Thu, 9 Feb 2017 18:59:03 -0800 (PST) Subject: FIST MD restart atom reordering not suppressed and problem with velocities & fixed atoms Message-ID: <932e7bcb-bbee-4ceb-9e17-d8e77ad687c9@googlegroups.com> Using prebuilt 4.1...with coordinates given in input &COORD.... Despite setting REORDER F in &TOPOPLOGY &GENERATE, atoms get reordered, but the LIST in &FIXED_ATOMS keeps input values, which are wrong after reordering. Deleting the FIXED_ATOMS_RESTART section prevents fixed atoms from being pulled hither and yon, but restarts also seem to get a nonphysical temperature bump which leads me to suspect that velocities might also be misordered (velocities initialization >1000K higher in restart; rescaling reduces this but it's noticeable). Setting NEIGHBOR_LISTS_FROM_SCRATCH F in &TOPOPLOGY &GENERATE and in &MM might influence this but doesn't eliminate the problem. Suggestions??? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjohns... at qub.ac.uk Fri Feb 10 07:35:29 2017 From: cjohns... at qub.ac.uk (Conrad) Date: Thu, 9 Feb 2017 23:35:29 -0800 (PST) Subject: PLUMED output files update In-Reply-To: <6bb70af6-2f02-4b6b-ae3a-5349fe4d3490@googlegroups.com> References: <6bb70af6-2f02-4b6b-ae3a-5349fe4d3490@googlegroups.com> Message-ID: Hi Luiz, This is a feature of Plumed. Try adding FLUSH STRIDE=1 to the end of your Plumed input. This will force the output to be written every step to HILLS and COLVAR. Normally writing is buffered, so this forces the buffer to be flushed regularly. Best wishes, Conrad -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjohns... at qub.ac.uk Fri Feb 10 07:37:57 2017 From: cjohns... at qub.ac.uk (Conrad) Date: Thu, 9 Feb 2017 23:37:57 -0800 (PST) Subject: collective variables in NPT metadynamics In-Reply-To: References: Message-ID: Dear Wei, One option is to use Plumed, if you've compiled CP2K with support for it. Please see the documentation for the collective variable, "CELL": http://plumed.github.io/doc-master/user-doc/html/_c_e_l_l.html Best wishes, Conrad -------------- next part -------------- An HTML attachment was scrubbed... URL: From wei.w... at gmail.com Fri Feb 10 14:33:30 2017 From: wei.w... at gmail.com (Wei Lai) Date: Fri, 10 Feb 2017 06:33:30 -0800 (PST) Subject: collective variables in NPT metadynamics In-Reply-To: References: Message-ID: Dear Conrad, Thanks for the suggestion. Regards, Wei On Friday, February 10, 2017 at 2:37:57 AM UTC-5, Conrad wrote: > > Dear Wei, > > One option is to use Plumed, if you've compiled CP2K with support for it. > > Please see the documentation for the collective variable, "CELL": > http://plumed.github.io/doc-master/user-doc/html/_c_e_l_l.html > > Best wishes, > Conrad > -------------- next part -------------- An HTML attachment was scrubbed... URL: From igla... at gmail.com Sun Feb 12 10:52:23 2017 From: igla... at gmail.com (Ivan Gladich) Date: Sun, 12 Feb 2017 13:52:23 +0300 Subject: [CP2K:8660] Re: Questions about AdBF-QM/MM in cp2k In-Reply-To: References: <070cc4e4-fded-429a-8975-bed3e2c420eb@googlegroups.com> Message-ID: Thank you Noam, I checked again and the labels seem fine now, probably I mis overlook them Thank you again for you answer and checking All the best Ivan On Tue, Feb 7, 2017 at 7:06 PM, Noam Bernstein wrote: > On Mon, Feb 6, 2017 at 4:17 PM, Noam Bernstein > wrote: > > > > If those lines are the only ones that are non-zero, then I agree > > there's a mismatch, but it's hard for me to imagine how that happens, > > since the files are written from the same internal data structures > > that are used to generate the counts that are printed above. I'll try > > to run with your input files. > > I ran with the input files on google drive (except only 5 time steps), > and do not see any problems. My output is entirely consistent: > > tin 1203 : fgrep N_QM stdout > QMMM FORCE MIXING final count (not including links): N_QM core_list > 2 N_QM core 0 N_QM extended 9 N_QM buffered 45 > QMMM FORCE MIXING final count (not including links): N_QM core_list > 2 N_QM core 0 N_QM extended 9 N_QM buffered 45 > QMMM FORCE MIXING final count (not including links): N_QM core_list > 2 N_QM core 0 N_QM extended 9 N_QM buffered 45 > QMMM FORCE MIXING final count (not including links): N_QM core_list > 2 N_QM core 0 N_QM extended 9 N_QM buffered 45 > QMMM FORCE MIXING final count (not including links): N_QM core_list > 2 N_QM core 0 N_QM extended 9 N_QM buffered 45 > QMMM FORCE MIXING final count (not including links): N_QM core_list > 2 N_QM core 0 N_QM extended 9 N_QM buffered 45 > > tin 1204 : fgrep -c ' 10.0' *fmlabel*xyz > BrO_md-fmlabels-1_0.xyz:2 > BrO_md-fmlabels-1_1.xyz:2 > BrO_md-fmlabels-1_2.xyz:2 > BrO_md-fmlabels-1_3.xyz:2 > BrO_md-fmlabels-1_4.xyz:2 > BrO_md-fmlabels-1_5.xyz:2 > > tin 1205 : fgrep -c ' 7.0' *fmlabel*xyz > BrO_md-fmlabels-1_0.xyz:9 > BrO_md-fmlabels-1_1.xyz:9 > BrO_md-fmlabels-1_2.xyz:9 > BrO_md-fmlabels-1_3.xyz:9 > BrO_md-fmlabels-1_4.xyz:9 > BrO_md-fmlabels-1_5.xyz:9 > > tin 1206 : fgrep -c ' 5.0' *fmlabel*xyz > BrO_md-fmlabels-1_0.xyz:45 > BrO_md-fmlabels-1_1.xyz:45 > BrO_md-fmlabels-1_2.xyz:45 > BrO_md-fmlabels-1_3.xyz:45 > BrO_md-fmlabels-1_4.xyz:45 > BrO_md-fmlabels-1_5.xyz:45 > > -- > You received this message because you are subscribed to a topic in the > Google Groups "cp2k" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/cp2k/u4xcztECsE0/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shun3... at gmail.com Mon Feb 13 09:38:32 2017 From: shun3... at gmail.com (Shun) Date: Mon, 13 Feb 2017 01:38:32 -0800 (PST) Subject: [CP2K:8652] Geometry optimization of SiO2 In-Reply-To: References: Message-ID: <23e3585d-1fc7-45dd-b2d6-56bf7bf97463@googlegroups.com> Dear Juerg Thank you very much for your advice. It goes well now. Shun 2017?2?7???? 15?19?13? UTC+1 jgh: > > Hi > > Please specify a XC functional > > &XC > &XC_FUNCTIONAL <--- here > <--- or here > &END XC_FUNCTIONAL > &END XC > > you can also optimize your SCF section for better convergence, > see examples > > regards > > Juerg > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: hut... at chem.uzh.ch > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----cp... at googlegroups.com wrote: -----To: cp2k > From: Shun > Sent by: cp... at googlegroups.com > Date: 02/06/2017 06:19PM > Subject: [CP2K:8652] Geometry optimization of SiO2 > > > Hi > > I am a beginner of cp2k and trying to optimize the structure of SiO2 to > make sure that cp2k works for zeolite I want to calculate. > The following input file was submitted and the BFGS Optimization was fine > first. But, 3rd and 4th SCF cycle of the optimization was not converged and > I saw the structure made big change. > What is the problem of this? I attempted also other structures of SiO2 but > same problem happened again. > If you have a advice, suggestion or solution, let me know please. > > > ************************** > &GLOBAL > PROJECT_NAME sio2 > RUN_TYPE GEO_OPT > &END GLOBAL > &MOTION > &GEO_OPT > OPTIMIZER BFGS > MAX_ITER 5000 > MAX_DR 1.0000000000000000E-4 > MAX_FORCE 1E-6 > &END GEO_OPT > &END MOTION > &FORCE_EVAL > METHOD QS > &DFT > BASIS_SET_FILE_~/cp2k-3.0/data/GTH_BASIS_SETS > POTENTIAL_FILE_NAME ~/cp2k-3.0/data/POTENTIAL > &SCF > EPS_SCF 1.0E-6 > MAX_SCF 200 > &MIXING T > ALPHA 0.1 > &END MIXING > &END SCF > &QS > METHOD GPW > &END QS > &MGRID > CUTOFF 300 > &END MGRID > &XC > &XC_FUNCTIONAL > &END XC_FUNCTIONAL > &END XC > &END DFT > &SUBSYS > > &CELL > PERIODIC XYZ > A 4.916000000000000 0.000000000000000 0.000000000000000 > B -2.458000000000000 4.257380885004300 0.000000000000000 > C 0.000000000000000 0.000000000000000 5.407000000000000 > &END CELL > > &COORD > Si -1.529859200000000 3.118957236354151 4.758700699999999 > Si -0.080622400000000 1.117988220402129 1.154394500000000 > Si 2.379098200000000 0.860416676859369 2.956006900000000 > O 0.000000000000000 0.000000000000000 0.000000000000000 > O -0.594098600000000 2.495250936701020 0.517990600000000 > O -0.600489400000000 3.740960583653279 3.594573599999999 > O 1.372301400000000 1.357678764227871 1.798908900000000 > O 2.451363400000000 1.978404897261498 4.123918900000000 > O 3.828826600000000 0.623706299653130 2.314736700000000 > &END COORD > > &KIND Si > BASIS_SET DZVP-GTH > POTENTIAL GTH-PBE-q4 > &END KIND > &KIND O > BASIS_SET DZVP-GTH > POTENTIAL GTH-PBE-q6 > &END KIND > &END SUBSYS > &END FORCE_EVAL > > ********************************************* > > > > > -- > > You received this message because you are subscribed to the Google Groups > "cp2k" group. > > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+... at googlegroups.com. > > To post to this group, send email to cp... at googlegroups.com. > > Visit this group at https://groups.google.com/group/cp2k. > > For more options, visit https://groups.google.com/d/optout. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ianpha... at gmail.com Mon Feb 13 16:58:23 2017 From: ianpha... at gmail.com (Ian Hamilton) Date: Mon, 13 Feb 2017 08:58:23 -0800 (PST) Subject: negative homo - lumo gap In-Reply-To: References: Message-ID: <334d6355-4ff5-46ea-9c3f-dfa3be07ed2e@googlegroups.com> Hi Marcella, One of my students has encountered this problem. He tried changing the OT and increasing the number of MOs (we don't know what you mean by "smearing the occupation numbers around the Fermi energy") but it didn't correct the problem. I?m posting this on his behalf because he was unable to- he got a message that he had ?limited access to public groups in his domain.? Do you (or anyone else) have another suggestion? In his pdos files all the levels look fine except for the HOMO and LUMO. >From his output: Fermi Energy [eV] : -5.966796 Lowest Eigenvalues of the unoccupied subspace spin 1 ----------------------------------------------------- Reached convergence in 149 iterations -0.23489989 -0.21167052 -0.18538586 -0.17943768 -0.13796253 -0.13007839 HOMO - LUMO gap [eV] : -0.425155 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -1076.972424168399129 Best regards, Ian Haminton On Sunday, November 22, 2009 at 6:13:06 AM UTC-5, Claudio wrote: > > Dear all, > > sometimes after I converge a calculation to an accuracy of say 1.0E-5 > I get things like > > HOMO - LUMO gap [eV] : -0.980594 > > This is because the Homo Energy is 0.22417642 and the Lumo Energy is > 0.18814027 in AU. > > I have requested the same accuracy for homo and lumo and have added > enough iterations to the lumo calculation loop to make sure the > program claims it is converged. I am using the OT method. How do I > prevent this from happening? I mean how do I ensure that the > calculation yields Lumo energies that are higher than the homo energy? > > > Sorry to bother you and thanks for your help! > > Claudio > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From yiyan... at asu.edu Mon Feb 13 23:44:54 2017 From: yiyan... at asu.edu (Yiyang) Date: Mon, 13 Feb 2017 15:44:54 -0800 (PST) Subject: Binary restart file does not work Message-ID: <43346873-8272-42f6-bc2f-15c0e37dad13@googlegroups.com> Dear CP2K experts, I am running a QS-MSST simulation (CP2K 4.1), during which i used: SPLIT_RESTART_FILE .TRUE. to write general restart files in both text format and binary format. I also used in the &EXT_RESTART section: EXTERNAL_FILE ${RESTART_FILE} BINARY_RESTART_FILE_NAME ${RESTART_FILE}.bin RESTART_DEFAULT .TRUE. to read from the restart files. However, I get following error message: * Section label read from the binary restart file * does not match the requested section name . In a test case (MD), the above settings worked, but as I switched to QS case, this did not. How can I use the restart files? Thanks. Regard Yiyang -------------- next part -------------- An HTML attachment was scrubbed... URL: From rdela... at gmail.com Tue Feb 14 12:11:15 2017 From: rdela... at gmail.com (rdela... at gmail.com) Date: Tue, 14 Feb 2017 04:11:15 -0800 (PST) Subject: Compilling problems Message-ID: <86455e94-4b40-4cf1-9cda-e62fdbd2022b@googlegroups.com> Hello all. I have been trying to compile and execute cp2k in my computer but i'm having problems. I use a modified arch file including my routes to files and libreries. When I compile it works but wher runing the tests it fails in all the cases. Could anyone help me with this? My computer is an intel i7-920 with 4 cores and 8 threadings. I have a CUDA capable graphic card so i like to enable it (I have installed the last version of the nvidia CUDA kit) About the software i run ubuntu 16.04.4 with gfortran and gcc, both versions 5.4.0. Also I have installed the last version of the intel MKL library (aditionally i also have ACML). Finally I'd like to compile cp2k with libint, libxc and fftw. All three are compiled and installed in my computer Any help for the creation of the appropiate arch file in wellcome. That you all in advance. Rafa -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.sassma... at ucl.ac.uk Tue Feb 14 12:14:21 2017 From: j.sassma... at ucl.ac.uk (=?ISO-8859-1?Q?J=F6rg_Sa=DFmannshausen?=) Date: Tue, 14 Feb 2017 12:14:21 +0000 Subject: [CP2K:8687] Compilling problems In-Reply-To: <86455e94-4b40-4cf1-9cda-e62fdbd2022b@googlegroups.com> References: <86455e94-4b40-4cf1-9cda-e62fdbd2022b@googlegroups.com> Message-ID: <1847908.CEVOnSOfLr@chemb105> Hi Refa, could you send us your modified makefile please and what is the error message? Without that information all we know is: it does not work! All the best from a sunny London J?rg On Tuesday 14 Feb 2017 04:11:15 rdela... at gmail.com wrote: > Hello all. > > I have been trying to compile and execute cp2k in my computer but i'm > having problems. > > I use a modified arch file including my routes to files and libreries. When > I compile it works but wher runing the tests it fails in all the cases. > > Could anyone help me with this? My computer is an intel i7-920 with 4 cores > and 8 threadings. I have a CUDA capable graphic card so i like to enable it > (I have installed the last version of the nvidia CUDA kit) > About the software i run ubuntu 16.04.4 with gfortran and gcc, both > versions 5.4.0. Also I have installed the last version of the intel MKL > library (aditionally i also have ACML). Finally I'd like to compile cp2k > with libint, libxc and fftw. All three are compiled and installed in my > computer > > Any help for the creation of the appropiate arch file in wellcome. > > That you all in advance. > > Rafa -- ************************************************************* Dr. J?rg Sa?mannshausen, MRSC University College London Department of Chemistry 20 Gordon Street London WC1H 0AJ email: j.sassma... at ucl.ac.uk web: http://sassy.formativ.net Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 220 bytes Desc: This is a digitally signed message part. URL: From rdela... at gmail.com Tue Feb 14 12:40:09 2017 From: rdela... at gmail.com (rdela... at gmail.com) Date: Tue, 14 Feb 2017 04:40:09 -0800 (PST) Subject: Compilling problems In-Reply-To: <86455e94-4b40-4cf1-9cda-e62fdbd2022b@googlegroups.com> References: <86455e94-4b40-4cf1-9cda-e62fdbd2022b@googlegroups.com> Message-ID: <902dc4bb-622f-42d5-8174-02685432681a@googlegroups.com> Hello and thank you J?rg I compile the next arch file: CC = gcc CPP = FC = gfortran LD = gfortran AR = ar -r ACML_INC = /home/ralf/ACML/gfortran64_mp/include ACML_LIB = /home/ralf/ACML/gfortran64_mp/lib FFTW_INC = /usr/local/include/ FFTW_LIB = /usr/local/lib/ LIBINT_INC = /usr/local/libint/1.1.4-stable/include LIBINT_LIB = /usr/local/libint/1.1.4-stable/lib LIBXC_INC = /opt/etsf/include LIBXC_LIB = /opt/etsf/lib DFLAGS = -D__FFTW3 -D__LIBINT -D__LIBXC2\ -D__LIBINT_MAX_AM=7 -D__LIBDERIV_MAX_AM1=6 -D__MAX_CONTR=4 CPPFLAGS = FCFLAGS = $(DFLAGS) -O2 -ffast-math -ffree-form -ffree-line-length-none\ -fopenmp -ftree-vectorize -funroll-loops\ -mtune=native\ -I$(ACML_INC) -I$(FFTW_INC) -I$(LIBINT_INC) -I$(LIBXC_INC) LDFLAGS = $(FCFLAGS) -static-libgfortran LIBS = $(ACML_LIB)/libacml_mp.so\ $(FFTW_LIB)/libfftw3.a\ $(FFTW_LIB)/libfftw3_threads.a\ $(LIBXC_LIB)/libxcf90.a\ $(LIBXC_LIB)/libxc.a\ $(LIBINT_LIB)/libderiv.a\ $(LIBINT_LIB)/libint.a And when I run the tests I obtain in all 2500 cases this kind of error /home/ralf/cp2k-4.1/regtesting/make/ssmp/TEST-make-ssmp-2017-02-14_13-35-10/optimize_input/regtest-1/driver-stride.inp.out /home/ralf/cp2k-4.1/regtesting/make/ssmp/../../..//exe/make/cp2k.ssmp: error while loading shared libraries: libacml_mp.so: cannot open shared object file: No such file or directory EXIT CODE: 127 MEANING: RUNTIME FAIL I should use libacml_mp.a for the compilling but in my installation this file doesn appear Rafa El martes, 14 de febrero de 2017, 13:11:16 (UTC+1), rdel... at gmail.com escribi?: > > Hello all. > > I have been trying to compile and execute cp2k in my computer but i'm > having problems. > > I use a modified arch file including my routes to files and libreries. > When I compile it works but wher runing the tests it fails in all the cases. > > Could anyone help me with this? My computer is an intel i7-920 with 4 > cores and 8 threadings. I have a CUDA capable graphic card so i like to > enable it (I have installed the last version of the nvidia CUDA kit) > About the software i run ubuntu 16.04.4 with gfortran and gcc, both > versions 5.4.0. Also I have installed the last version of the intel MKL > library (aditionally i also have ACML). Finally I'd like to compile cp2k > with libint, libxc and fftw. All three are compiled and installed in my > computer > > Any help for the creation of the appropiate arch file in wellcome. > > That you all in advance. > > Rafa > -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.sassma... at ucl.ac.uk Tue Feb 14 12:49:58 2017 From: j.sassma... at ucl.ac.uk (=?ISO-8859-1?Q?J=F6rg_Sa=DFmannshausen?=) Date: Tue, 14 Feb 2017 12:49:58 +0000 Subject: [CP2K:8689] Re: Compilling problems In-Reply-To: <902dc4bb-622f-42d5-8174-02685432681a@googlegroups.com> References: <86455e94-4b40-4cf1-9cda-e62fdbd2022b@googlegroups.com> <902dc4bb-622f-42d5-8174-02685432681a@googlegroups.com> Message-ID: <1961523.tVKKaFDGU5@chemb105> Hi Rafa, there are two things: a) why do you use ACML when you got an Intel CPU? ACML is for AMD Opterons and I am not sure whether it makes sense to use a high performance BLAS library which was tuned for a different chip family. If you want to stay clear of proprietary BLAS libs I would suggest to use OpenBLAS or ATLAS. b) it appears that your library is not in the search path for the libraries. There are three ways of fixing this. - $ export LD_LIBRARY_PATH=/path/to/libacml_mp.so:$LD_LIBRARY_PATH - add /path/to/libacml_mp.so in /etc/ld.so.conf and run ldconfig - use -Wl,--rpath=/path/to/libacml_mp.so when you compile for the linking. The first will only last for the current shell session and the second is a global setting. The third means you hard-code the path into your binary file. Like all things, there are pros and cons for all of that. ;-) All the best J?rg On Tuesday 14 Feb 2017 04:40:09 rdela... at gmail.com wrote: > Hello and thank you J?rg > > I compile the next arch file: > > CC = gcc > CPP = > FC = gfortran > LD = gfortran > AR = ar -r > ACML_INC = /home/ralf/ACML/gfortran64_mp/include > ACML_LIB = /home/ralf/ACML/gfortran64_mp/lib > FFTW_INC = /usr/local/include/ > FFTW_LIB = /usr/local/lib/ > LIBINT_INC = /usr/local/libint/1.1.4-stable/include > LIBINT_LIB = /usr/local/libint/1.1.4-stable/lib > LIBXC_INC = /opt/etsf/include > LIBXC_LIB = /opt/etsf/lib > DFLAGS = -D__FFTW3 -D__LIBINT -D__LIBXC2\ > -D__LIBINT_MAX_AM=7 -D__LIBDERIV_MAX_AM1=6 -D__MAX_CONTR=4 > CPPFLAGS = > FCFLAGS = $(DFLAGS) -O2 -ffast-math -ffree-form -ffree-line-length-none\ > -fopenmp -ftree-vectorize -funroll-loops\ > -mtune=native\ > -I$(ACML_INC) -I$(FFTW_INC) -I$(LIBINT_INC) -I$(LIBXC_INC) > LDFLAGS = $(FCFLAGS) -static-libgfortran > LIBS = $(ACML_LIB)/libacml_mp.so\ > $(FFTW_LIB)/libfftw3.a\ > $(FFTW_LIB)/libfftw3_threads.a\ > $(LIBXC_LIB)/libxcf90.a\ > $(LIBXC_LIB)/libxc.a\ > $(LIBINT_LIB)/libderiv.a\ > $(LIBINT_LIB)/libint.a > > And when I run the tests I obtain in all 2500 cases this kind of error > > /home/ralf/cp2k-4.1/regtesting/make/ssmp/TEST-make-ssmp-2017-02-14_13-35-10/ > optimize_input/regtest-1/driver-stride.inp.out > /home/ralf/cp2k-4.1/regtesting/make/ssmp/../../..//exe/make/cp2k.ssmp: > error while loading shared libraries: libacml_mp.so: cannot open shared > object file: No such file or directory > EXIT CODE: 127 MEANING: RUNTIME FAIL > > I should use libacml_mp.a for the compilling but in my installation this > file doesn appear > > Rafa > > > El martes, 14 de febrero de 2017, 13:11:16 (UTC+1), rdel... at gmail.com > > escribi?: > > Hello all. > > > > I have been trying to compile and execute cp2k in my computer but i'm > > having problems. > > > > I use a modified arch file including my routes to files and libreries. > > When I compile it works but wher runing the tests it fails in all the > > cases. > > > > Could anyone help me with this? My computer is an intel i7-920 with 4 > > cores and 8 threadings. I have a CUDA capable graphic card so i like to > > enable it (I have installed the last version of the nvidia CUDA kit) > > About the software i run ubuntu 16.04.4 with gfortran and gcc, both > > versions 5.4.0. Also I have installed the last version of the intel MKL > > library (aditionally i also have ACML). Finally I'd like to compile cp2k > > with libint, libxc and fftw. All three are compiled and installed in my > > computer > > > > Any help for the creation of the appropiate arch file in wellcome. > > > > That you all in advance. > > > > Rafa -- ************************************************************* Dr. J?rg Sa?mannshausen, MRSC University College London Department of Chemistry 20 Gordon Street London WC1H 0AJ email: j.sassma... at ucl.ac.uk web: http://sassy.formativ.net Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 220 bytes Desc: This is a digitally signed message part. URL: From rdela... at gmail.com Tue Feb 14 13:03:45 2017 From: rdela... at gmail.com (rdela... at gmail.com) Date: Tue, 14 Feb 2017 05:03:45 -0800 (PST) Subject: [CP2K:8689] Re: Compilling problems In-Reply-To: <1961523.tVKKaFDGU5@chemb105> References: <86455e94-4b40-4cf1-9cda-e62fdbd2022b@googlegroups.com> <902dc4bb-622f-42d5-8174-02685432681a@googlegroups.com> <1961523.tVKKaFDGU5@chemb105> Message-ID: I use ACML because i red that for using MKL ifort compiler is needed, and i don't have it. Anyway I'm going to try ATLAS. I'll tell you. Thank you Rafa El martes, 14 de febrero de 2017, 13:50:05 (UTC+1), sassy escribi?: > > Hi Rafa, > > there are two things: > > a) why do you use ACML when you got an Intel CPU? ACML is for AMD Opterons > and > I am not sure whether it makes sense to use a high performance BLAS > library > which was tuned for a different chip family. > If you want to stay clear of proprietary BLAS libs I would suggest to use > OpenBLAS or ATLAS. > > b) it appears that your library is not in the search path for the > libraries. > There are three ways of fixing this. > - $ export LD_LIBRARY_PATH=/path/to/libacml_mp.so:$LD_LIBRARY_PATH > - add /path/to/libacml_mp.so in /etc/ld.so.conf and run ldconfig > - use -Wl,--rpath=/path/to/libacml_mp.so when you compile for the > linking. > > The first will only last for the current shell session and the second is a > global setting. The third means you hard-code the path into your binary > file. > > Like all things, there are pros and cons for all of that. ;-) > > All the best > > J?rg > > On Tuesday 14 Feb 2017 04:40:09 rdel... at gmail.com wrote: > > Hello and thank you J?rg > > > > I compile the next arch file: > > > > CC = gcc > > CPP = > > FC = gfortran > > LD = gfortran > > AR = ar -r > > ACML_INC = /home/ralf/ACML/gfortran64_mp/include > > ACML_LIB = /home/ralf/ACML/gfortran64_mp/lib > > FFTW_INC = /usr/local/include/ > > FFTW_LIB = /usr/local/lib/ > > LIBINT_INC = /usr/local/libint/1.1.4-stable/include > > LIBINT_LIB = /usr/local/libint/1.1.4-stable/lib > > LIBXC_INC = /opt/etsf/include > > LIBXC_LIB = /opt/etsf/lib > > DFLAGS = -D__FFTW3 -D__LIBINT -D__LIBXC2\ > > -D__LIBINT_MAX_AM=7 -D__LIBDERIV_MAX_AM1=6 -D__MAX_CONTR=4 > > CPPFLAGS = > > FCFLAGS = $(DFLAGS) -O2 -ffast-math -ffree-form > -ffree-line-length-none\ > > -fopenmp -ftree-vectorize -funroll-loops\ > > -mtune=native\ > > -I$(ACML_INC) -I$(FFTW_INC) -I$(LIBINT_INC) -I$(LIBXC_INC) > > LDFLAGS = $(FCFLAGS) -static-libgfortran > > LIBS = $(ACML_LIB)/libacml_mp.so\ > > $(FFTW_LIB)/libfftw3.a\ > > $(FFTW_LIB)/libfftw3_threads.a\ > > $(LIBXC_LIB)/libxcf90.a\ > > $(LIBXC_LIB)/libxc.a\ > > $(LIBINT_LIB)/libderiv.a\ > > $(LIBINT_LIB)/libint.a > > > > And when I run the tests I obtain in all 2500 cases this kind of error > > > > > /home/ralf/cp2k-4.1/regtesting/make/ssmp/TEST-make-ssmp-2017-02-14_13-35-10/ > > > optimize_input/regtest-1/driver-stride.inp.out > > /home/ralf/cp2k-4.1/regtesting/make/ssmp/../../..//exe/make/cp2k.ssmp: > > error while loading shared libraries: libacml_mp.so: cannot open shared > > object file: No such file or directory > > EXIT CODE: 127 MEANING: RUNTIME FAIL > > > > I should use libacml_mp.a for the compilling but in my installation this > > file doesn appear > > > > Rafa > > > > > > El martes, 14 de febrero de 2017, 13:11:16 (UTC+1), rdel... at gmail.com > > > > escribi?: > > > Hello all. > > > > > > I have been trying to compile and execute cp2k in my computer but i'm > > > having problems. > > > > > > I use a modified arch file including my routes to files and libreries. > > > When I compile it works but wher runing the tests it fails in all the > > > cases. > > > > > > Could anyone help me with this? My computer is an intel i7-920 with 4 > > > cores and 8 threadings. I have a CUDA capable graphic card so i like > to > > > enable it (I have installed the last version of the nvidia CUDA kit) > > > About the software i run ubuntu 16.04.4 with gfortran and gcc, both > > > versions 5.4.0. Also I have installed the last version of the intel > MKL > > > library (aditionally i also have ACML). Finally I'd like to compile > cp2k > > > with libint, libxc and fftw. All three are compiled and installed in > my > > > computer > > > > > > Any help for the creation of the appropiate arch file in wellcome. > > > > > > That you all in advance. > > > > > > Rafa > > > -- > ************************************************************* > Dr. J?rg Sa?mannshausen, MRSC > University College London > Department of Chemistry > 20 Gordon Street > London > WC1H 0AJ > > email: j.sas... at ucl.ac.uk > web: http://sassy.formativ.net > > Please avoid sending me Word or PowerPoint attachments. > See http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.sassma... at ucl.ac.uk Tue Feb 14 13:43:36 2017 From: j.sassma... at ucl.ac.uk (=?ISO-8859-1?Q?J=F6rg_Sa=DFmannshausen?=) Date: Tue, 14 Feb 2017 13:43:36 +0000 Subject: [CP2K:8692] Re: Compilling problems In-Reply-To: References: <86455e94-4b40-4cf1-9cda-e62fdbd2022b@googlegroups.com> <1961523.tVKKaFDGU5@chemb105> Message-ID: <2329725.vlm8EUzt7q@chemb105> Hi Rafa, that is not correct. You can use MKL with gfortran. You will need the libmkl_gf* libs for that. Good luck! J?rg On Tuesday 14 Feb 2017 05:03:45 rdela... at gmail.com wrote: > I use ACML because i red that for using MKL ifort compiler is needed, and i > don't have it. > > Anyway I'm going to try ATLAS. > > I'll tell you. Thank you > > Rafa > > El martes, 14 de febrero de 2017, 13:50:05 (UTC+1), sassy escribi?: > > Hi Rafa, > > > > there are two things: > > > > a) why do you use ACML when you got an Intel CPU? ACML is for AMD Opterons > > and > > I am not sure whether it makes sense to use a high performance BLAS > > library > > which was tuned for a different chip family. > > If you want to stay clear of proprietary BLAS libs I would suggest to use > > OpenBLAS or ATLAS. > > > > b) it appears that your library is not in the search path for the > > libraries. > > There are three ways of fixing this. > > - $ export LD_LIBRARY_PATH=/path/to/libacml_mp.so:$LD_LIBRARY_PATH > > - add /path/to/libacml_mp.so in /etc/ld.so.conf and run ldconfig > > - use -Wl,--rpath=/path/to/libacml_mp.so when you compile for the > > linking. > > > > The first will only last for the current shell session and the second is a > > global setting. The third means you hard-code the path into your binary > > file. > > > > Like all things, there are pros and cons for all of that. ;-) > > > > All the best > > > > J?rg > > > > On Tuesday 14 Feb 2017 04:40:09 rdel... at gmail.com wrote: > > > Hello and thank you J?rg > > > > > > I compile the next arch file: > > > > > > CC = gcc > > > CPP = > > > FC = gfortran > > > LD = gfortran > > > AR = ar -r > > > ACML_INC = /home/ralf/ACML/gfortran64_mp/include > > > ACML_LIB = /home/ralf/ACML/gfortran64_mp/lib > > > FFTW_INC = /usr/local/include/ > > > FFTW_LIB = /usr/local/lib/ > > > LIBINT_INC = /usr/local/libint/1.1.4-stable/include > > > LIBINT_LIB = /usr/local/libint/1.1.4-stable/lib > > > LIBXC_INC = /opt/etsf/include > > > LIBXC_LIB = /opt/etsf/lib > > > DFLAGS = -D__FFTW3 -D__LIBINT -D__LIBXC2\ > > > > > > -D__LIBINT_MAX_AM=7 -D__LIBDERIV_MAX_AM1=6 -D__MAX_CONTR=4 > > > > > > CPPFLAGS = > > > FCFLAGS = $(DFLAGS) -O2 -ffast-math -ffree-form > > > > -ffree-line-length-none\ > > > > > -fopenmp -ftree-vectorize -funroll-loops\ > > > -mtune=native\ > > > -I$(ACML_INC) -I$(FFTW_INC) -I$(LIBINT_INC) -I$(LIBXC_INC) > > > > > > LDFLAGS = $(FCFLAGS) -static-libgfortran > > > LIBS = $(ACML_LIB)/libacml_mp.so\ > > > > > > $(FFTW_LIB)/libfftw3.a\ > > > $(FFTW_LIB)/libfftw3_threads.a\ > > > $(LIBXC_LIB)/libxcf90.a\ > > > $(LIBXC_LIB)/libxc.a\ > > > $(LIBINT_LIB)/libderiv.a\ > > > $(LIBINT_LIB)/libint.a > > > > > > And when I run the tests I obtain in all 2500 cases this kind of error > > > > /home/ralf/cp2k-4.1/regtesting/make/ssmp/TEST-make-ssmp-2017-02-14_13-35-1 > > 0/> > > > optimize_input/regtest-1/driver-stride.inp.out > > > /home/ralf/cp2k-4.1/regtesting/make/ssmp/../../..//exe/make/cp2k.ssmp: > > > error while loading shared libraries: libacml_mp.so: cannot open shared > > > object file: No such file or directory > > > EXIT CODE: 127 MEANING: RUNTIME FAIL > > > > > > I should use libacml_mp.a for the compilling but in my installation this > > > file doesn appear > > > > > > Rafa > > > > > > > > > El martes, 14 de febrero de 2017, 13:11:16 (UTC+1), rdel... at gmail.com > > > > > > escribi?: > > > > Hello all. > > > > > > > > I have been trying to compile and execute cp2k in my computer but i'm > > > > having problems. > > > > > > > > I use a modified arch file including my routes to files and libreries. > > > > When I compile it works but wher runing the tests it fails in all the > > > > cases. > > > > > > > > Could anyone help me with this? My computer is an intel i7-920 with 4 > > > > cores and 8 threadings. I have a CUDA capable graphic card so i like > > > > to > > > > > > enable it (I have installed the last version of the nvidia CUDA kit) > > > > About the software i run ubuntu 16.04.4 with gfortran and gcc, both > > > > versions 5.4.0. Also I have installed the last version of the intel > > > > MKL > > > > > > library (aditionally i also have ACML). Finally I'd like to compile > > > > cp2k > > > > > > with libint, libxc and fftw. All three are compiled and installed in > > > > my > > > > > > computer > > > > > > > > Any help for the creation of the appropiate arch file in wellcome. > > > > > > > > That you all in advance. > > > > > > > > Rafa > > > > email: j.sas... at ucl.ac.uk > > web: http://sassy.formativ.net > > > > Please avoid sending me Word or PowerPoint attachments. > > See http://www.gnu.org/philosophy/no-word-attachments.html -- ************************************************************* Dr. J?rg Sa?mannshausen, MRSC University College London Department of Chemistry 20 Gordon Street London WC1H 0AJ email: j.sassma... at ucl.ac.uk web: http://sassy.formativ.net Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 220 bytes Desc: This is a digitally signed message part. URL: From amazing... at gmail.com Tue Feb 14 15:29:46 2017 From: amazing... at gmail.com (David T) Date: Tue, 14 Feb 2017 07:29:46 -0800 (PST) Subject: meaning of global and subconfigurations in bsse calculation Message-ID: <14e22ed2-71e5-4d7a-8378-b8a2da22c04b@googlegroups.com> Dear all I am trying to understand the meaning of global and subsystem configuration in a bsse calculation. I guess the sybsystem is simply the different parts of the system I would like to study, for instance AB I will define 2 fragment and then I will have subsystem 1 0 and 0 1. On the other hand I am lost in the possible meaning of global configuration, the only information I could find here on the group was an topic from which I've seen it is defined several time so I wonder if the input I found is correct and the meaning of it. &BSSE &FRAGMENT LIST ... &END FRAGMENT &FRAGMENT LIST .... &END FRAGMENT &CONFIGURATION GLB_CONF 1 1 SUB_CONF 1 1 &END &CONFIGURATION GLB_CONF 1 0 SUB_CONF 1 0 &END &CONFIGURATION GLB_CONF 0 1 SUB_CONF 0 1 &END &CONFIGURATION GLB_CONF 1 1 SUB_CONF 1 0 &END &CONFIGURATION GLB_CONF 1 1 SUB_CONF 0 1 &END &END BSSE what I would have done is GLB_CONF 1 1 SUB_CONF 1 1 GLB_CONF 1 1 SUB_COND 1 0 GLB_CONF 1 1 SUB_CONF 0 1 Nevertheless also in this case it seems strange to me have to define the global configuration so that I imagine I'm missing something. Any comment, advice or even link to examples which I could not find are more than welcome Cheers Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From manoo... at gmail.com Tue Feb 14 18:21:43 2017 From: manoo... at gmail.com (Babgen Manookian) Date: Tue, 14 Feb 2017 10:21:43 -0800 (PST) Subject: Isolated system Geometry Optimizations Message-ID: <1a744090-32fc-4286-a8ff-a32fbcb27c07@googlegroups.com> Hey Everyone, I am a new cp2k user and have been working on a test system in order to get a feel for how the program works. My test system is a cyclohexane molecule and I am interested in determining the energy difference between boat and chair conformations. I am using a wavelet poisson solver with periodicity turned off and the molecule centered in the cell. I attached the template input file which I used to create the different inputs with varying cells size. What I have noticed is that as I increase my cell size the energy does not converge on a single value, instead it seems to oscillate. The graphs below show the energies of each conformation and their differences as functions of cell size. I am very curious as to what is causing these oscillations. If I have a single cyclohexane molecule centered in my cell, as I increase my cell size, I would think that the extra vacuum space around the molecule will not affect the energy. If there is anyone out there who could provide any sort of input on this it would be much appreciated. Thanks, Bobby -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cychex_boat_temp.inp Type: chemical/x-gamess-input Size: 2796 bytes Desc: not available URL: From lingsa... at gmail.com Tue Feb 14 19:15:46 2017 From: lingsa... at gmail.com (S Ling) Date: Tue, 14 Feb 2017 19:15:46 +0000 Subject: [CP2K:8694] meaning of global and subconfigurations in bsse calculation In-Reply-To: References: <14e22ed2-71e5-4d7a-8378-b8a2da22c04b@googlegroups.com> Message-ID: Hi My understanding is that GLB_CONF defines whether there are basis sets imposed on each fragment (including the ghost atoms, 1: yes, 0: no), and SUB_CONF defines whether a fragment is included in the electronic structure calculation. If both fragments are neutral and closed-shell, I think you don't need to specify the &CONFIGURATION sections. SL On 14 Feb 2017 15:29, "David T" wrote: Dear all I am trying to understand the meaning of global and subsystem configuration in a bsse calculation. I guess the sybsystem is simply the different parts of the system I would like to study, for instance AB I will define 2 fragment and then I will have subsystem 1 0 and 0 1. On the other hand I am lost in the possible meaning of global configuration, the only information I could find here on the group was an topic from which I've seen it is defined several time so I wonder if the input I found is correct and the meaning of it. &BSSE &FRAGMENT LIST ... &END FRAGMENT &FRAGMENT LIST .... &END FRAGMENT &CONFIGURATION GLB_CONF 1 1 SUB_CONF 1 1 &END &CONFIGURATION GLB_CONF 1 0 SUB_CONF 1 0 &END &CONFIGURATION GLB_CONF 0 1 SUB_CONF 0 1 &END &CONFIGURATION GLB_CONF 1 1 SUB_CONF 1 0 &END &CONFIGURATION GLB_CONF 1 1 SUB_CONF 0 1 &END &END BSSE what I would have done is GLB_CONF 1 1 SUB_CONF 1 1 GLB_CONF 1 1 SUB_COND 1 0 GLB_CONF 1 1 SUB_CONF 0 1 Nevertheless also in this case it seems strange to me have to define the global configuration so that I imagine I'm missing something. Any comment, advice or even link to examples which I could not find are more than welcome Cheers Davide -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From yiyan... at asu.edu Tue Feb 14 21:33:24 2017 From: yiyan... at asu.edu (Yiyang) Date: Tue, 14 Feb 2017 13:33:24 -0800 (PST) Subject: Binary restart file does not work In-Reply-To: <43346873-8272-42f6-bc2f-15c0e37dad13@googlegroups.com> References: <43346873-8272-42f6-bc2f-15c0e37dad13@googlegroups.com> Message-ID: <5dad361b-d4cd-4739-b4c8-d1516ff0e1f9@googlegroups.com> Even if i specify RESTART_SHELL_POS .FALSE. RESTART_SHELL_THERMOSTAT .FALSE. RESTART_SHELL_VELOCITY .FALSE. in the &EXT_RESTART section, the same error message is still generated. The position of the above commands do not matter. For example, the error message will not change if I put RESTART_SHELL_POS .FALSE. in front of RESTART_VEL .TRUE. in the &EXT_RESTART section. Is this a bug? -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Wed Feb 15 08:32:00 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Wed, 15 Feb 2017 09:32:00 +0100 Subject: [CP2K:8695] Isolated system Geometry Optimizations In-Reply-To: <1a744090-32fc-4286-a8ff-a32fbcb27c07@googlegroups.com> References: <1a744090-32fc-4286-a8ff-a32fbcb27c07@googlegroups.com> Message-ID: Hi the problem is connected to the fact that the plane wave basis depends on the box size. The same is true for the XC integration grid. Now with a very small cutoff for the PW this will show the dramatic effects you have. To solve this proble you have to use a much higher cutoff, especially the relative cutoff. I would suggest values of 80 and 400, respectively. The smoothing you use for the XC will also have an effect. I don't know how bad this is in your case. I would start without the smoothing and make later some tests to see if it helps. In general, it is a good idea for such tests to increase accuracy in all parts of the calculation. regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Babgen Manookian Sent by: cp... at googlegroups.com Date: 02/14/2017 07:21PM Subject: [CP2K:8695] Isolated system Geometry Optimizations Hey Everyone, I am a new cp2k user and have been working on a test system in order to get a feel for how the program works. My test system is a cyclohexane molecule and I am interested in determining the energy difference between boat and chair conformations. I am using a wavelet poisson solver with periodicity turned off and the molecule centered in the cell. I attached the template input file which I used to create the different inputs with varying cells size. What I have noticed is that as I increase my cell size the energy does not converge on a single value, instead it seems to oscillate. The graphs below show the energies of each conformation and their differences as functions of cell size. I am very curious as to what is causing these oscillations. If I have a single cyclohexane molecule centered in my cell, as I increase my cell size, I would think that the extra vacuum space around the molecule will not affect the energy.? If there is anyone out there who could provide any sort of input on this it would be much appreciated. Thanks,Bobby -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. [attachment "cychex_boat_temp.inp" removed by J?rg Hutter/at/UZH] From liufe... at gmail.com Wed Feb 15 09:06:47 2017 From: liufe... at gmail.com (feihu liu) Date: Wed, 15 Feb 2017 01:06:47 -0800 (PST) Subject: Is there some code to read, write and modify WFN files In-Reply-To: <09b7ddc0-0ad8-4898-9626-0cdc32d0577d@googlegroups.com> References: <3df8e4f7-907e-48dd-a412-61622a04ba0e@googlegroups.com> <09b7ddc0-0ad8-4898-9626-0cdc32d0577d@googlegroups.com> Message-ID: <289f38c2-d681-4d58-bbae-8ce0d19c3090@googlegroups.com> Hi Yi, I also want to read the WFN file, but I cannot find the RestartTool in tools folder in version 2.6.2 and 2.6.0. Would you like to tell more. Thank you! Bests, Feihu ? 2015?4?23???? UTC+8??12:57:32?????? > > I found it. > > In version 2.6, there is a tool named RestartTool in the tools folder can > do it. > > Yi > > On Wednesday, April 22, 2015 at 8:39:14 AM UTC-4, ?? wrote: >> >> I would like to do a SCF calculation for a system then add some atom >> without electron into it. So, the number of basis set is not consistent. >> Would you please point out how to read and write WFN file so that I can >> make the first SCF WFN file suitable for the latter restart. >> >> Yi >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amazing... at gmail.com Wed Feb 15 21:29:46 2017 From: amazing... at gmail.com (David T) Date: Wed, 15 Feb 2017 13:29:46 -0800 (PST) Subject: [CP2K:8694] meaning of global and subconfigurations in bsse calculation In-Reply-To: References: <14e22ed2-71e5-4d7a-8378-b8a2da22c04b@googlegroups.com> Message-ID: <338517d1-c575-4595-a965-80542d1e7a6e@googlegroups.com> Thanks On Tuesday, 14 February 2017 19:15:49 UTC, S Ling wrote: > Hi > > My understanding is that GLB_CONF defines whether there are basis sets > imposed on each fragment (including the ghost atoms, 1: yes, 0: no), and > SUB_CONF defines whether a fragment is included in the electronic structure > calculation. If both fragments are neutral and closed-shell, I think you > don't need to specify the &CONFIGURATION sections. > > SL > > On 14 Feb 2017 15:29, "David T" > > wrote: > > Dear all > > I am trying to understand the meaning of global and subsystem > configuration in a bsse calculation. > > I guess the sybsystem is simply the different parts of the system I would > like to study, for instance AB I will define 2 fragment and then I will > have subsystem 1 0 and 0 1. > > On the other hand I am lost in the possible meaning of global > configuration, the only information I could find here on the group was an > topic from which I've seen it is defined several time so I wonder if the > input I found is correct and the meaning of it. > > &BSSE > &FRAGMENT > LIST ... > &END FRAGMENT > &FRAGMENT > LIST .... > &END FRAGMENT > &CONFIGURATION > GLB_CONF 1 1 > SUB_CONF 1 1 > &END > > &CONFIGURATION > GLB_CONF 1 0 > SUB_CONF 1 0 > &END > > &CONFIGURATION > GLB_CONF 0 1 > SUB_CONF 0 1 > &END > &CONFIGURATION > GLB_CONF 1 1 > SUB_CONF 1 0 > &END > &CONFIGURATION > GLB_CONF 1 1 > SUB_CONF 0 1 > &END > &END BSSE > > what I would have done is > > GLB_CONF 1 1 > SUB_CONF 1 1 > > GLB_CONF 1 1 > SUB_COND 1 0 > > GLB_CONF 1 1 > SUB_CONF 0 1 > > Nevertheless also in this case it seems strange to me have to define the > global configuration so that I imagine I'm missing something. > > Any comment, advice or even link to examples which I could not find are > more than welcome > > Cheers > Davide > > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+... at googlegroups.com . > To post to this group, send email to cp... at googlegroups.com . > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shun3... at gmail.com Thu Feb 16 11:14:56 2017 From: shun3... at gmail.com (Shun) Date: Thu, 16 Feb 2017 03:14:56 -0800 (PST) Subject: Error of Hybrid DFT Message-ID: <462af447-ec77-4fa8-a812-eb489e75c801@googlegroups.com> Dear all HI. I am trying to calculate Band-gap of ZnO by means of Hybrid-DFT (PBE and HF) with reference to this example file (https://www.cp2k.org/exercises:2014_ethz_mmm:tio2_gap) But, an Error message appeared immediately after starting this calculation. the message is as follows. What do I have to do to solve this problem? I guess this question is very stupid but I have no idea. ********************** *** WARNING in hfx_energy_potential.F:626 :: The Kohn Sham matrix is not *** *** 100% occupied. This may result in uncorrect Hartree-Fock results. Try *** *** to decrease EPS_PGF_ORB and EPS_FILTER_MATRIX in the QS section. *** *********************** ****input**** &GLOBAL PROJECT_NAME zno RUN_TYPE CELL_OPT &END GLOBAL &MOTION &GEO_OPT OPTIMIZER BFGS MAX_ITER 500 MAX_DR 1E-6 MAX_FORCE 1E-06 &END GEO_OPT &CELL_OPT OPTIMIZER BFGS MAX_ITER 500 MAX_DR 1E-6 MAX_FORCE 1E-06 &END CELL_OPT &END MOTION &FORCE_EVAL STRESS_TENSOR ANALYTICAL METHOD QS &DFT BASIS_SET_FILE_NAME /cp2k-3.0/data/BASIS_MOLOPT POTENTIAL_FILE_NAME /cp2k-3.0/data/POTENTIAL &SCF SCF_GUESS RESTART EPS_SCF 1.0E-8 MAX_SCF 10 &OUTER_SCF EPS_SCF 1.0E-8 MAX_SCF 1000 &END OUTER_SCF &OT ON PRECONDITIONER FULL_SINGLE_INVERSE MINIMIZER DIIS &END OT &END SCF &QS METHOD GPW &END QS &MGRID CUTOFF 500 &END MGRID &PRINT ! section required to obtain the HOMO-LUMO gap. &MO_CUBES WRITE_CUBE .FALSE. ! no cube file is generated NHOMO 1 ! but we require 1 HOMO and 1 LUMO in the output NLUMO 1 ! so that we get the band gap &END &END &XC ! this is the section to define the electronic exchange &XC_FUNCTIONAL ! our functional is hybrid &PBE ! it has 75% of PBE SCALE_X 0.75 SCALE_C 1.0 &END &PBE_HOLE_T_C_LR SCALE_X 0.25 ! + 25% of truncated PBE0 functional - that includes exact hfx CUTOFF_RADIUS 3.5 ! that has interaction truncated at 3.5 A from the atomic core &END &END XC_FUNCTIONAL &HF FRACTION 0.25 ! this is the hfx section. The amount of hfx must be consistent with above &SCREENING ! Screening of the electronic repulsion up to the given threshold. This section is needed EPS_SCHWARZ 1.0E-6 SCREEN_ON_INITIAL_P TRUE ! having an external wave-function, a preliminary screening &END ! can be performed to speed up calculations &INTERACTION_POTENTIAL ! Sets up interaction potential between the two regions POTENTIAL_TYPE TRUNCATED ! the potential is truncated CUTOFF_RADIUS 3.5 ! at 3.5 A (see above) # T_C_G_DATA ./t_c_g.dat ! external file with parameters needed to truncate the potential &END &END &END &END DFT &SUBSYS &CELL PERIODIC XYZ A 2.814062947057155 -1.624700000000000 0.000000000000000 B 0.000000000000000 3.249400000000000 0.000000000000000 C 0.000000000000000 0.000000000000000 5.203800000000000 MULTIPLE_UNIT_CELL 3 3 3 ! a 2x2x1 system is required to get realistic results &END CELL &COORD Zn 0.938020982352385 1.624700000000000 0.000000000000000 Zn 1.876041964704770 0.000000000000000 2.601900000000000 O 0.938020982352385 1.624700000000000 1.988371980000000 O 1.876041964704770 0.000000000000000 4.590271980000001 &END COORD &TOPOLOGY MULTIPLE_UNIT_CELL 3 3 3 &END TOPOLOGY &TOPOLOGY MULTIPLE_UNIT_CELL 3 3 3 &END TOPOLOGY @set FUNCTIONAL PBE &KIND Zn BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-${FUNCTIONAL}-q12 &END KIND &KIND O BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-${FUNCTIONAL}-q6 &END KIND &END SUBSYS &END FORCE_EVAL **************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From lingsa... at gmail.com Thu Feb 16 11:46:53 2017 From: lingsa... at gmail.com (S Ling) Date: Thu, 16 Feb 2017 11:46:53 +0000 Subject: [CP2K:8701] Error of Hybrid DFT In-Reply-To: <462af447-ec77-4fa8-a812-eb489e75c801@googlegroups.com> References: <462af447-ec77-4fa8-a812-eb489e75c801@googlegroups.com> Message-ID: See here: https://www.cp2k.org/faq:hfx_eps_warning You may need to use the ADMM method for hybrid DFT calculation of a 3x3x3 supercell of ZnO. Please have a look at my slides ( https://www.cp2k.org/_media/events:2015_cecam_tutorial:ling_hybrids.pdf) on how to use ADMM method for hybrid DFT calculations in CP2K. SL On 16 February 2017 at 11:14, Shun wrote: > > Dear all > > HI. I am trying to calculate Band-gap of ZnO by means of Hybrid-DFT (PBE > and HF) with reference to this example file (https://www.cp2k.org/ > exercises:2014_ethz_mmm:tio2_gap) > But, an Error message appeared immediately after starting this > calculation. the message is as follows. What do I have to do to solve this > problem? I guess this question is very stupid but I have no idea. > > > ********************** > *** WARNING in hfx_energy_potential.F:626 :: The Kohn Sham matrix is not > *** > *** 100% occupied. This may result in uncorrect Hartree-Fock results. Try > *** > *** to decrease EPS_PGF_ORB and EPS_FILTER_MATRIX in the QS section. > *** > *********************** > > ****input**** > > &GLOBAL > PROJECT_NAME zno > RUN_TYPE CELL_OPT > &END GLOBAL > &MOTION > &GEO_OPT > OPTIMIZER BFGS > MAX_ITER 500 > MAX_DR 1E-6 > MAX_FORCE 1E-06 > &END GEO_OPT > &CELL_OPT > OPTIMIZER BFGS > MAX_ITER 500 > MAX_DR 1E-6 > MAX_FORCE 1E-06 > &END CELL_OPT > &END MOTION > &FORCE_EVAL > STRESS_TENSOR ANALYTICAL > METHOD QS > &DFT > BASIS_SET_FILE_NAME /cp2k-3.0/data/BASIS_MOLOPT > POTENTIAL_FILE_NAME /cp2k-3.0/data/POTENTIAL > &SCF > SCF_GUESS RESTART > EPS_SCF 1.0E-8 > MAX_SCF 10 > &OUTER_SCF > EPS_SCF 1.0E-8 > MAX_SCF 1000 > &END OUTER_SCF > &OT ON > PRECONDITIONER FULL_SINGLE_INVERSE > MINIMIZER DIIS > &END OT > &END SCF > &QS > METHOD GPW > &END QS > &MGRID > CUTOFF 500 > &END MGRID > > &PRINT ! section required to obtain the HOMO-LUMO gap. > &MO_CUBES > WRITE_CUBE .FALSE. ! no cube file is generated > NHOMO 1 ! but we require 1 HOMO and 1 LUMO in the output > NLUMO 1 ! so that we get the band gap > &END > &END > &XC ! this is the section to define the > electronic exchange > &XC_FUNCTIONAL ! our functional is hybrid > > &PBE ! it has 75% of PBE > SCALE_X 0.75 > SCALE_C 1.0 > &END > &PBE_HOLE_T_C_LR > SCALE_X 0.25 ! + 25% of truncated PBE0 functional - that > includes exact hfx > CUTOFF_RADIUS 3.5 ! that has interaction truncated at 3.5 A > from the atomic core > &END > &END XC_FUNCTIONAL > &HF > FRACTION 0.25 ! this is the hfx section. The amount of hfx > must be consistent with above > &SCREENING ! Screening of the electronic repulsion up > to the given threshold. This section is needed > EPS_SCHWARZ 1.0E-6 > SCREEN_ON_INITIAL_P TRUE ! having an external wave-function, a > preliminary screening > &END ! can be performed to speed up > calculations > &INTERACTION_POTENTIAL ! Sets up interaction potential > between the two regions > POTENTIAL_TYPE TRUNCATED ! the potential is truncated > CUTOFF_RADIUS 3.5 ! at 3.5 A (see above) > # T_C_G_DATA ./t_c_g.dat ! external file with parameters > needed to truncate the potential > &END > &END > &END > &END DFT > &SUBSYS > > &CELL > PERIODIC XYZ > A 2.814062947057155 -1.624700000000000 0.000000000000000 > B 0.000000000000000 3.249400000000000 0.000000000000000 > C 0.000000000000000 0.000000000000000 5.203800000000000 > MULTIPLE_UNIT_CELL 3 3 3 ! a 2x2x1 system is required to get > realistic results > &END CELL > > &COORD > Zn 0.938020982352385 1.624700000000000 0.000000000000000 > Zn 1.876041964704770 0.000000000000000 2.601900000000000 > O 0.938020982352385 1.624700000000000 1.988371980000000 > O 1.876041964704770 0.000000000000000 4.590271980000001 > &END COORD > > &TOPOLOGY > MULTIPLE_UNIT_CELL 3 3 3 > &END TOPOLOGY > > &TOPOLOGY > MULTIPLE_UNIT_CELL 3 3 3 > &END TOPOLOGY > > > @set FUNCTIONAL PBE > &KIND Zn > BASIS_SET DZVP-MOLOPT-SR-GTH > POTENTIAL GTH-${FUNCTIONAL}-q12 > &END KIND > &KIND O > BASIS_SET DZVP-MOLOPT-SR-GTH > POTENTIAL GTH-${FUNCTIONAL}-q6 > &END KIND > &END SUBSYS > &END FORCE_EVAL > > **************************************************** > > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuri.a.... at gmail.com Thu Feb 16 15:24:15 2017 From: nuri.a.... at gmail.com (Nuri Yazdani) Date: Thu, 16 Feb 2017 07:24:15 -0800 (PST) Subject: Computing total energy with -RESTART.wfn and no SCF iterations In-Reply-To: References: Message-ID: HI again, Thanks for all the help! Indeed the ADDED_MOS did the trick! Just to add: the ADDED_MOS can be used for both addition or removing of charge from the system! To calculate with charge removed: Generate the RESTART file with the neutral system, then in the calculation of the system with charge removed but with the wavefunctions of the neutral system include ADDED_MOS dC, where dC is the removed charge. To calculate with charge added: Generate the RESTART file with the neutral system including ADDED_MOS dC, where dC is the charge you want to add in the next step, then in the calculation of the system with charge added do not include the ADDED_MOS. Cheers, Nuri -------------- next part -------------- An HTML attachment was scrubbed... URL: From reza.... at gmail.com Fri Feb 17 06:56:17 2017 From: reza.... at gmail.com (Reza) Date: Thu, 16 Feb 2017 22:56:17 -0800 (PST) Subject: Libinit compilation Message-ID: Dear Users, I have compile libint and linked it in cp2k ssmp and psmp versions. I used ifort, icc, icpc of intel. speed of GGA BLYP method for fullerene (C240 molecule in 30*30*30 box) is good, but when I use PBE0, a hybrid method, speed is very low. Is it possible to compile libint with mpicc? I think libint should be very fast for HFX, but my performance is very low. I used 6-31G** basis set for C atoms in C240. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Fri Feb 17 09:07:30 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Fri, 17 Feb 2017 10:07:30 +0100 Subject: [CP2K:8704] Libinit compilation In-Reply-To: References: Message-ID: Hi without more information I will have to guess: this is most likely NOT a libint problem. Doing a basic PBE0 calculation will cost you about 10 times more than a PBE calculation. Now, if you didn't have enough memory (check the output) this will be even longer. The settings of the HFX part are also crucial for performance (screening). regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Reza Sent by: cp... at googlegroups.com Date: 02/17/2017 07:44AM Subject: [CP2K:8704] Libinit compilation Dear Users, I have compile libint and linked it in cp2k ssmp and psmp versions. I used ifort, icc, icpc of intel. speed of GGA BLYP method for fullerene (C240 molecule in 30*30*30 box) is good, but when I use PBE0, a hybrid method, speed is very low. Is it possible to compile libint with mpicc? I think libint should be very fast for HFX, but my performance is very low. I used 6-31G** basis set for C atoms in C240. -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. From reza.... at gmail.com Fri Feb 17 09:48:24 2017 From: reza.... at gmail.com (Reza) Date: Fri, 17 Feb 2017 01:48:24 -0800 (PST) Subject: [CP2K:8704] Libinit compilation In-Reply-To: References: Message-ID: <4eb14ada-2833-4cc8-b70e-c0646e2b3426@googlegroups.com> Dear Juerg; Thank you for your answer. I calculated nearly the same job for Gaussian09 and CP2K for C240 molecule (contains 240 carbon atom). For BLYP, wall clock times of Gaussian09 and CP2K are similar (about 20min), but for hybrid methods such as PBE0 and B3LYP, the wall clock times are very different. For Gaussian09, PBE0 time is about 40 min, and B3LYP is about 45 min, but for CP2K, PBE0 two cycles of SCF needs 96 min!!!!. It needs at least 10 cycles to SCF to be converged. Please see the attached files. I think this is because I didn't use parallel compiling for Libint (googling doesn't show any parallel compiling for Libint). Thanks again. On Friday, February 17, 2017 at 12:37:35 PM UTC+3:30, jgh wrote: > > Hi > > without more information I will have to guess: > > this is most likely NOT a libint problem. Doing a basic PBE0 > calculation will cost you about 10 times more than a PBE calculation. > Now, if you didn't have enough memory (check the output) this will > be even longer. The settings of the HFX part are also crucial for > performance > (screening). > > regards > > Juerg > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: hut... at chem.uzh.ch > > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----cp... at googlegroups.com wrote: -----To: cp2k < > cp... at googlegroups.com > > From: Reza > Sent by: cp... at googlegroups.com > Date: 02/17/2017 07:44AM > Subject: [CP2K:8704] Libinit compilation > > Dear Users, > I have compile libint and linked it in cp2k ssmp and psmp versions. I used > ifort, icc, icpc of intel. > speed of GGA BLYP method for fullerene (C240 molecule in 30*30*30 box) is > good, but when I use PBE0, a hybrid method, speed is very low. > Is it possible to compile libint with mpicc? I think libint should be very > fast for HFX, but my performance is very low. > I used 6-31G** basis set for C atoms in C240. > > > > > -- > > You received this message because you are subscribed to the Google Groups > "cp2k" group. > > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+... at googlegroups.com . > > To post to this group, send email to cp... at googlegroups.com . > > > Visit this group at https://groups.google.com/group/cp2k. > > For more options, visit https://groups.google.com/d/optout. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: C240_6_31Gxx_SCF_Conv_blyp.inp Type: chemical/x-gamess-input Size: 15733 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: C240_6_31Gxx_SCF_Conv_blyp_cpu40_psmp_mpirun_Good_Perf.out Type: application/octet-stream Size: 67575 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: C240_6_31Gxx_2SCF_40cpu_ssmp_Bad_Perf.out Type: application/octet-stream Size: 104772 bytes Desc: not available URL: From hut... at chem.uzh.ch Fri Feb 17 10:55:39 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Fri, 17 Feb 2017 11:55:39 +0100 Subject: [CP2K:8706] Libinit compilation In-Reply-To: <4eb14ada-2833-4cc8-b70e-c0646e2b3426@googlegroups.com> References: <4eb14ada-2833-4cc8-b70e-c0646e2b3426@googlegroups.com>, Message-ID: Hi from your output one can see that your settings (no input to confirm) are far from optimal. I'm also sure you didn't use the same tight settings in your Gaussian calculations. three obvious points: - no screening of integrals (10^-16) - recalculation of almost all integrals (not enough memory allocated) - very tight SCF convergence and non-optimal OT settings (your BLYP calculation could converge 10 times faster) regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Reza Sent by: cp... at googlegroups.com Date: 02/17/2017 10:48AM Subject: Re: [CP2K:8706] Libinit compilation Dear Juerg; Thank you for your answer. I calculated nearly the same job for Gaussian09 and CP2K for C240 molecule (contains 240 carbon atom). For BLYP, wall clock times of Gaussian09 and CP2K are similar (about 20min), but for hybrid methods such as PBE0 and B3LYP, the wall clock times are very different. For Gaussian09, PBE0 time is about 40 min, and B3LYP is about 45 min, but? for CP2K, PBE0 two cycles of SCF needs 96 min!!!!. It needs at least 10 cycles to SCF to be converged. Please see the attached files. I think this is because I didn't use parallel compiling for Libint (googling doesn't show any parallel compiling for Libint). Thanks again. On Friday, February 17, 2017 at 12:37:35 PM UTC+3:30, jgh wrote:Hi without more information I will have to guess: this is most likely NOT a libint problem. Doing a basic PBE0 calculation will cost you about 10 times more than a PBE calculation. Now, if you didn't have enough memory (check the output) this will be even longer. The settings of the HFX part are also crucial for performance (screening). regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Reza Sent by: cp... at googlegroups.com Date: 02/17/2017 07:44AM Subject: [CP2K:8704] Libinit compilation Dear Users, I have compile libint and linked it in cp2k ssmp and psmp versions. I used ifort, icc, icpc of intel. speed of GGA BLYP method for fullerene (C240 molecule in 30*30*30 box) is good, but when I use PBE0, a hybrid method, speed is very low. Is it possible to compile libint with mpicc? I think libint should be very fast for HFX, but my performance is very low. I used 6-31G** basis set for C atoms in C240. -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. [attachment "C240_6_31Gxx_SCF_Conv_blyp.inp" removed by J?rg Hutter/at/UZH] [attachment "C240_6_31Gxx_SCF_Conv_blyp_cpu40_psmp_mpirun_Good_Perf.out" removed by J?rg Hutter/at/UZH] [attachment "C240_6_31Gxx_2SCF_40cpu_ssmp_Bad_Perf.out" removed by J?rg Hutter/at/UZH] From reza.... at gmail.com Fri Feb 17 17:17:55 2017 From: reza.... at gmail.com (Reza) Date: Fri, 17 Feb 2017 09:17:55 -0800 (PST) Subject: [CP2K:8706] Libinit compilation In-Reply-To: References: <4eb14ada-2833-4cc8-b70e-c0646e2b3426@googlegroups.com>,> Message-ID: Hi again, I have set parameters to obtain the same total energy to the Gaussian, as could as possible. the change of total energy in the last SCF converged in Gaussian is about 5*10(-9) and for CP2K is 8*10(-9). the grid of Gaussian is 75 for radial and 302 for angular point. Setting lower or higher cutoff of grids in CP2K changes total energy in CP2K. total energy of Gaussian is -9143.41735963 and for CP2K is -9142.9538484165. About memory, you are right. I forgot to increase it in CP2K. You can see the output of Gaussian as attached file. On Friday, February 17, 2017 at 2:25:42 PM UTC+3:30, jgh wrote: > > Hi > > from your output one can see that your settings (no input to confirm) > are far from optimal. I'm also sure you didn't use the same tight settings > in your Gaussian calculations. > > three obvious points: > > - no screening of integrals (10^-16) > - recalculation of almost all integrals (not enough memory allocated) > - very tight SCF convergence and non-optimal OT settings (your BLYP > calculation could converge 10 times faster) > > regards > > Juerg > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: hut... at chem.uzh.ch > > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----cp... at googlegroups.com wrote: -----To: cp2k < > cp... at googlegroups.com > > From: Reza > Sent by: cp... at googlegroups.com > Date: 02/17/2017 10:48AM > Subject: Re: [CP2K:8706] Libinit compilation > > Dear Juerg; > Thank you for your answer. I calculated nearly the same job for Gaussian09 > and CP2K for C240 molecule (contains 240 carbon atom). > For BLYP, wall clock times of Gaussian09 and CP2K are similar (about > 20min), but for hybrid methods such as PBE0 and B3LYP, the wall clock times > are very different. For Gaussian09, PBE0 time is about 40 min, and B3LYP is > about 45 min, but for CP2K, PBE0 two cycles of SCF needs 96 min!!!!. It > needs at least 10 cycles to SCF to be converged. > > Please see the attached files. > > I think this is because I didn't use parallel compiling for Libint > (googling doesn't show any parallel compiling for Libint). > > Thanks again. > > On Friday, February 17, 2017 at 12:37:35 PM UTC+3:30, jgh wrote:Hi > > > > without more information I will have to guess: > > > > this is most likely NOT a libint problem. Doing a basic PBE0 > > calculation will cost you about 10 times more than a PBE calculation. > > Now, if you didn't have enough memory (check the output) this will > > be even longer. The settings of the HFX part are also crucial for > performance > > (screening). > > > > regards > > > > Juerg > > -------------------------------------------------------------- > > Juerg Hutter Phone : ++41 44 635 4491 > > Institut f?r Chemie C FAX : ++41 44 635 6838 > > Universit?t Z?rich E-mail: hut... at chem.uzh.ch > > Winterthurerstrasse 190 > > CH-8057 Z?rich, Switzerland > > --------------------------------------------------------------- > > > > -----cp... at googlegroups.com wrote: -----To: cp2k > > From: Reza > > Sent by: cp... at googlegroups.com > > Date: 02/17/2017 07:44AM > > Subject: [CP2K:8704] Libinit compilation > > > > Dear Users, > > I have compile libint and linked it in cp2k ssmp and psmp versions. I used > ifort, icc, icpc of intel. > > speed of GGA BLYP method for fullerene (C240 molecule in 30*30*30 box) is > good, but when I use PBE0, a hybrid method, speed is very low. > > Is it possible to compile libint with mpicc? I think libint should be very > fast for HFX, but my performance is very low. > > I used 6-31G** basis set for C atoms in C240. > > > > > > > > > > -- > > > > You received this message because you are subscribed to the Google Groups > "cp2k" group. > > > > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+... at googlegroups.com. > > > > To post to this group, send email to cp... at googlegroups.com. > > > > Visit this group at https://groups.google.com/group/cp2k. > > > > For more options, visit https://groups.google.com/d/optout. > > > > > > > > > > -- > > You received this message because you are subscribed to the Google Groups > "cp2k" group. > > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+... at googlegroups.com . > > To post to this group, send email to cp... at googlegroups.com . > > > Visit this group at https://groups.google.com/group/cp2k. > > For more options, visit https://groups.google.com/d/optout. > > > > [attachment "C240_6_31Gxx_SCF_Conv_blyp.inp" removed by J?rg > Hutter/at/UZH] > [attachment "C240_6_31Gxx_SCF_Conv_blyp_cpu40_psmp_mpirun_Good_Perf.out" > removed by J?rg Hutter/at/UZH] > [attachment "C240_6_31Gxx_2SCF_40cpu_ssmp_Bad_Perf.out" removed by J?rg > Hutter/at/UZH] > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- Entering Gaussian System, Link 0=/root/g09/g09 Input=Fullerene_C240_BLYP.gjf Output=Fullerene_C240_BLYP.log Initial command: /root/g09/l1.exe "/root/runs/nwchem/Gau-13715.inp" -scrdir="/root/runs/nwchem/" Entering Link 1 = /root/g09/l1.exe PID= 13716. Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2015, Gaussian, Inc. All Rights Reserved. This is part of the Gaussian(R) 09 program. It is based on the Gaussian(R) 03 system (copyright 2003, Gaussian, Inc.), the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.), the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.), the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.), the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.), the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.), the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon University), and the Gaussian 82(TM) system (copyright 1983, Carnegie Mellon University). Gaussian is a federally registered trademark of Gaussian, Inc. This software contains proprietary and confidential information, including trade secrets, belonging to Gaussian, Inc. This software is provided under written license and may be used, copied, transmitted, or stored only in accord with that written license. The following legend is applicable only to US Government contracts under FAR: RESTRICTED RIGHTS LEGEND Use, reproduction and disclosure by the US Government is subject to restrictions as set forth in subparagraphs (a) and (c) of the Commercial Computer Software - Restricted Rights clause in FAR 52.227-19. Gaussian, Inc. 340 Quinnipiac St., Bldg. 40, Wallingford CT 06492 --------------------------------------------------------------- Warning -- This program may not be used in any manner that competes with the business of Gaussian, Inc. or will provide assistance to any competitor of Gaussian, Inc. The licensee of this program is prohibited from giving any competitor of Gaussian, Inc. access to this program. By using this program, the user acknowledges that Gaussian, Inc. is engaged in the business of creating and licensing software in the field of computational chemistry and represents and warrants to the licensee that it is not a competitor of Gaussian, Inc. and that it will not use this program in any manner prohibited above. --------------------------------------------------------------- Cite this work as: Gaussian 09, Revision E.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2013. ****************************************** Gaussian 09: ES64L-G09RevE.01 30-Nov-2015 14-Feb-2017 ****************************************** %chk=./Fullerene_C240.chk %mem=120GB %nprocshared=40 Will use up to 40 processors via shared memory. -------------- #p BLYP/6-31G* -------------- 1/38=1/1; 2/12=2,17=6,18=5,40=1/2; 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=402/1,2,3; 4//1; 5/5=2,38=5/2; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; Leave Link 1 at Tue Feb 14 12:30:12 2017, MaxMem= 16106127360 cpu: 3.8 (Enter /root/g09/l101.exe) ------------------- Title Card Required ------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C C 1 B1 C 2 B2 1 A1 C 3 B3 2 A2 1 D1 0 C 1 B4 2 A3 3 D2 0 C 1 B5 2 A4 3 D3 0 C 6 B6 1 A5 2 D4 0 C 7 B7 6 A6 1 D5 0 C 8 B8 7 A7 6 D6 0 C 6 B9 1 A8 2 D7 0 C 7 B10 6 A9 1 D8 0 C 11 B11 7 A10 6 D9 0 C 12 B12 11 A11 7 D10 0 C 13 B13 12 A12 11 D11 0 C 11 B14 7 A13 6 D12 0 C 12 B15 11 A14 7 D13 0 C 16 B16 12 A15 11 D14 0 C 17 B17 16 A16 12 D15 0 C 18 B18 17 A17 16 D16 0 C 16 B19 12 A18 11 D17 0 C 17 B20 16 A19 12 D18 0 C 21 B21 17 A20 16 D19 0 C 22 B22 21 A21 17 D20 0 C 23 B23 22 A22 21 D21 0 C 21 B24 17 A23 16 D22 0 C 9 B25 8 A24 7 D23 0 C 26 B26 9 A25 8 D24 0 C 27 B27 26 A26 9 D25 0 C 28 B28 27 A27 26 D26 0 C 26 B29 9 A28 8 D27 0 C 25 B30 21 A29 17 D28 0 C 31 B31 25 A30 21 D29 0 C 32 B32 31 A31 25 D30 0 C 33 B33 32 A32 31 D31 0 C 34 B34 33 A33 32 D32 0 C 16 B35 12 A34 11 D33 0 C 36 B36 16 A35 12 D34 0 C 37 B37 36 A36 16 D35 0 C 38 B38 37 A37 36 D36 0 C 36 B39 16 A38 12 D37 0 C 11 B40 7 A39 6 D38 0 C 41 B41 11 A40 7 D39 0 C 42 B42 41 A41 11 D40 0 C 43 B43 42 A42 41 D41 0 C 44 B44 43 A43 42 D42 0 C 6 B45 1 A44 2 D43 0 C 46 B46 6 A45 1 D44 0 C 47 B47 46 A46 6 D45 0 C 48 B48 47 A47 46 D46 0 C 49 B49 48 A48 47 D47 0 C 26 B50 9 A49 8 D48 0 C 51 B51 26 A50 9 D49 0 C 52 B52 51 A51 26 D50 0 C 53 B53 52 A52 51 D51 0 C 51 B54 26 A53 9 D52 0 C 21 B55 17 A54 16 D53 0 C 56 B56 21 A55 17 D54 0 C 57 B57 56 A56 21 D55 0 C 58 B58 57 A57 56 D56 0 C 59 B59 58 A58 57 D57 0 C 59 B60 58 A59 57 D58 0 C 61 B61 59 A60 58 D59 0 C 62 B62 61 A61 59 D60 0 C 63 B63 62 A62 61 D61 0 C 64 B64 63 A63 62 D62 0 C 61 B65 59 A64 58 D63 0 C 54 B66 53 A65 52 D64 0 C 67 B67 54 A66 53 D65 0 C 68 B68 67 A67 54 D66 0 C 69 B69 68 A68 67 D67 0 C 70 B70 69 A69 68 D68 0 C 67 B71 54 A70 53 D69 0 C 49 B72 48 A71 47 D70 0 C 73 B73 49 A72 48 D71 0 C 74 B74 73 A73 49 D72 0 C 75 B75 74 A74 73 D73 0 C 76 B76 75 A75 74 D74 0 C 73 B77 49 A76 48 D75 0 C 44 B78 43 A77 42 D76 0 C 79 B79 44 A78 43 D77 0 C 80 B80 79 A79 44 D78 0 C 81 B81 80 A80 79 D79 0 C 82 B82 81 A81 80 D80 0 C 79 B83 44 A82 43 D81 0 C 39 B84 38 A83 37 D82 0 C 85 B85 39 A84 38 D83 0 C 86 B86 85 A85 39 D84 0 C 87 B87 86 A86 85 D85 0 C 88 B88 87 A87 86 D86 0 C 85 B89 39 A88 38 D87 0 C 14 B90 13 A89 12 D88 0 C 91 B91 14 A90 13 D89 0 C 92 B92 91 A91 14 D90 0 C 93 B93 92 A92 91 D91 0 C 94 B94 93 A93 92 D92 0 C 91 B95 14 A94 13 D93 0 C 9 B96 8 A95 7 D94 0 C 97 B97 9 A96 8 D95 0 C 98 B98 97 A97 9 D96 0 C 99 B99 98 A98 97 D97 0 C 100 B100 99 A99 98 D98 0 C 97 B101 9 A100 8 D99 0 C 29 B102 28 A101 27 D100 0 C 103 B103 29 A102 28 D101 0 C 104 B104 103 A103 29 D102 0 C 105 B105 104 A104 103 D103 0 C 106 B106 105 A105 104 D104 0 C 103 B107 29 A106 28 D105 0 C 24 B108 23 A107 22 D106 0 C 109 B109 24 A108 23 D107 0 C 110 B110 109 A109 24 D108 0 C 111 B111 110 A110 109 D109 0 C 112 B112 111 A111 110 D110 0 C 109 B113 24 A112 23 D111 0 C 19 B114 18 A113 17 D112 0 C 115 B115 19 A114 18 D113 0 C 116 B116 115 A115 19 D114 0 C 117 B117 116 A116 115 D115 0 C 118 B118 117 A117 116 D116 0 C 115 B119 19 A118 18 D117 0 C 56 B120 21 A119 17 D118 0 C 121 B121 56 A120 21 D119 0 C 122 B122 121 A121 56 D120 0 C 123 B123 122 A122 121 D121 0 C 124 B124 123 A123 122 D122 0 C 121 B125 56 A124 21 D123 0 C 57 B126 56 A125 21 D124 0 C 127 B127 57 A126 56 D125 0 C 128 B128 127 A127 57 D126 0 C 129 B129 128 A128 127 D127 0 C 130 B130 129 A129 128 D128 0 C 127 B131 57 A130 56 D129 0 C 36 B132 16 A131 12 D130 0 C 133 B133 36 A132 16 D131 0 C 134 B134 133 A133 36 D132 0 C 135 B135 134 A134 133 D133 0 C 136 B136 135 A135 134 D134 0 C 133 B137 36 A136 16 D135 0 C 37 B138 36 A137 16 D136 0 C 139 B139 37 A138 36 D137 0 C 140 B140 139 A139 37 D138 0 C 141 B141 140 A140 139 D139 0 C 142 B142 141 A141 140 D140 0 C 139 B143 37 A142 36 D141 0 C 41 B144 11 A143 7 D142 0 C 145 B145 41 A144 11 D143 0 C 146 B146 145 A145 41 D144 0 C 147 B147 146 A146 145 D145 0 C 148 B148 147 A147 146 D146 0 C 145 B149 41 A148 11 D147 0 C 42 B150 41 A149 11 D148 0 C 151 B151 42 A150 41 D149 0 C 152 B152 151 A151 42 D150 0 C 153 B153 152 A152 151 D151 0 C 154 B154 153 A153 152 D152 0 C 151 B155 42 A154 41 D153 0 C 46 B156 6 A155 1 D154 0 C 157 B157 46 A156 6 D155 0 C 158 B158 157 A157 46 D156 0 C 159 B159 158 A158 157 D157 0 C 160 B160 159 A159 158 D158 0 C 157 B161 46 A160 6 D159 0 C 47 B162 46 A161 6 D160 0 C 163 B163 47 A162 46 D161 0 C 164 B164 163 A163 47 D162 0 C 165 B165 164 A164 163 D163 0 C 166 B166 165 A165 164 D164 0 C 163 B167 47 A166 46 D165 0 C 51 B168 26 A167 9 D166 0 C 169 B169 51 A168 26 D167 0 C 170 B170 169 A169 51 D168 0 C 171 B171 170 A170 169 D169 0 C 172 B172 171 A171 170 D170 0 C 169 B173 51 A172 26 D171 0 C 60 B174 59 A173 58 D172 0 C 175 B175 60 A174 59 D173 0 C 176 B176 175 A175 60 D174 0 C 177 B177 176 A176 175 D175 0 C 178 B178 177 A177 176 D176 0 C 175 B179 60 A178 59 D177 0 C 34 B180 33 A179 32 D178 0 C 53 B181 52 A180 51 D179 0 C 52 B182 51 A181 26 D180 0 C 59 B183 58 A182 57 D181 0 C 58 B184 57 A183 56 D182 0 C 35 B185 34 A184 33 D183 0 C 33 B186 32 A185 31 D184 0 C 48 B187 47 A186 46 D185 0 C 47 B188 46 A187 6 D186 0 C 54 B189 53 A188 52 D187 0 C 32 B190 31 A189 25 D188 0 C 43 B191 42 A190 41 D189 0 C 42 B192 41 A191 11 D190 0 C 49 B193 48 A192 47 D191 0 C 31 B194 25 A193 21 D192 0 C 38 B195 37 A194 36 D193 0 C 37 B196 36 A195 16 D194 0 C 44 B197 43 A196 42 D195 0 C 57 B198 56 A197 21 D196 0 C 39 B199 38 A198 37 D197 0 C 1 B200 2 A199 3 D198 0 C 8 B201 7 A200 6 D199 0 C 7 B202 6 A201 1 D200 0 C 14 B203 13 A202 12 D201 0 C 13 B204 12 A203 11 D202 0 C 2 B205 1 A204 201 D203 0 C 5 B206 1 A205 201 D204 0 C 28 B207 27 A206 26 D205 0 C 27 B208 26 A207 9 D206 0 C 9 B209 8 A208 7 D207 0 C 4 B210 3 A209 2 D208 0 C 23 B211 22 A210 21 D209 0 C 22 B212 21 A211 17 D210 0 C 29 B213 28 A212 27 D211 0 C 3 B214 2 A213 1 D212 0 C 18 B215 17 A214 16 D213 0 C 17 B216 16 A215 12 D214 0 C 24 B217 23 A216 22 D215 0 C 12 B218 11 A217 7 D216 0 C 19 B219 18 A218 17 D217 0 C 21 B220 17 A219 16 D218 0 C 56 B221 21 A220 17 D219 0 C 60 B222 59 A221 58 D220 0 C 30 B223 26 A222 9 D221 0 C 25 B224 21 A223 17 D222 0 C 40 B225 36 A224 16 D223 0 C 16 B226 12 A225 11 D224 0 C 36 B227 16 A226 12 D225 0 C 20 B228 16 A227 12 D226 0 C 45 B229 44 A228 43 D227 0 C 11 B230 7 A229 6 D228 0 C 41 B231 11 A230 7 D229 0 C 15 B232 11 A231 7 D230 0 C 50 B233 49 A232 48 D231 0 C 6 B234 1 A233 201 D232 0 C 46 B235 6 A234 1 D233 0 C 10 B236 6 A235 1 D234 0 C 55 B237 51 A236 26 D235 0 C 26 B238 9 A237 8 D236 0 C 51 B239 26 A238 9 D237 0 Variables: B1 1.38793 B2 1.38819 B3 1.38847 B4 1.38797 B5 7.2813 B6 1.38844 B7 1.38802 B8 1.38906 B9 1.38803 B10 7.28028 B11 1.38815 B12 1.38868 B13 1.38764 B14 1.38771 B15 7.28118 B16 1.3882 B17 1.38869 B18 1.38802 B19 1.38797 B20 7.28088 B21 1.38835 B22 1.38855 B23 1.38825 B24 1.3884 B25 6.15644 B26 1.38775 B27 1.38835 B28 1.38823 B29 1.38819 B30 10.89161 B31 1.38784 B32 1.38841 B33 1.38847 B34 1.38819 B35 5.34289 B36 1.38818 B37 1.38906 B38 1.38802 B39 1.38803 B40 5.34347 B41 1.38842 B42 1.38823 B43 1.38835 B44 1.38775 B45 5.34374 B46 1.38869 B47 1.38868 B48 1.38873 B49 1.38776 B50 5.34427 B51 1.3883 B52 1.38802 B53 1.38869 B54 1.38797 B55 5.34273 B56 1.38873 B57 1.38764 B58 1.38868 B59 1.38815 B60 2.36834 B61 1.4498 B62 1.4196 B63 1.44931 B64 1.42012 B65 1.41973 B66 2.36942 B67 1.44981 B68 1.41879 B69 1.44933 B70 1.42013 B71 1.41953 B72 2.36904 B73 1.44975 B74 1.42013 B75 1.44952 B76 1.41966 B77 1.41986 B78 2.36962 B79 1.45007 B80 1.41966 B81 1.44976 B82 1.41952 B83 1.41864 B84 2.3691 B85 1.44928 B86 1.41952 B87 1.44988 B88 1.41825 B89 1.41907 B90 2.3688 B91 1.45 B92 1.41825 B93 1.44988 B94 1.41952 B95 1.41953 B96 2.36951 B97 1.44993 B98 1.41952 B99 1.44976 B100 1.41966 B101 1.41864 B102 2.36822 B103 1.44892 B104 1.41966 B105 1.44952 B106 1.42004 B107 1.41986 B108 2.36819 B109 1.44882 B110 1.42013 B111 1.44933 B112 1.41879 B113 1.41953 B114 2.36922 B115 1.45007 B116 1.42012 B117 1.44931 B118 1.41905 B119 1.41875 B120 2.36883 B121 1.44892 B122 1.41951 B123 1.44925 B124 1.41916 B125 1.41983 B126 2.36973 B127 1.45012 B128 1.41884 B129 1.44948 B130 1.4201 B131 1.41922 B132 2.36867 B133 1.44895 B134 1.41874 B135 1.45003 B136 1.41953 B137 1.42 B138 2.36889 B139 1.4501 B140 1.41911 B141 1.44976 B142 1.41852 B143 1.41953 B144 2.36895 B145 1.44931 B146 1.419 B147 1.44903 B148 1.41973 B149 1.42009 B150 2.36889 B151 1.44925 B152 1.41951 B153 1.44952 B154 1.41981 B155 1.41916 B156 2.36923 B157 1.44901 B158 1.41884 B159 1.45012 B160 1.41922 B161 1.41958 B162 2.3688 B163 1.44998 B164 1.41959 B165 1.44895 B166 1.42 B167 1.41953 B168 2.36958 B169 1.44976 B170 1.41911 B171 1.4501 B172 1.41953 B173 1.41852 B174 2.36895 B175 1.44934 B176 1.41973 B177 1.44903 B178 1.41976 B179 1.42009 B180 1.38394 B181 1.38447 B182 1.38496 B183 1.38456 B184 1.38458 B185 1.3851 B186 1.38432 B187 1.38394 B188 1.38447 B189 1.38402 B190 1.38517 B191 1.38456 B192 1.38446 B193 1.38441 B194 1.38389 B195 1.38456 B196 1.38439 B197 1.38509 B198 1.38504 B199 1.38342 B200 1.38441 B201 1.38456 B202 1.38342 B203 1.38504 B204 1.38458 B205 1.3851 B206 1.38517 B207 1.38456 B208 1.38509 B209 1.38439 B210 1.38432 B211 1.38468 B212 1.38441 B213 1.38446 B214 1.3844 B215 1.38447 B216 1.38402 B217 1.38447 B218 1.38456 B219 1.38496 B220 1.3842 B221 1.38412 B222 1.38515 B223 1.3841 B224 1.38395 B225 1.38504 B226 1.38434 B227 1.38436 B228 1.38486 B229 1.38474 B230 1.38515 B231 1.3841 B232 1.3845 B233 1.38407 B234 1.38504 B235 1.38395 B236 1.38436 B237 1.38434 B238 1.38474 B239 1.38486 A1 108.02584 A2 107.98576 A3 107.99195 A4 111.52024 A5 32.51523 A6 107.9656 A7 108.00842 A8 84.54917 A9 111.55949 A10 84.55664 A11 107.95997 A12 108.0145 A13 32.51164 A14 111.55453 A15 84.52258 A16 108.00454 A17 107.9928 A18 32.51063 A19 111.52924 A20 84.56351 A21 107.99152 A22 108.00421 A23 32.51836 A24 128.03931 A25 48.7161 A26 107.98869 A27 108.01872 A28 140.51926 A29 89.98341 A30 120.02223 A31 108.03714 A32 107.97767 A33 107.98576 A34 118.44305 A35 120.01304 A36 107.99258 A37 108.00842 A38 120.0307 A39 118.4518 A40 120.00088 A41 107.97128 A42 108.01872 A43 107.98869 A44 118.44878 A45 120.02457 A46 108.01834 A47 107.96957 A48 108.04253 A49 71.25269 A50 119.97921 A51 107.98804 A52 107.9928 A53 119.98763 A54 118.45624 A55 120.0301 A56 108.03488 A57 108.0145 A58 107.95997 A59 90.73355 A60 89.2874 A61 120.00144 A62 120.0074 A63 120.02539 A64 145.89937 A65 90.7507 A66 89.26654 A67 120.02287 A68 120.00358 A69 119.98306 A70 145.92506 A71 90.6955 A72 89.24809 A73 119.97415 A74 119.99328 A75 120.00508 A76 145.90298 A77 90.73964 A78 89.24483 A79 119.99857 A80 119.99384 A81 120.00333 A82 145.91624 A83 90.74737 A84 89.23262 A85 119.98424 A86 119.97373 A87 120.02285 A88 145.90342 A89 90.75299 A90 89.27238 A91 120.0194 A92 120.02285 A93 119.97373 A94 145.8888 A95 90.73445 A96 89.23616 A97 119.97453 A98 120.00333 A99 119.99384 A100 145.9111 A101 90.75604 A102 89.28512 A103 120.0189 A104 120.00508 A105 119.96734 A106 145.91363 A107 90.77135 A108 89.25377 A109 120.006 A110 119.98306 A111 120.00358 A112 145.90241 A113 90.7395 A114 89.23525 A115 119.95645 A116 120.02539 A117 119.9745 A118 145.91903 A119 34.11433 A120 89.28612 A121 119.9991 A122 119.99827 A123 120.01731 A124 145.87523 A125 90.69451 A126 89.25373 A127 119.96929 A128 120.05006 A129 119.95698 A130 145.92478 A131 34.10742 A132 89.28499 A133 120.03085 A134 120.02109 A135 119.95501 A136 145.89352 A137 90.75243 A138 89.25359 A139 119.99089 A140 120.01155 A141 120.00144 A142 145.93384 A143 34.10275 A144 89.30094 A145 120.0119 A146 120.03041 A147 119.97521 A148 145.88287 A149 90.72603 A150 89.26883 A151 119.99827 A152 120.01199 A153 119.96926 A154 145.88012 A155 34.10988 A156 89.28761 A157 120.01566 A158 119.96929 A159 120.01654 A160 145.87294 A161 90.70361 A162 89.26486 A163 119.96539 A164 120.04864 A165 119.97743 A166 145.90634 A167 34.07033 A168 89.23887 A169 120.01155 A170 119.99089 A171 119.99425 A172 145.92921 A173 90.70439 A174 89.27927 A175 120.02347 A176 119.97521 A177 120.04101 A178 145.922 A179 124.23811 A180 124.24995 A181 124.22314 A182 124.20989 A183 124.24093 A184 124.19732 A185 124.23705 A186 124.18318 A187 124.16677 A188 124.20463 A189 124.22029 A190 124.19316 A191 124.18326 A192 124.1621 A193 49.10855 A194 124.21372 A195 124.21906 A196 124.18643 A197 124.14489 A198 124.23307 A199 124.19712 A200 124.21282 A201 124.23969 A202 124.24864 A203 124.19755 A204 124.22511 A205 124.25036 A206 124.22831 A207 124.26033 A208 124.1968 A209 124.18921 A210 124.23832 A211 124.23417 A212 124.26722 A213 124.25837 A214 124.18033 A215 124.23563 A216 124.26968 A217 124.26741 A218 124.21086 A219 130.68738 A220 14.79761 A221 124.17703 A222 124.1957 A223 124.19694 A224 124.17592 A225 130.622 A226 14.79105 A227 124.20967 A228 124.16737 A229 130.68448 A230 14.80746 A231 124.25799 A232 124.26399 A233 130.64406 A234 14.80458 A235 124.21814 A236 124.20471 A237 77.00523 A238 14.78794 D1 0.00713 D2 0.02535 D3 135.81462 D4 67.55728 D5 45.83728 D6 -0.01002 D7 -155.65063 D8 -90.00551 D9 155.68032 D10 22.79995 D11 0.01707 D12 -67.56507 D13 -113.01836 D14 155.67435 D15 22.81802 D16 -0.00808 D17 -67.64925 D18 -113.02531 D19 155.73456 D20 22.81382 D21 -0.01069 D22 -67.61055 D23 -133.08874 D24 -47.17029 D25 142.6373 D26 -0.0144 D27 18.09623 D28 75.82277 D29 -110.88892 D30 100.81127 D31 -0.01415 D32 0.03688 D33 34.39262 D34 -37.40441 D35 142.61155 D36 0.02634 D37 100.81208 D38 34.40556 D39 -37.38199 D40 142.6151 D41 0.00699 D42 0.0144 D43 -34.38556 D44 -100.80288 D45 142.60763 D46 0.02497 D47 -0.03267 D48 132.82417 D49 -138.207 D50 142.6216 D51 -0.00622 D52 -0.0049 D53 34.41653 D54 -37.33612 D55 142.57691 D56 0.01298 D57 -0.01707 D58 -161.04449 D59 -0.02058 D60 161.55978 D61 0.08852 D62 -0.0775 D63 150.83644 D64 -161.02871 D65 0.00595 D66 161.60102 D67 -0.04192 D68 0.06359 D69 150.80814 D70 -161.02147 D71 0. D72 161.60692 D73 0.0399 D74 -0.06128 D75 150.79212 D76 -161.03212 D77 0.02138 D78 161.6251 D79 -0.03707 D80 -0.00668 D81 150.76312 D82 -161.03498 D83 0.00742 D84 161.62596 D85 -0.0373 D86 0.03576 D87 150.85418 D88 -161.0337 D89 -0.00727 D90 161.59303 D91 0.0116 D92 -0.03576 D93 150.72923 D94 -160.99695 D95 -0.02484 D96 161.64347 D97 -0.0281 D98 0.00668 D99 150.86193 D100 -161.00695 D101 -0.03745 D102 161.61353 D103 -0.02136 D104 0.0967 D105 150.85844 D106 -160.9895 D107 0.04092 D108 161.60144 D109 0.03669 D110 -0.06359 D111 150.84226 D112 -161.0018 D113 -0.01971 D114 161.62027 D115 -0.04089 D116 0.06972 D117 150.77936 D118 135.07229 D119 -150.82468 D120 161.56638 D121 0.05552 D122 -0.05754 D123 0.01003 D124 -18.40871 D125 0. D126 161.61473 D127 0.00307 D128 0.03657 D129 150.88597 D130 135.07149 D131 -150.79527 D132 161.6273 D133 -0.03977 D134 0.02124 D135 -0.01863 D136 -18.36871 D137 -0.04118 D138 161.58235 D139 0.03684 D140 -0.02712 D141 150.79994 D142 135.07094 D143 -150.83472 D144 161.56124 D145 0.04673 D146 -0.03199 D147 0. D148 -18.3958 D149 0.00653 D150 161.64527 D151 -0.0888 D152 0.09679 D153 150.82584 D154 71.61906 D155 -150.83039 D156 161.59821 D157 -0.01034 D158 0.03631 D159 0.05169 D160 -18.41307 D161 0.01566 D162 161.59746 D163 0.01414 D164 -0.03778 D165 150.81446 D166 34.25615 D167 -150.82578 D168 161.635 D169 -0.03684 D170 0.04919 D171 -0.01828 D172 -161.01978 D173 0.01893 D174 161.61966 D175 -0.01262 D176 0.00405 D177 150.82745 D178 -159.38372 D179 -159.35449 D180 -16.73135 D181 -159.4242 D182 -159.42284 D183 -159.43777 D184 -159.31156 D185 -159.37975 D186 -16.77711 D187 -159.41439 D188 -58.56175 D189 -159.40191 D190 -16.75045 D191 -159.37279 D192 138.01556 D193 -159.36368 D194 -16.70104 D195 -159.38781 D196 -16.80609 D197 -159.39339 D198 159.34457 D199 -159.40027 D200 -113.56444 D201 -159.36944 D202 -159.42981 D203 -0.07898 D204 0.04218 D205 -159.41432 D206 -16.74601 D207 -159.34465 D208 -159.34658 D209 -159.29486 D210 -136.52862 D211 -159.35102 D212 -159.41066 D213 -159.37418 D214 -136.59654 D215 -159.36086 D216 -136.59246 D217 -159.34987 D218 24.20948 D219 -148.26356 D220 -159.42177 D221 113.52828 D222 113.49905 D223 16.73529 D224 24.19282 D225 -148.39403 D226 113.47353 D227 -159.37488 D228 24.21011 D229 -148.4002 D230 113.58081 D231 -159.38571 D232 -150.75377 D233 148.2491 D234 136.60082 D235 16.74869 D236 146.98464 D237 110.92277 NAtoms= 240 NQM= 240 NQMF= 0 NMMI= 0 NMMIF= 0 NMic= 0 NMicF= 0. Isotopes and Nuclear Properties: (Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM) in nuclear magnetons) Atom 1 2 3 4 5 6 7 8 9 10 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 11 12 13 14 15 16 17 18 19 20 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 21 22 23 24 25 26 27 28 29 30 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 31 32 33 34 35 36 37 38 39 40 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 41 42 43 44 45 46 47 48 49 50 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 51 52 53 54 55 56 57 58 59 60 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 61 62 63 64 65 66 67 68 69 70 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 71 72 73 74 75 76 77 78 79 80 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 81 82 83 84 85 86 87 88 89 90 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 91 92 93 94 95 96 97 98 99 100 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 101 102 103 104 105 106 107 108 109 110 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 111 112 113 114 115 116 117 118 119 120 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 121 122 123 124 125 126 127 128 129 130 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 131 132 133 134 135 136 137 138 139 140 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 141 142 143 144 145 146 147 148 149 150 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 151 152 153 154 155 156 157 158 159 160 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 161 162 163 164 165 166 167 168 169 170 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 171 172 173 174 175 176 177 178 179 180 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 181 182 183 184 185 186 187 188 189 190 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 191 192 193 194 195 196 197 198 199 200 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 201 202 203 204 205 206 207 208 209 210 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 211 212 213 214 215 216 217 218 219 220 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 221 222 223 224 225 226 227 228 229 230 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Atom 231 232 233 234 235 236 237 238 239 240 IAtWgt= 12 12 12 12 12 12 12 12 12 12 AtmWgt= 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 0 0 0 0 0 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 AtZNuc= 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 6.0000000 Leave Link 101 at Tue Feb 14 12:30:13 2017, MaxMem= 16106127360 cpu: 37.8 (Enter /root/g09/l202.exe) Stoichiometry C240 Framework group C1[X(C240)] Deg. of freedom 714 Full point group C1 NOp 1 Largest Abelian subgroup C1 NOp 1 Largest concise Abelian subgroup C1 NOp 1 Standard orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 3.374436 -6.118982 1.212478 2 6 0 3.478957 -6.177200 -0.170289 3 6 0 4.563672 -5.399639 -0.552209 4 6 0 5.129995 -4.860657 0.595231 5 6 0 4.394205 -5.304925 1.685611 6 6 0 -3.526935 -5.172244 3.331934 7 6 0 -2.587649 -6.006636 2.740933 8 6 0 -1.441520 -5.983133 3.523510 9 6 0 -1.672623 -5.133863 4.598138 10 6 0 -2.961531 -4.632320 4.478857 11 6 0 -2.284596 -5.013255 -4.464887 12 6 0 -0.995293 -5.513919 -4.346642 13 6 0 -0.933879 -6.267976 -3.182145 14 6 0 -2.184529 -6.233263 -2.581954 15 6 0 -3.019643 -5.456866 -3.374632 16 6 0 3.996647 -0.428820 -5.842623 17 6 0 4.831190 -1.204496 -5.049552 18 6 0 4.326851 -2.498256 -5.032889 19 6 0 3.180722 -2.521760 -5.815466 20 6 0 2.976878 -1.242878 -6.315756 21 6 0 6.635211 2.245294 1.103148 22 6 0 6.840148 0.966847 1.604224 23 6 0 7.071599 0.117356 0.530507 24 6 0 7.009442 0.870756 -0.633865 25 6 0 6.740303 2.186356 -0.280013 26 6 0 1.986078 -0.685970 6.773434 27 6 0 2.254298 -2.000627 6.419065 28 6 0 3.505518 -2.036061 5.818481 29 6 0 4.010428 -0.743023 5.801424 30 6 0 3.070793 0.091591 6.391514 31 6 0 -3.373906 6.118248 -1.212859 32 6 0 -4.394246 5.304911 -1.685599 33 6 0 -5.130036 4.860643 -0.595218 34 6 0 -4.563712 5.399625 0.552222 35 6 0 -3.478998 6.177186 0.170302 36 6 0 2.961490 4.632307 -4.478844 37 6 0 1.672582 5.133849 -4.598125 38 6 0 1.441479 5.983119 -3.523497 39 6 0 2.587608 6.006623 -2.740920 40 6 0 3.526894 5.172230 -3.331921 41 6 0 -3.070834 -0.091605 -6.391501 42 6 0 -4.010469 0.743009 -5.801411 43 6 0 -3.505559 2.036048 -5.818468 44 6 0 -2.254339 2.000614 -6.419052 45 6 0 -1.986119 0.685956 -6.773421 46 6 0 -6.740344 -2.186369 0.280026 47 6 0 -7.009483 -0.870769 0.633877 48 6 0 -7.070897 -0.116712 -0.530619 49 6 0 -6.840189 -0.966861 -1.604212 50 6 0 -6.635601 -2.245086 -1.104046 51 6 0 -2.976919 1.242864 6.315769 52 6 0 -3.180763 2.521746 5.815479 53 6 0 -4.326892 2.498242 5.032902 54 6 0 -4.831231 1.204483 5.049565 55 6 0 -3.996688 0.428807 5.842636 56 6 0 3.020345 5.457509 3.374520 57 6 0 2.184488 6.233249 2.581967 58 6 0 0.933838 6.267963 3.182158 59 6 0 0.995252 5.513905 4.346654 60 6 0 2.284555 5.013241 4.464900 61 6 0 -1.365236 5.325031 4.384997 62 6 0 -1.429912 6.112677 3.169529 63 6 0 -2.602133 6.087931 2.369185 64 6 0 -3.735076 5.276831 2.767993 65 6 0 -3.672601 4.505212 3.958555 66 6 0 -2.474809 4.530044 4.775486 67 6 0 -6.097891 1.639763 3.095016 68 6 0 -5.571469 2.990504 3.077174 69 6 0 -5.634340 3.761245 1.887647 70 6 0 -6.224123 3.198086 0.689501 71 6 0 -6.740247 1.875178 0.706878 72 6 0 -6.676490 1.088474 1.921830 73 6 0 -6.304521 0.879574 -2.988439 74 6 0 -6.545685 1.765952 -1.866855 75 6 0 -6.029529 3.088847 -1.884237 76 6 0 -5.262656 3.552541 -3.023541 77 6 0 -5.026462 2.683920 -4.121333 78 6 0 -5.552147 1.333856 -4.103592 79 6 0 -1.700068 4.094739 -5.458581 80 6 0 -3.006799 4.131148 -4.831024 81 6 0 -3.243049 4.999774 -3.733247 82 6 0 -2.177539 5.849746 -3.239237 83 6 0 -0.898104 5.813353 -3.853049 84 6 0 -0.657626 4.926314 -4.974492 85 6 0 1.351382 6.842016 -0.900679 86 6 0 0.154904 6.817120 -1.718127 87 6 0 -1.124531 6.853513 -1.104315 88 6 0 -1.233471 6.914754 0.340172 89 6 0 -0.062342 6.939065 1.139730 90 6 0 1.244738 6.902434 0.513083 91 6 0 -1.244779 -6.902447 -0.513071 92 6 0 0.062301 -6.939078 -1.139717 93 6 0 1.233430 -6.914768 -0.340160 94 6 0 1.124490 -6.853527 1.104328 95 6 0 -0.154945 -6.817134 1.718140 96 6 0 -1.351994 -6.841309 0.901085 97 6 0 0.657585 -4.926328 4.974504 98 6 0 0.898063 -5.813367 3.853062 99 6 0 2.177498 -5.849760 3.239250 100 6 0 3.243008 -4.999787 3.733260 101 6 0 3.006758 -4.131162 4.831036 102 6 0 1.700027 -4.094752 5.458593 103 6 0 5.552106 -1.333870 4.103605 104 6 0 5.026428 -2.683954 4.121321 105 6 0 5.262678 -3.552580 3.023545 106 6 0 6.029578 -3.088877 1.884261 107 6 0 6.546050 -1.766191 1.867795 108 6 0 6.304480 -0.879588 2.988451 109 6 0 6.676449 -1.088488 -1.921817 110 6 0 6.740206 -1.875192 -0.706866 111 6 0 6.224082 -3.198099 -0.689489 112 6 0 5.634299 -3.761259 -1.887634 113 6 0 5.571429 -2.990518 -3.077162 114 6 0 6.097850 -1.639776 -3.095003 115 6 0 2.474768 -4.530057 -4.775473 116 6 0 3.672560 -4.505226 -3.958543 117 6 0 3.735035 -5.276845 -2.767980 118 6 0 2.602092 -6.087945 -2.369173 119 6 0 1.430615 -6.112034 -3.169641 120 6 0 1.365939 -5.324388 -4.385109 121 6 0 4.630057 3.756218 3.729209 122 6 0 3.862810 3.292737 4.867582 123 6 0 4.071130 1.985006 5.378906 124 6 0 5.052091 1.113944 4.763035 125 6 0 5.803722 1.567569 3.648006 126 6 0 5.590752 2.902769 3.125380 127 6 0 3.643844 5.968829 0.733730 128 6 0 4.515833 5.158954 1.562328 129 6 0 5.475930 4.306210 0.958874 130 6 0 5.585794 4.244062 -0.485098 131 6 0 4.732170 5.038023 -1.296048 132 6 0 3.751231 5.909068 -0.680157 133 6 0 4.571164 2.894677 -4.492032 134 6 0 5.161517 3.457116 -3.294280 135 6 0 6.014997 2.664806 -2.483954 136 6 0 6.296492 1.291168 -2.853358 137 6 0 5.717893 0.739880 -4.026544 138 6 0 4.846220 1.549480 -4.854250 139 6 0 1.090645 3.373703 -6.072875 140 6 0 2.437302 2.850259 -5.949180 141 6 0 2.711787 1.505783 -6.311004 142 6 0 1.646277 0.655810 -6.805014 143 6 0 0.328955 1.167832 -6.926243 144 6 0 0.047460 2.541470 -6.556839 145 6 0 -1.742582 -2.050323 -6.496799 146 6 0 -0.609639 -1.239224 -6.895607 147 6 0 0.708032 -1.751467 -6.773466 148 6 0 0.921745 -3.086011 -6.250964 149 6 0 -0.187828 -3.880998 -5.860476 150 6 0 -1.533909 -3.358272 -5.984560 151 6 0 -5.052132 -1.113957 -4.763023 152 6 0 -4.071171 -1.985020 -5.378893 153 6 0 -3.862850 -3.292750 -4.867569 154 6 0 -4.629750 -3.756453 -3.728286 155 6 0 -5.590793 -2.902783 -3.125367 156 6 0 -5.803763 -1.567582 -3.647994 157 6 0 -5.585318 -4.244831 0.484679 158 6 0 -5.476030 -4.306293 -0.958897 159 6 0 -4.515906 -5.159021 -1.562333 160 6 0 -3.643885 -5.968843 -0.733717 161 6 0 -3.751272 -5.909082 0.680170 162 6 0 -4.732233 -5.038019 1.296041 163 6 0 -6.296533 -1.291181 2.853371 164 6 0 -6.015387 -2.664598 2.483056 165 6 0 -5.161558 -3.457129 3.294292 166 6 0 -4.571205 -2.894691 4.492044 167 6 0 -4.846261 -1.549493 4.854262 168 6 0 -5.717934 -0.739893 4.026556 169 6 0 -1.646318 -0.655824 6.805027 170 6 0 -2.711828 -1.505796 6.311017 171 6 0 -2.437343 -2.850273 5.949192 172 6 0 -1.090686 -3.373717 6.072887 173 6 0 -0.047501 -2.541484 6.556852 174 6 0 -0.328996 -1.167846 6.926256 175 6 0 1.533872 3.358261 5.984577 176 6 0 0.187787 3.880985 5.860489 177 6 0 -0.921786 3.085997 6.250977 178 6 0 -0.708073 1.751454 6.773479 179 6 0 0.610169 1.238489 6.895226 180 6 0 1.742541 2.050310 6.496812 181 6 0 -4.743357 4.885609 1.824544 182 6 0 -4.625574 3.437010 4.060143 183 6 0 -2.192799 3.487693 5.720644 184 6 0 -0.109934 4.980802 4.988027 185 6 0 -0.240418 6.580477 2.518435 186 6 0 -2.441809 6.535310 1.015578 187 6 0 -5.943791 3.740846 -0.608874 188 6 0 -6.912761 1.257397 -0.576410 189 6 0 -6.782278 -0.342278 1.893181 190 6 0 -5.695352 0.693950 4.096586 191 6 0 -4.384594 4.682940 -2.923235 192 6 0 -3.940943 3.052432 -4.985156 193 6 0 -5.010894 0.307994 -4.948983 194 6 0 -6.422772 -0.544290 -2.854723 195 6 0 -2.219764 6.410212 -1.918450 196 6 0 0.182957 6.342542 -3.071892 197 6 0 0.672947 4.540855 -5.350204 198 6 0 -1.286123 2.978017 -6.258683 199 6 0 2.414625 6.505563 1.243604 200 6 0 2.615211 6.392069 -1.412570 201 6 0 2.219723 -6.410226 1.918462 202 6 0 -0.182998 -6.342556 3.071904 203 6 0 -2.615252 -6.392083 1.412583 204 6 0 -2.414666 -6.505577 -1.243591 205 6 0 0.240377 -6.580491 -2.518423 206 6 0 2.441768 -6.535324 -1.015566 207 6 0 4.384554 -4.682954 2.923248 208 6 0 3.940903 -3.052446 4.985169 209 6 0 1.286082 -2.978031 6.258696 210 6 0 -0.672988 -4.540869 5.350217 211 6 0 5.943750 -3.740860 0.608887 212 6 0 6.912721 -1.257411 0.576423 213 6 0 6.422731 0.544276 2.854735 214 6 0 5.010853 -0.308008 4.948996 215 6 0 4.744060 -4.884965 -1.824656 216 6 0 4.625533 -3.437024 -4.060130 217 6 0 5.695311 -0.693964 -4.096573 218 6 0 6.782237 0.342265 -1.893168 219 6 0 0.109893 -4.980815 -4.988014 220 6 0 2.192758 -3.487707 -5.720632 221 6 0 5.989991 3.257261 1.792796 222 6 0 4.185608 4.860205 2.925996 223 6 0 2.625668 3.917455 5.240482 224 6 0 3.017429 1.461570 6.201667 225 6 0 6.212036 3.132163 -1.141232 226 6 0 4.608240 4.621613 -2.664206 227 6 0 3.923756 0.952115 -5.778571 228 6 0 3.408550 3.477508 -5.097749 229 6 0 1.760018 -0.774722 -6.782571 230 6 0 -0.715922 0.188118 -7.010620 231 6 0 -2.625709 -3.917468 -5.240469 232 6 0 -3.017470 -1.461583 -6.201655 233 6 0 -4.185649 -4.860219 -2.925983 234 6 0 -5.990032 -3.257275 -1.792784 235 6 0 -4.608281 -4.621627 2.664219 236 6 0 -6.212077 -3.132177 1.141244 237 6 0 -3.408590 -3.477521 5.097762 238 6 0 -3.923797 -0.952129 5.778584 239 6 0 0.715881 -0.188132 7.010633 240 6 0 -1.760059 0.774708 6.782583 --------------------------------------------------------------------- Rotational constants (GHZ): 0.0052937 0.0052937 0.0052937 Leave Link 202 at Tue Feb 14 12:30:13 2017, MaxMem= 16106127360 cpu: 1.4 (Enter /root/g09/l301.exe) Standard basis: 6-31G(d) (6D, 7F) Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F. There are 3600 symmetry adapted cartesian basis functions of A symmetry. There are 3600 symmetry adapted basis functions of A symmetry. 3600 basis functions, 6720 primitive gaussians, 3600 cartesian basis functions 720 alpha electrons 720 beta electrons nuclear repulsion energy 72448.4428787464 Hartrees. IExCor= 402 DFT=T Ex=B Corr=LYP ExCW=0 ScaHFX= 0.000000 ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 NAtoms= 240 NActive= 240 NUniq= 240 SFac= 1.00D+00 NAtFMM= 60 NAOKFM=T Big=T Integral buffers will be 131072 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. Leave Link 301 at Tue Feb 14 12:30:13 2017, MaxMem= 16106127360 cpu: 3.0 (Enter /root/g09/l302.exe) NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. One-electron integrals computed using PRISM. NBasis= 3600 RedAO= T EigKep= 3.04D-05 NBF= 3600 NBsUse= 3600 1.00D-06 EigRej= -1.00D+00 NBFU= 3600 Precomputing XC quadrature grid using IXCGrd= 4 IRadAn= 0 IRanWt= -1 IRanGd= 0 AccXCQ= 0.00D+00. Generated NRdTot= 0 NPtTot= 0 NUsed= 0 NTot= 32 NSgBfM= 1454 1454 1454 1454 1454 MxSgAt= 240 MxSgA2= 163. Leave Link 302 at Tue Feb 14 12:31:25 2017, MaxMem= 16106127360 cpu: 2799.1 (Enter /root/g09/l303.exe) DipDrv: MaxL=1. Leave Link 303 at Tue Feb 14 12:31:28 2017, MaxMem= 16106127360 cpu: 77.3 (Enter /root/g09/l401.exe) ExpMin= 1.69D-01 ExpMax= 3.05D+03 ExpMxC= 4.57D+02 IAcc=1 IRadAn= 1 AccDes= 0.00D+00 Harris functional with IExCor= 402 and IRadAn= 1 diagonalized for initial guess. HarFok: IExCor= 402 AccDes= 0.00D+00 IRadAn= 1 IDoV= 1 UseB2=F ITyADJ=14 ICtDFT= 3500011 ScaDFX= 1.000000 1.000000 1.000000 1.000000 FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 2001 NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 200000004 NGrid= 0 NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 Petite list used in FoFCou. Harris En= -9145.28256315004 JPrj=0 DoOrth=F DoCkMO=F. Leave Link 401 at Tue Feb 14 12:32:13 2017, MaxMem= 16106127360 cpu: 1767.1 (Enter /root/g09/l502.exe) Closed shell SCF: Using DIIS extrapolation, IDIIS= 1040. Integral symmetry usage will be decided dynamically. IVT= 39069190 IEndB= 39069190 NGot= 16106127360 MDV= 16080038411 LenX= 16080038411 LenY= 16067074811 Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. Fock matrices will be formed incrementally for 20 cycles. Integral accuracy reduced to 1.0D-05 until final iterations. Cycle 1 Pass 0 IDiag 1: FoFJK: IHMeth= 1 ICntrl= 500 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F IRaf= 300000000 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0. FoFCou: FMM=T IPFlag= 0 FMFlag= 100000 FMFlg1= 2001 NFxFlg= 0 DoJE=T BraDBF=F KetDBF=F FulRan=T wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 0 NGrid= 0 NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 Symmetry not used in FoFCou. FMM levels: 10 Number of levels for PrismC: 9 E= -9141.32264680337 DIIS: error= 2.68D-02 at cycle 1 NSaved= 1. NSaved= 1 IEnMin= 1 EnMin= -9141.32264680337 IErMin= 1 ErrMin= 2.68D-02 ErrMax= 2.68D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.97D+00 BMatP= 1.97D+00 IDIUse=3 WtCom= 7.32D-01 WtEn= 2.68D-01 Coeff-Com: 0.100D+01 Coeff-En: 0.100D+01 Coeff: 0.100D+01 Gap= 0.041 Goal= None Shift= 0.000 GapD= 0.041 DampG=0.250 DampE=0.500 DampFc=0.2500 IDamp=-1. Damping current iteration by 2.50D-01 RMSDP=1.48D+01 MaxDP=4.97D+02 OVMax= 8.74D-01 Problem detected with inexpensive integrals. Switching to full accuracy and repeating last cycle. Cycle 2 Pass 1 IDiag 1: E= -9141.32319083890 Delta-E= -0.000544035531 Rises=F Damp=F DIIS: error= 2.68D-02 at cycle 1 NSaved= 1. NSaved= 1 IEnMin= 1 EnMin= -9141.32319083890 IErMin= 1 ErrMin= 2.68D-02 ErrMax= 2.68D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.96D+00 BMatP= 1.96D+00 IDIUse=3 WtCom= 7.32D-01 WtEn= 2.68D-01 Coeff-Com: 0.100D+01 Coeff-En: 0.100D+01 Coeff: 0.100D+01 Gap= 0.041 Goal= None Shift= 0.000 GapD= 0.041 DampG=0.250 DampE=0.500 DampFc=0.2500 IDamp=-1. Damping current iteration by 2.50D-01 RMSDP=1.61D-03 MaxDP=1.16D-01 DE=-5.44D-04 OVMax= 3.62D-01 Cycle 3 Pass 1 IDiag 1: RMSU= 3.68D-04 CP: 9.74D-01 E= -9141.95662958729 Delta-E= -0.633438748395 Rises=F Damp=T DIIS: error= 1.59D-02 at cycle 2 NSaved= 2. NSaved= 2 IEnMin= 2 EnMin= -9141.95662958729 IErMin= 2 ErrMin= 1.59D-02 ErrMax= 1.59D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.87D-01 BMatP= 1.96D+00 IDIUse=3 WtCom= 8.41D-01 WtEn= 1.59D-01 Coeff-Com: -0.512D+00 0.151D+01 Coeff-En: 0.000D+00 0.100D+01 Coeff: -0.430D+00 0.143D+01 Gap= 0.031 Goal= None Shift= 0.000 GapD= 0.031 DampG=0.250 DampE=0.500 DampFc=0.2500 IDamp=-1. Damping current iteration by 2.50D-01 RMSDP=7.83D-04 MaxDP=3.69D-02 DE=-6.33D-01 OVMax= 3.42D-01 Cycle 4 Pass 1 IDiag 1: RMSU= 1.78D-04 CP: 9.64D-01 1.12D+00 E= -9142.26916024942 Delta-E= -0.312530662122 Rises=F Damp=T DIIS: error= 1.10D-02 at cycle 3 NSaved= 3. NSaved= 3 IEnMin= 3 EnMin= -9142.26916024942 IErMin= 3 ErrMin= 1.10D-02 ErrMax= 1.10D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.17D-01 BMatP= 5.87D-01 IDIUse=3 WtCom= 8.90D-01 WtEn= 1.10D-01 Coeff-Com: -0.603D+00-0.936D-01 0.170D+01 Coeff-En: 0.000D+00 0.000D+00 0.100D+01 Coeff: -0.537D+00-0.833D-01 0.162D+01 Gap= 0.042 Goal= None Shift= 0.000 RMSDP=3.70D-04 MaxDP=2.73D-02 DE=-3.13D-01 OVMax= 1.96D-01 Cycle 5 Pass 1 IDiag 1: RMSU= 2.29D-04 CP: 9.43D-01 1.74D+00 1.69D+00 E= -9143.35820281880 Delta-E= -1.089042569380 Rises=F Damp=F DIIS: error= 3.66D-03 at cycle 4 NSaved= 4. NSaved= 4 IEnMin= 4 EnMin= -9143.35820281880 IErMin= 4 ErrMin= 3.66D-03 ErrMax= 3.66D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 6.40D-02 BMatP= 3.17D-01 IDIUse=3 WtCom= 9.63D-01 WtEn= 3.66D-02 Coeff-Com: -0.311D+00-0.198D+00 0.106D+01 0.453D+00 Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.100D+01 Coeff: -0.300D+00-0.191D+00 0.102D+01 0.473D+00 Gap= 0.042 Goal= None Shift= 0.000 RMSDP=1.59D-04 MaxDP=1.16D-02 DE=-1.09D+00 OVMax= 2.99D-02 Cycle 6 Pass 1 IDiag 1: RMSU= 7.09D-05 CP: 9.37D-01 1.81D+00 2.00D+00 4.60D-01 E= -9143.41381301577 Delta-E= -0.055610196971 Rises=F Damp=F DIIS: error= 1.04D-03 at cycle 5 NSaved= 5. NSaved= 5 IEnMin= 5 EnMin= -9143.41381301577 IErMin= 5 ErrMin= 1.04D-03 ErrMax= 1.04D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.33D-03 BMatP= 6.40D-02 IDIUse=3 WtCom= 9.90D-01 WtEn= 1.04D-02 Coeff-Com: -0.355D-01 0.231D-01 0.429D-01 0.170D+00 0.799D+00 Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.496D-01 0.950D+00 Coeff: -0.351D-01 0.228D-01 0.424D-01 0.169D+00 0.801D+00 Gap= 0.042 Goal= None Shift= 0.000 RMSDP=2.91D-05 MaxDP=2.32D-03 DE=-5.56D-02 OVMax= 1.14D-02 Cycle 7 Pass 1 IDiag 1: RMSU= 1.07D-05 CP: 9.38D-01 1.82D+00 1.93D+00 5.50D-01 8.53D-01 E= -9143.41685578835 Delta-E= -0.003042772587 Rises=F Damp=F DIIS: error= 5.17D-04 at cycle 6 NSaved= 6. NSaved= 6 IEnMin= 6 EnMin= -9143.41685578835 IErMin= 6 ErrMin= 5.17D-04 ErrMax= 5.17D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.39D-04 BMatP= 3.33D-03 IDIUse=3 WtCom= 9.95D-01 WtEn= 5.17D-03 Coeff-Com: -0.248D-01 0.180D-01 0.264D-01 0.125D+00 0.609D+00 0.246D+00 Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.605D-01 0.940D+00 Coeff: -0.247D-01 0.179D-01 0.262D-01 0.125D+00 0.606D+00 0.250D+00 Gap= 0.042 Goal= None Shift= 0.000 RMSDP=1.11D-05 MaxDP=1.14D-03 DE=-3.04D-03 OVMax= 1.03D-02 Cycle 8 Pass 1 IDiag 1: RMSU= 4.81D-06 CP: 9.38D-01 1.82D+00 1.93D+00 5.48D-01 8.60D-01 CP: 6.66D-02 E= -9143.41725766775 Delta-E= -0.000401879399 Rises=F Damp=F DIIS: error= 2.32D-04 at cycle 7 NSaved= 7. NSaved= 7 IEnMin= 7 EnMin= -9143.41725766775 IErMin= 7 ErrMin= 2.32D-04 ErrMax= 2.32D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 6.70D-05 BMatP= 3.39D-04 IDIUse=3 WtCom= 9.98D-01 WtEn= 2.32D-03 Coeff-Com: -0.121D-01 0.891D-02 0.121D-01 0.616D-01 0.314D+00 0.243D+00 Coeff-Com: 0.373D+00 Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.253D+00 Coeff-En: 0.747D+00 Coeff: -0.120D-01 0.889D-02 0.120D-01 0.614D-01 0.313D+00 0.243D+00 Coeff: 0.374D+00 Gap= 0.042 Goal= None Shift= 0.000 RMSDP=4.11D-06 MaxDP=4.17D-04 DE=-4.02D-04 OVMax= 4.86D-03 Cycle 9 Pass 1 IDiag 1: RMSU= 1.65D-06 CP: 9.38D-01 1.82D+00 1.93D+00 5.47D-01 8.60D-01 CP: 3.22D-01 4.64D-01 E= -9143.41735461811 Delta-E= -0.000096950360 Rises=F Damp=F DIIS: error= 2.65D-05 at cycle 8 NSaved= 8. NSaved= 8 IEnMin= 8 EnMin= -9143.41735461811 IErMin= 8 ErrMin= 2.65D-05 ErrMax= 2.65D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 4.81D-06 BMatP= 6.70D-05 IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 Coeff-Com: -0.399D-02 0.245D-02 0.445D-02 0.186D-01 0.102D+00 0.124D+00 Coeff-Com: 0.266D+00 0.487D+00 Coeff: -0.399D-02 0.245D-02 0.445D-02 0.186D-01 0.102D+00 0.124D+00 Coeff: 0.266D+00 0.487D+00 Gap= 0.042 Goal= None Shift= 0.000 RMSDP=9.87D-07 MaxDP=1.06D-04 DE=-9.70D-05 OVMax= 5.07D-04 Cycle 10 Pass 1 IDiag 1: RMSU= 5.51D-07 CP: 9.38D-01 1.82D+00 1.93D+00 5.47D-01 8.61D-01 CP: 3.02D-01 5.00D-01 5.66D-01 E= -9143.41735892667 Delta-E= -0.000004308560 Rises=F Damp=F DIIS: error= 1.05D-05 at cycle 9 NSaved= 9. NSaved= 9 IEnMin= 9 EnMin= -9143.41735892667 IErMin= 9 ErrMin= 1.05D-05 ErrMax= 1.05D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.48D-07 BMatP= 4.81D-06 IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 Coeff-Com: -0.202D-02 0.119D-02 0.225D-02 0.878D-02 0.499D-01 0.711D-01 Coeff-Com: 0.163D+00 0.341D+00 0.364D+00 Coeff: -0.202D-02 0.119D-02 0.225D-02 0.878D-02 0.499D-01 0.711D-01 Coeff: 0.163D+00 0.341D+00 0.364D+00 Gap= 0.042 Goal= None Shift= 0.000 RMSDP=4.78D-07 MaxDP=4.50D-05 DE=-4.31D-06 OVMax= 3.14D-04 Cycle 11 Pass 1 IDiag 1: RMSU= 3.14D-07 CP: 9.38D-01 1.82D+00 1.93D+00 5.47D-01 8.61D-01 CP: 3.01D-01 5.05D-01 5.98D-01 3.57D-01 E= -9143.41735927865 Delta-E= -0.000000351982 Rises=F Damp=F DIIS: error= 8.95D-06 at cycle 10 NSaved= 10. NSaved=10 IEnMin=10 EnMin= -9143.41735927865 IErMin=10 ErrMin= 8.95D-06 ErrMax= 8.95D-06 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.65D-07 BMatP= 5.48D-07 IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 Coeff-Com: -0.588D-03 0.364D-03 0.564D-03 0.196D-02 0.130D-01 0.268D-01 Coeff-Com: 0.684D-01 0.169D+00 0.355D+00 0.365D+00 Coeff: -0.588D-03 0.364D-03 0.564D-03 0.196D-02 0.130D-01 0.268D-01 Coeff: 0.684D-01 0.169D+00 0.355D+00 0.365D+00 Gap= 0.042 Goal= None Shift= 0.000 RMSDP=2.39D-07 MaxDP=2.70D-05 DE=-3.52D-07 OVMax= 1.83D-04 Cycle 12 Pass 1 IDiag 1: RMSU= 9.71D-08 CP: 9.38D-01 1.82D+00 1.93D+00 5.47D-01 8.61D-01 CP: 3.03D-01 5.11D-01 5.86D-01 5.18D-01 3.79D-01 E= -9143.41735959605 Delta-E= -0.000000317392 Rises=F Damp=F DIIS: error= 3.98D-06 at cycle 11 NSaved= 11. NSaved=11 IEnMin=11 EnMin= -9143.41735959605 IErMin=11 ErrMin= 3.98D-06 ErrMax= 3.98D-06 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.61D-08 BMatP= 2.65D-07 IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 Coeff-Com: -0.371D-03 0.258D-03 0.303D-03 0.108D-02 0.770D-02 0.177D-01 Coeff-Com: 0.463D-01 0.118D+00 0.265D+00 0.292D+00 0.252D+00 Coeff: -0.371D-03 0.258D-03 0.303D-03 0.108D-02 0.770D-02 0.177D-01 Coeff: 0.463D-01 0.118D+00 0.265D+00 0.292D+00 0.252D+00 Gap= 0.042 Goal= None Shift= 0.000 RMSDP=7.77D-08 MaxDP=1.02D-05 DE=-3.17D-07 OVMax= 6.65D-05 Cycle 13 Pass 1 IDiag 1: RMSU= 4.51D-08 CP: 9.38D-01 1.82D+00 1.93D+00 5.47D-01 8.61D-01 CP: 3.03D-01 5.11D-01 5.87D-01 5.11D-01 4.32D-01 CP: 3.80D-01 E= -9143.41735962743 Delta-E= -0.000000031388 Rises=F Damp=F DIIS: error= 1.06D-06 at cycle 12 NSaved= 12. NSaved=12 IEnMin=12 EnMin= -9143.41735962743 IErMin=12 ErrMin= 1.06D-06 ErrMax= 1.06D-06 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.38D-09 BMatP= 2.61D-08 IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 Coeff-Com: -0.736D-04 0.110D-03-0.304D-04 0.447D-04 0.775D-03 0.355D-02 Coeff-Com: 0.102D-01 0.290D-01 0.757D-01 0.937D-01 0.218D+00 0.569D+00 Coeff: -0.736D-04 0.110D-03-0.304D-04 0.447D-04 0.775D-03 0.355D-02 Coeff: 0.102D-01 0.290D-01 0.757D-01 0.937D-01 0.218D+00 0.569D+00 Gap= 0.042 Goal= None Shift= 0.000 RMSDP=2.88D-08 MaxDP=2.62D-06 DE=-3.14D-08 OVMax= 1.72D-05 Cycle 14 Pass 1 IDiag 1: RMSU= 1.38D-08 CP: 9.38D-01 1.82D+00 1.93D+00 5.47D-01 8.61D-01 CP: 3.03D-01 5.11D-01 5.90D-01 5.15D-01 4.33D-01 CP: 4.82D-01 6.55D-01 E= -9143.41735962947 Delta-E= -0.000000002037 Rises=F Damp=F DIIS: error= 2.95D-07 at cycle 13 NSaved= 13. NSaved=13 IEnMin=13 EnMin= -9143.41735962947 IErMin=13 ErrMin= 2.95D-07 ErrMax= 2.95D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.75D-10 BMatP= 3.38D-09 IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 Coeff-Com: -0.339D-04 0.727D-04-0.477D-04-0.407D-04 0.770D-04 0.159D-02 Coeff-Com: 0.493D-02 0.149D-01 0.417D-01 0.541D-01 0.155D+00 0.451D+00 Coeff-Com: 0.277D+00 Coeff: -0.339D-04 0.727D-04-0.477D-04-0.407D-04 0.770D-04 0.159D-02 Coeff: 0.493D-02 0.149D-01 0.417D-01 0.541D-01 0.155D+00 0.451D+00 Coeff: 0.277D+00 Gap= 0.042 Goal= None Shift= 0.000 RMSDP=1.13D-08 MaxDP=9.63D-07 DE=-2.04D-09 OVMax= 9.29D-06 Cycle 15 Pass 1 IDiag 1: RMSU= 4.72D-09 CP: 9.38D-01 1.82D+00 1.93D+00 5.47D-01 8.61D-01 CP: 3.03D-01 5.11D-01 5.90D-01 5.17D-01 4.31D-01 CP: 4.83D-01 6.86D-01 2.80D-01 E= -9143.41735963043 Delta-E= -0.000000000960 Rises=F Damp=F DIIS: error= 1.23D-07 at cycle 14 NSaved= 14. NSaved=14 IEnMin=14 EnMin= -9143.41735963043 IErMin=14 ErrMin= 1.23D-07 ErrMax= 1.23D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.28D-11 BMatP= 5.75D-10 IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 Coeff-Com: -0.178D-04 0.432D-04-0.324D-04-0.342D-04-0.216D-04 0.800D-03 Coeff-Com: 0.255D-02 0.793D-02 0.226D-01 0.297D-01 0.900D-01 0.269D+00 Coeff-Com: 0.203D+00 0.375D+00 Coeff: -0.178D-04 0.432D-04-0.324D-04-0.342D-04-0.216D-04 0.800D-03 Coeff: 0.255D-02 0.793D-02 0.226D-01 0.297D-01 0.900D-01 0.269D+00 Coeff: 0.203D+00 0.375D+00 Gap= 0.042 Goal= None Shift= 0.000 RMSDP=4.33D-09 MaxDP=3.81D-07 DE=-9.60D-10 OVMax= 4.13D-06 SCF Done: E(RB-LYP) = -9143.41735963 A.U. after 15 cycles NFock= 15 Conv=0.43D-08 -V/T= 2.0079 KE= 9.071345381904D+03 PE=-1.660875477189D+05 EE= 7.542434209867D+04 Leave Link 502 at Tue Feb 14 12:54:46 2017, MaxMem= 16106127360 cpu: 53631.4 (Enter /root/g09/l601.exe) Copying SCF densities to generalized density rwf, IOpCl= 0 IROHF=0. Hyperfine terms turned off by default for NAtoms > 100. ********************************************************************** Population analysis using the SCF density. ********************************************************************** Orbital symmetries: Occupied (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) 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(A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) The electronic state is 1-A. Alpha occ. eigenvalues -- -9.95983 -9.95983 -9.95983 -9.95983 -9.95982 Alpha occ. eigenvalues -- -9.95982 -9.95982 -9.95982 -9.95982 -9.95981 Alpha occ. eigenvalues -- -9.95981 -9.95981 -9.95981 -9.95980 -9.95980 Alpha occ. eigenvalues -- -9.95980 -9.95980 -9.95979 -9.95979 -9.95979 Alpha occ. eigenvalues -- -9.95971 -9.95971 -9.95970 -9.95970 -9.95970 Alpha occ. eigenvalues -- -9.95970 -9.95970 -9.95970 -9.95970 -9.95969 Alpha occ. eigenvalues -- -9.95969 -9.95969 -9.95969 -9.95969 -9.95969 Alpha occ. eigenvalues -- -9.95968 -9.95968 -9.95968 -9.95968 -9.95968 Alpha occ. eigenvalues -- -9.95968 -9.95967 -9.95967 -9.95967 -9.95967 Alpha occ. eigenvalues -- -9.95967 -9.95967 -9.95966 -9.95966 -9.95966 Alpha occ. eigenvalues -- -9.95966 -9.95966 -9.95966 -9.95966 -9.95966 Alpha occ. eigenvalues -- -9.95965 -9.95965 -9.95965 -9.95965 -9.95965 Alpha occ. eigenvalues -- -9.95944 -9.95944 -9.95943 -9.95943 -9.95943 Alpha occ. eigenvalues -- -9.95943 -9.95943 -9.95943 -9.95942 -9.95942 Alpha occ. eigenvalues -- -9.95942 -9.95942 -9.95942 -9.95942 -9.95941 Alpha occ. eigenvalues -- -9.95941 -9.95941 -9.95941 -9.95941 -9.95941 Alpha occ. eigenvalues -- -9.95941 -9.95941 -9.95940 -9.95940 -9.95940 Alpha occ. eigenvalues -- -9.95940 -9.95940 -9.95940 -9.95940 -9.95939 Alpha occ. eigenvalues -- -9.95939 -9.95939 -9.95939 -9.95939 -9.95938 Alpha occ. eigenvalues -- -9.95938 -9.95938 -9.95938 -9.95938 -9.95937 Alpha occ. eigenvalues -- -9.95931 -9.95931 -9.95931 -9.95930 -9.95929 Alpha occ. eigenvalues -- -9.95928 -9.95928 -9.95928 -9.95928 -9.95928 Alpha occ. eigenvalues -- -9.95928 -9.95928 -9.95928 -9.95927 -9.95927 Alpha occ. eigenvalues -- -9.95927 -9.95927 -9.95927 -9.95927 -9.95926 Alpha occ. eigenvalues -- -9.95164 -9.95164 -9.95164 -9.95163 -9.95163 Alpha occ. eigenvalues -- -9.95163 -9.95163 -9.95163 -9.95163 -9.95162 Alpha occ. eigenvalues -- -9.95162 -9.95162 -9.95162 -9.95162 -9.95162 Alpha occ. eigenvalues -- -9.95162 -9.95162 -9.95162 -9.95162 -9.95161 Alpha occ. eigenvalues -- -9.95161 -9.95161 -9.95161 -9.95160 -9.95160 Alpha occ. eigenvalues -- -9.95160 -9.95160 -9.95160 -9.95160 -9.95160 Alpha occ. eigenvalues -- -9.95160 -9.95159 -9.95159 -9.95159 -9.95159 Alpha occ. eigenvalues -- -9.95159 -9.95159 -9.95159 -9.95158 -9.95158 Alpha occ. eigenvalues -- -9.95158 -9.95158 -9.95158 -9.95158 -9.95158 Alpha occ. eigenvalues -- -9.95158 -9.95158 -9.95157 -9.95157 -9.95157 Alpha occ. eigenvalues -- -9.95157 -9.95157 -9.95157 -9.95157 -9.95157 Alpha occ. eigenvalues -- -9.95156 -9.95155 -9.95155 -9.95153 -9.95153 Alpha occ. eigenvalues -- -9.92717 -9.92714 -9.92713 -9.92712 -9.92712 Alpha occ. eigenvalues -- -9.92711 -9.92710 -9.92710 -9.92710 -9.92710 Alpha occ. eigenvalues -- -9.92709 -9.92709 -9.92690 -9.92688 -9.92687 Alpha occ. eigenvalues -- -9.92687 -9.92687 -9.92686 -9.92685 -9.92684 Alpha occ. eigenvalues -- -9.92684 -9.92684 -9.92683 -9.92683 -9.92683 Alpha occ. eigenvalues -- -9.92683 -9.92682 -9.92682 -9.92682 -9.92682 Alpha occ. 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0.73718 0.74074 Alpha virt. eigenvalues -- 0.74075 0.74078 0.74080 0.74389 0.74402 Alpha virt. eigenvalues -- 0.74405 0.74406 0.74408 0.74905 0.74905 Alpha virt. eigenvalues -- 0.74906 0.75029 0.75764 0.75765 0.75766 Alpha virt. eigenvalues -- 0.76538 0.76540 0.76541 0.76542 0.76543 Alpha virt. eigenvalues -- 0.77595 0.77598 0.77599 0.78481 0.78484 Alpha virt. eigenvalues -- 0.78485 0.78869 0.78872 0.78875 0.78876 Alpha virt. eigenvalues -- 0.78879 0.81986 0.81986 0.81990 0.81991 Alpha virt. eigenvalues -- 0.81992 0.83231 0.83233 0.83234 0.83235 Alpha virt. eigenvalues -- 0.87618 0.87624 0.87626 0.87629 0.87779 Alpha virt. eigenvalues -- 0.87782 0.87791 0.88251 0.88257 0.88258 Alpha virt. eigenvalues -- 0.88263 0.88272 0.88276 0.88277 0.88278 Alpha virt. eigenvalues -- 0.88280 0.88393 0.88396 0.88401 0.89160 Alpha virt. eigenvalues -- 0.89162 0.89170 0.89172 0.89470 0.89475 Alpha virt. eigenvalues -- 0.89478 0.89610 0.89613 0.89615 0.89705 Alpha virt. eigenvalues -- 0.89708 0.89711 0.89712 0.89714 0.89715 Alpha virt. eigenvalues -- 0.89717 0.89720 0.89956 0.89964 0.89967 Alpha virt. eigenvalues -- 0.89971 0.89975 0.90295 0.90301 0.90302 Alpha virt. eigenvalues -- 0.90305 0.91025 0.91029 0.91031 0.91032 Alpha virt. eigenvalues -- 0.91035 0.91192 0.91196 0.91201 0.91462 Alpha virt. eigenvalues -- 0.91464 0.91465 0.91467 0.91470 0.91799 Alpha virt. eigenvalues -- 0.91800 0.91803 0.92261 0.92263 0.92266 Alpha virt. eigenvalues -- 0.92267 0.92268 0.92831 0.92834 0.92836 Alpha virt. eigenvalues -- 0.92838 0.92932 0.92936 0.92938 0.93258 Alpha virt. eigenvalues -- 0.93264 0.93269 0.93461 0.93553 0.93559 Alpha virt. eigenvalues -- 0.93560 0.93561 0.93744 0.93748 0.93753 Alpha virt. eigenvalues -- 0.93759 0.93763 0.93953 0.93957 0.93959 Alpha virt. eigenvalues -- 0.93960 0.94101 0.94104 0.94106 0.94924 Alpha virt. eigenvalues -- 0.94926 0.94930 0.94933 0.95732 0.95735 Alpha virt. eigenvalues -- 0.95737 0.95810 0.95811 0.95814 0.95870 Alpha virt. eigenvalues -- 0.95877 0.95879 0.95882 0.95883 0.96055 Alpha virt. eigenvalues -- 0.96056 0.96059 0.96529 0.96533 0.96535 Alpha virt. eigenvalues -- 0.96540 0.96601 0.96603 0.96604 0.96606 Alpha virt. eigenvalues -- 0.96607 0.96668 0.96671 0.96677 0.96678 Alpha virt. eigenvalues -- 0.97022 0.97027 0.97032 0.97042 0.97045 Alpha virt. eigenvalues -- 0.97047 0.97048 0.97052 0.97245 0.97248 Alpha virt. eigenvalues -- 0.97253 0.97562 0.97569 0.97570 0.98053 Alpha virt. eigenvalues -- 0.98058 0.98060 0.98062 0.98177 0.98184 Alpha virt. eigenvalues -- 0.98191 0.98507 0.98510 0.98518 0.98519 Alpha virt. eigenvalues -- 0.98879 0.98883 0.98887 0.98889 0.98894 Alpha virt. eigenvalues -- 0.99769 0.99777 0.99781 0.99944 0.99947 Alpha virt. eigenvalues -- 0.99947 0.99949 0.99951 1.00511 1.00513 Alpha virt. eigenvalues -- 1.00516 1.00519 1.00522 1.00979 1.00983 Alpha virt. eigenvalues -- 1.00985 1.00987 1.01485 1.01487 1.01491 Alpha virt. eigenvalues -- 1.01494 1.01494 1.01497 1.01499 1.01501 Alpha virt. eigenvalues -- 1.01610 1.01612 1.01616 1.01617 1.01619 Alpha virt. eigenvalues -- 1.01872 1.01873 1.01874 1.01876 1.02096 Alpha virt. eigenvalues -- 1.03278 1.03280 1.03281 1.03284 1.03286 Alpha virt. eigenvalues -- 1.03489 1.03495 1.03496 1.03499 1.03674 Alpha virt. eigenvalues -- 1.03678 1.03682 1.03851 1.03853 1.03857 Alpha virt. eigenvalues -- 1.04506 1.04509 1.04511 1.04514 1.04517 Alpha virt. eigenvalues -- 1.05147 1.05151 1.05155 1.05175 1.05177 Alpha virt. eigenvalues -- 1.05181 1.05183 1.05186 1.05825 1.05829 Alpha virt. eigenvalues -- 1.05832 1.06556 1.06561 1.06562 1.06569 Alpha virt. eigenvalues -- 1.06573 1.06584 1.06585 1.06589 1.06597 Alpha virt. eigenvalues -- 1.07340 1.07341 1.07343 1.07610 1.07611 Alpha virt. eigenvalues -- 1.07620 1.07624 1.08495 1.11718 1.11720 Alpha virt. eigenvalues -- 1.11722 1.11724 1.11731 1.11737 1.11740 Alpha virt. eigenvalues -- 1.11741 1.11745 1.11747 1.12018 1.12022 Alpha virt. eigenvalues -- 1.12030 1.13522 1.13529 1.13539 1.14599 Alpha virt. eigenvalues -- 1.14599 1.14603 1.14604 1.14935 1.14940 Alpha virt. eigenvalues -- 1.14944 1.15524 1.15533 1.15536 1.15543 Alpha virt. eigenvalues -- 1.15554 1.16086 1.16089 1.16091 1.16111 Alpha virt. eigenvalues -- 1.16112 1.16117 1.16120 1.17580 1.17735 Alpha virt. eigenvalues -- 1.17737 1.17741 1.17959 1.17963 1.17967 Alpha virt. eigenvalues -- 1.18050 1.18050 1.18055 1.18058 1.18060 Alpha virt. eigenvalues -- 1.19896 1.19896 1.19898 1.19900 1.19902 Alpha virt. eigenvalues -- 1.19905 1.19907 1.19909 1.20233 1.20236 Alpha virt. eigenvalues -- 1.20238 1.20241 1.20346 1.20357 1.20364 Alpha virt. eigenvalues -- 1.20805 1.20808 1.20810 1.20815 1.20815 Alpha virt. eigenvalues -- 1.20949 1.20951 1.20955 1.20959 1.21768 Alpha virt. eigenvalues -- 1.21769 1.21776 1.21779 1.21781 1.22600 Alpha virt. eigenvalues -- 1.22710 1.22723 1.22725 1.22730 1.22731 Alpha virt. eigenvalues -- 1.22807 1.22810 1.22817 1.22886 1.22888 Alpha virt. eigenvalues -- 1.22893 1.22992 1.22994 1.22997 1.22999 Alpha virt. eigenvalues -- 1.23453 1.23455 1.23459 1.24176 1.24177 Alpha virt. eigenvalues -- 1.24180 1.24909 1.24913 1.24917 1.24918 Alpha virt. eigenvalues -- 1.24920 1.25675 1.25681 1.25685 1.25686 Alpha virt. eigenvalues -- 1.25687 1.25688 1.25689 1.25692 1.25694 Alpha virt. eigenvalues -- 1.26010 1.26010 1.26011 1.26014 1.26020 Alpha virt. eigenvalues -- 1.26026 1.26026 1.26030 1.26037 1.26592 Alpha virt. eigenvalues -- 1.26594 1.26599 1.26914 1.26920 1.26921 Alpha virt. eigenvalues -- 1.27011 1.27014 1.27019 1.27022 1.27457 Alpha virt. eigenvalues -- 1.27458 1.27460 1.27569 1.27571 1.27581 Alpha virt. eigenvalues -- 1.27716 1.27717 1.27721 1.27726 1.27728 Alpha virt. eigenvalues -- 1.28061 1.28074 1.28082 1.28085 1.28090 Alpha virt. eigenvalues -- 1.28919 1.28923 1.28924 1.28931 1.28942 Alpha virt. eigenvalues -- 1.29090 1.29099 1.29101 1.29107 1.29108 Alpha virt. eigenvalues -- 1.29111 1.29116 1.29505 1.29509 1.29517 Alpha virt. eigenvalues -- 1.30754 1.30756 1.30760 1.30764 1.30859 Alpha virt. eigenvalues -- 1.30865 1.30869 1.33013 1.33021 1.33024 Alpha virt. eigenvalues -- 1.33031 1.33217 1.33221 1.33224 1.33225 Alpha virt. eigenvalues -- 1.33229 1.33773 1.33781 1.33785 1.34044 Alpha virt. eigenvalues -- 1.34047 1.34052 1.34056 1.34059 1.34564 Alpha virt. eigenvalues -- 1.34573 1.34579 1.34580 1.35319 1.35323 Alpha virt. eigenvalues -- 1.35328 1.35334 1.35426 1.35429 1.35438 Alpha virt. eigenvalues -- 1.36075 1.36081 1.36088 1.36090 1.36096 Alpha virt. eigenvalues -- 1.36637 1.36645 1.36647 1.36653 1.36861 Alpha virt. eigenvalues -- 1.36866 1.36871 1.37415 1.37417 1.37422 Alpha virt. eigenvalues -- 1.37878 1.37881 1.37883 1.37886 1.37888 Alpha virt. eigenvalues -- 1.37889 1.37892 1.37895 1.37896 1.37904 Alpha virt. eigenvalues -- 1.38012 1.38022 1.38029 1.38035 1.38211 Alpha virt. eigenvalues -- 1.38287 1.38298 1.38301 1.38702 1.38862 Alpha virt. eigenvalues -- 1.38862 1.38866 1.38868 1.38870 1.39108 Alpha virt. eigenvalues -- 1.39111 1.39122 1.39897 1.39903 1.39910 Alpha virt. eigenvalues -- 1.40728 1.40738 1.40740 1.40746 1.41015 Alpha virt. eigenvalues -- 1.41017 1.41021 1.41027 1.41028 1.41371 Alpha virt. eigenvalues -- 1.41382 1.41387 1.41733 1.41735 1.41739 Alpha virt. eigenvalues -- 1.41742 1.41750 1.42787 1.42790 1.42791 Alpha virt. eigenvalues -- 1.42885 1.42888 1.42892 1.42894 1.43054 Alpha virt. eigenvalues -- 1.43069 1.43083 1.43178 1.43184 1.43188 Alpha virt. eigenvalues -- 1.43454 1.43460 1.43461 1.43467 1.43472 Alpha virt. eigenvalues -- 1.43477 1.43478 1.43483 1.43486 1.44297 Alpha virt. eigenvalues -- 1.44312 1.44315 1.44320 1.44326 1.44426 Alpha virt. eigenvalues -- 1.44431 1.44442 1.44448 1.44940 1.44945 Alpha virt. eigenvalues -- 1.44948 1.45452 1.45457 1.45461 1.45464 Alpha virt. eigenvalues -- 1.45470 1.45918 1.45923 1.45925 1.45934 Alpha virt. eigenvalues -- 1.46670 1.46674 1.46679 1.46681 1.46687 Alpha virt. eigenvalues -- 1.46764 1.46770 1.46775 1.46777 1.46782 Alpha virt. eigenvalues -- 1.47301 1.47704 1.47713 1.47715 1.47717 Alpha virt. eigenvalues -- 1.48431 1.48438 1.48444 1.48738 1.48741 Alpha virt. eigenvalues -- 1.48742 1.48743 1.48745 1.49044 1.49051 Alpha virt. eigenvalues -- 1.49052 1.49826 1.49832 1.49833 1.50039 Alpha virt. eigenvalues -- 1.50045 1.50054 1.50060 1.50064 1.50133 Alpha virt. eigenvalues -- 1.50135 1.50136 1.50142 1.51329 1.51332 Alpha virt. eigenvalues -- 1.51336 1.51440 1.51441 1.51444 1.51717 Alpha virt. eigenvalues -- 1.51720 1.51727 1.52557 1.52560 1.52565 Alpha virt. eigenvalues -- 1.52566 1.52570 1.53204 1.53207 1.53208 Alpha virt. eigenvalues -- 1.53656 1.53657 1.53661 1.53669 1.53722 Alpha virt. eigenvalues -- 1.53727 1.53733 1.53737 1.53741 1.54140 Alpha virt. eigenvalues -- 1.54142 1.54147 1.54148 1.54348 1.54351 Alpha virt. eigenvalues -- 1.54364 1.54675 1.54676 1.54679 1.54680 Alpha virt. eigenvalues -- 1.54687 1.55378 1.55384 1.55394 1.56143 Alpha virt. eigenvalues -- 1.56146 1.56150 1.56156 1.56159 1.56477 Alpha virt. eigenvalues -- 1.56479 1.56484 1.56777 1.56781 1.56783 Alpha virt. eigenvalues -- 1.56785 1.56788 1.57841 1.57847 1.57849 Alpha virt. eigenvalues -- 1.58184 1.58188 1.58190 1.58192 1.58293 Alpha virt. eigenvalues -- 1.58297 1.58301 1.58304 1.58578 1.58583 Alpha virt. eigenvalues -- 1.58587 1.58825 1.58865 1.58871 1.58876 Alpha virt. eigenvalues -- 1.58879 1.58883 1.59629 1.59632 1.59637 Alpha virt. eigenvalues -- 1.59642 1.59647 1.59777 1.59779 1.59793 Alpha virt. eigenvalues -- 1.59963 1.59969 1.59972 1.59975 1.59993 Alpha virt. eigenvalues -- 1.59997 1.60001 1.60003 1.60006 1.60246 Alpha virt. eigenvalues -- 1.60250 1.60254 1.60525 1.60528 1.60533 Alpha virt. eigenvalues -- 1.60535 1.61621 1.61633 1.61638 1.61643 Alpha virt. eigenvalues -- 1.61647 1.61730 1.61731 1.61744 1.61746 Alpha virt. eigenvalues -- 1.61845 1.61848 1.61851 1.61909 1.61913 Alpha virt. eigenvalues -- 1.61926 1.62431 1.62436 1.62437 1.62442 Alpha virt. eigenvalues -- 1.62453 1.62454 1.62460 1.62966 1.63037 Alpha virt. eigenvalues -- 1.63046 1.63072 1.63685 1.63692 1.63700 Alpha virt. eigenvalues -- 1.63702 1.64106 1.64114 1.64121 1.64196 Alpha virt. eigenvalues -- 1.64200 1.64209 1.64210 1.64289 1.64296 Alpha virt. eigenvalues -- 1.64296 1.64299 1.64303 1.64594 1.64596 Alpha virt. eigenvalues -- 1.64598 1.64601 1.64603 1.65557 1.65558 Alpha virt. eigenvalues -- 1.65560 1.65562 1.65564 1.65711 1.65715 Alpha virt. eigenvalues -- 1.65717 1.65720 1.66308 1.66327 1.66328 Alpha virt. eigenvalues -- 1.66336 1.66345 1.66351 1.66550 1.66556 Alpha virt. eigenvalues -- 1.66564 1.66571 1.66751 1.66763 1.66773 Alpha virt. eigenvalues -- 1.67541 1.67858 1.67868 1.67872 1.67877 Alpha virt. eigenvalues -- 1.67935 1.67941 1.67945 1.67956 1.67970 Alpha virt. eigenvalues -- 1.68331 1.68345 1.68352 1.68358 1.68910 Alpha virt. eigenvalues -- 1.68915 1.68926 1.69190 1.69198 1.69204 Alpha virt. eigenvalues -- 1.69550 1.69552 1.69555 1.69557 1.69564 Alpha virt. eigenvalues -- 1.69654 1.69664 1.69669 1.70895 1.70900 Alpha virt. eigenvalues -- 1.70906 1.71323 1.71328 1.71331 1.71332 Alpha virt. eigenvalues -- 1.71337 1.73105 1.73473 1.73481 1.73489 Alpha virt. eigenvalues -- 1.73494 1.73501 1.73506 1.73512 1.73513 Alpha virt. eigenvalues -- 1.74519 1.74529 1.74533 1.74542 1.74543 Alpha virt. eigenvalues -- 1.75188 1.75192 1.75198 1.75519 1.75523 Alpha virt. eigenvalues -- 1.75529 1.75531 1.75538 1.75651 1.75660 Alpha virt. eigenvalues -- 1.75662 1.75669 1.75676 1.76571 1.76576 Alpha virt. eigenvalues -- 1.76581 1.77588 1.77597 1.77601 1.77613 Alpha virt. eigenvalues -- 1.77731 1.77736 1.77741 1.77743 1.77748 Alpha virt. eigenvalues -- 1.77750 1.77756 1.77761 1.79675 1.79680 Alpha virt. eigenvalues -- 1.79692 1.79700 1.80667 1.80673 1.80684 Alpha virt. eigenvalues -- 1.80768 1.80780 1.80783 1.80784 1.80789 Alpha virt. eigenvalues -- 1.81163 1.81166 1.81168 1.81170 1.81174 Alpha virt. eigenvalues -- 1.81482 1.81491 1.81493 1.82027 1.82029 Alpha virt. eigenvalues -- 1.82035 1.82040 1.82306 1.82310 1.82315 Alpha virt. eigenvalues -- 1.82317 1.82381 1.82391 1.82395 1.83021 Alpha virt. eigenvalues -- 1.83527 1.83529 1.83537 1.83540 1.83566 Alpha virt. eigenvalues -- 1.83635 1.83643 1.83684 1.83797 1.83800 Alpha virt. eigenvalues -- 1.83803 1.83805 1.83815 1.85084 1.85090 Alpha virt. eigenvalues -- 1.85096 1.85102 1.85714 1.85722 1.85728 Alpha virt. eigenvalues -- 1.85884 1.85887 1.85888 1.85895 1.85900 Alpha virt. eigenvalues -- 1.86239 1.86241 1.86247 1.86689 1.86698 Alpha virt. eigenvalues -- 1.86701 1.86706 1.86711 1.87021 1.87032 Alpha virt. eigenvalues -- 1.87033 1.87791 1.87793 1.87803 1.87811 Alpha virt. eigenvalues -- 1.88868 1.88871 1.88883 1.89340 1.89346 Alpha virt. eigenvalues -- 1.89351 1.89354 1.89810 1.89821 1.89832 Alpha virt. eigenvalues -- 1.89836 1.90430 1.90441 1.90456 1.91383 Alpha virt. eigenvalues -- 1.91391 1.91400 1.91688 1.91693 1.91697 Alpha virt. eigenvalues -- 1.91701 1.91709 1.92051 1.92058 1.92060 Alpha virt. eigenvalues -- 1.92100 1.92107 1.92111 1.92121 1.92900 Alpha virt. eigenvalues -- 1.92901 1.92903 1.92910 1.92915 1.93279 Alpha virt. eigenvalues -- 1.93283 1.93284 1.93291 1.93295 1.93355 Alpha virt. eigenvalues -- 1.93368 1.93374 1.93383 1.93812 1.93818 Alpha virt. eigenvalues -- 1.93826 1.93836 1.94490 1.94508 1.94513 Alpha virt. eigenvalues -- 1.94651 1.94667 1.94676 1.94691 1.94697 Alpha virt. eigenvalues -- 1.94797 1.94806 1.94811 1.94821 1.95185 Alpha virt. eigenvalues -- 1.96069 1.96072 1.96081 1.96610 1.96613 Alpha virt. eigenvalues -- 1.96622 1.96623 1.96668 1.96675 1.96679 Alpha virt. eigenvalues -- 1.96683 1.96685 1.96819 1.96825 1.96829 Alpha virt. eigenvalues -- 1.96839 1.96843 1.97068 1.97071 1.97078 Alpha virt. eigenvalues -- 1.97576 1.97578 1.97581 1.97593 1.97597 Alpha virt. eigenvalues -- 1.97801 1.97810 1.97813 1.99094 1.99097 Alpha virt. eigenvalues -- 1.99111 1.99274 1.99282 1.99286 1.99796 Alpha virt. eigenvalues -- 1.99808 1.99830 1.99839 1.99999 2.00002 Alpha virt. eigenvalues -- 2.00009 2.00575 2.00578 2.00582 2.00586 Alpha virt. eigenvalues -- 2.00590 2.01020 2.01227 2.01237 2.01248 Alpha virt. eigenvalues -- 2.01447 2.01450 2.01458 2.01462 2.01488 Alpha virt. eigenvalues -- 2.01491 2.01497 2.01504 2.01510 2.01790 Alpha virt. eigenvalues -- 2.01799 2.01803 2.01805 2.01815 2.01816 Alpha virt. eigenvalues -- 2.01830 2.01841 2.02691 2.02702 2.02708 Alpha virt. eigenvalues -- 2.03164 2.03171 2.03172 2.03175 2.03178 Alpha virt. eigenvalues -- 2.03643 2.03660 2.03688 2.03817 2.03824 Alpha virt. eigenvalues -- 2.03835 2.04660 2.04664 2.04669 2.04672 Alpha virt. eigenvalues -- 2.04676 2.04924 2.04930 2.04938 2.04940 Alpha virt. eigenvalues -- 2.04949 2.04950 2.04954 2.04962 2.04964 Alpha virt. eigenvalues -- 2.05268 2.05578 2.05586 2.05588 2.05593 Alpha virt. eigenvalues -- 2.05980 2.05998 2.06005 2.06324 2.06335 Alpha virt. eigenvalues -- 2.06336 2.06338 2.06347 2.06710 2.06714 Alpha virt. eigenvalues -- 2.06726 2.06901 2.06911 2.06918 2.06919 Alpha virt. eigenvalues -- 2.06927 2.06927 2.06930 2.06933 2.06939 Alpha virt. eigenvalues -- 2.07091 2.07098 2.07116 2.07764 2.07780 Alpha virt. eigenvalues -- 2.07785 2.07790 2.07797 2.08570 2.08692 Alpha virt. eigenvalues -- 2.08699 2.08703 2.08708 2.08713 2.09010 Alpha virt. eigenvalues -- 2.09023 2.09029 2.09115 2.09120 2.09123 Alpha virt. eigenvalues -- 2.09133 2.09291 2.09317 2.09325 2.10021 Alpha virt. eigenvalues -- 2.10028 2.10046 2.10052 2.10057 2.10126 Alpha virt. eigenvalues -- 2.10142 2.10147 2.10256 2.10263 2.10272 Alpha virt. eigenvalues -- 2.10289 2.11143 2.11159 2.11169 2.11654 Alpha virt. eigenvalues -- 2.11659 2.11668 2.11673 2.11680 2.11872 Alpha virt. eigenvalues -- 2.11879 2.11887 2.11895 2.12130 2.12137 Alpha virt. eigenvalues -- 2.12143 2.12146 2.12150 2.12175 2.12191 Alpha virt. eigenvalues -- 2.12199 2.12394 2.12402 2.12409 2.13916 Alpha virt. eigenvalues -- 2.13920 2.13926 2.13929 2.15018 2.15020 Alpha virt. eigenvalues -- 2.15027 2.15030 2.15036 2.15043 2.15045 Alpha virt. eigenvalues -- 2.15056 2.15073 2.15085 2.15090 2.15445 Alpha virt. eigenvalues -- 2.15450 2.15452 2.15456 2.15475 2.15864 Alpha virt. eigenvalues -- 2.15867 2.15878 2.15887 2.16723 2.16732 Alpha virt. eigenvalues -- 2.16744 2.16752 2.17459 2.17465 2.17471 Alpha virt. eigenvalues -- 2.17613 2.17616 2.17625 2.17922 2.17923 Alpha virt. eigenvalues -- 2.17926 2.17930 2.17933 2.18725 2.18728 Alpha virt. eigenvalues -- 2.18731 2.19766 2.19780 2.19784 2.19790 Alpha virt. eigenvalues -- 2.19798 2.19825 2.19830 2.19833 2.19842 Alpha virt. eigenvalues -- 2.19945 2.19951 2.19956 2.19966 2.19992 Alpha virt. eigenvalues -- 2.20675 2.20686 2.20699 2.21644 2.21648 Alpha virt. eigenvalues -- 2.21653 2.21911 2.21921 2.21927 2.22118 Alpha virt. eigenvalues -- 2.22125 2.22135 2.22140 2.22142 2.22145 Alpha virt. eigenvalues -- 2.22148 2.22152 2.22164 2.22169 2.22251 Alpha virt. eigenvalues -- 2.22262 2.22277 2.22284 2.22772 2.22776 Alpha virt. eigenvalues -- 2.22780 2.22785 2.22791 2.22975 2.22978 Alpha virt. eigenvalues -- 2.22988 2.23169 2.23174 2.23176 2.23180 Alpha virt. eigenvalues -- 2.25001 2.25004 2.25013 2.25014 2.25016 Alpha virt. eigenvalues -- 2.25323 2.25329 2.25334 2.25341 2.26379 Alpha virt. eigenvalues -- 2.26383 2.26391 2.28469 2.28487 2.28493 Alpha virt. eigenvalues -- 2.28503 2.29048 2.29054 2.29057 2.30048 Alpha virt. eigenvalues -- 2.30052 2.30060 2.30102 2.30106 2.30110 Alpha virt. eigenvalues -- 2.30116 2.30117 2.30443 2.30451 2.30457 Alpha virt. eigenvalues -- 2.31096 2.31097 2.31103 2.31107 2.31508 Alpha virt. eigenvalues -- 2.31522 2.31524 2.31528 2.32321 2.32323 Alpha virt. eigenvalues -- 2.32328 2.32333 2.32338 2.33735 2.33742 Alpha virt. eigenvalues -- 2.33743 2.33750 2.33755 2.34351 2.34357 Alpha virt. eigenvalues -- 2.34360 2.34362 2.34365 2.34775 2.34781 Alpha virt. eigenvalues -- 2.34787 2.37063 2.37064 2.37068 2.37080 Alpha virt. eigenvalues -- 2.37085 2.37211 2.37219 2.37225 2.37233 Alpha virt. eigenvalues -- 2.37859 2.37863 2.37870 2.39226 2.39231 Alpha virt. eigenvalues -- 2.39238 2.39248 2.40595 2.40599 2.40605 Alpha virt. eigenvalues -- 2.40726 2.40734 2.40744 2.40745 2.40751 Alpha virt. eigenvalues -- 2.41695 2.41701 2.41705 2.41711 2.42128 Alpha virt. eigenvalues -- 2.42137 2.42143 2.42472 2.42475 2.42476 Alpha virt. eigenvalues -- 2.42490 2.43152 2.43153 2.43159 2.45467 Alpha virt. eigenvalues -- 2.45475 2.45480 2.45488 2.45491 2.45666 Alpha virt. eigenvalues -- 2.45669 2.45676 2.46397 2.46403 2.46406 Alpha virt. eigenvalues -- 2.46407 2.48283 2.48286 2.48293 2.49009 Alpha virt. eigenvalues -- 2.49011 2.49014 2.49022 2.49035 2.49313 Alpha virt. eigenvalues -- 2.49320 2.49324 2.49331 2.50743 2.50748 Alpha virt. eigenvalues -- 2.50756 2.50760 2.50770 2.52760 2.52773 Alpha virt. eigenvalues -- 2.52781 2.52790 2.52794 2.53383 2.53394 Alpha virt. eigenvalues -- 2.53396 2.53402 2.53409 2.53793 2.53796 Alpha virt. eigenvalues -- 2.53800 2.53805 2.53813 2.54675 2.54676 Alpha virt. eigenvalues -- 2.54698 2.55777 2.55780 2.55785 2.55951 Alpha virt. eigenvalues -- 2.56013 2.56022 2.56026 2.56029 2.56056 Alpha virt. eigenvalues -- 2.56068 2.56076 2.56081 2.56205 2.56213 Alpha virt. eigenvalues -- 2.56223 2.56225 2.56234 2.57054 2.57058 Alpha virt. eigenvalues -- 2.57060 2.57380 2.57640 2.57645 2.57649 Alpha virt. eigenvalues -- 2.57653 2.57654 2.57659 2.57662 2.57665 Alpha virt. eigenvalues -- 2.57987 2.57999 2.58003 2.58883 2.58886 Alpha virt. eigenvalues -- 2.58888 2.59204 2.59214 2.59222 2.59226 Alpha virt. eigenvalues -- 2.59235 2.60237 2.60247 2.60252 2.60262 Alpha virt. eigenvalues -- 2.60722 2.60728 2.60737 2.60778 2.60783 Alpha virt. eigenvalues -- 2.60787 2.60831 2.60837 2.60841 2.60847 Alpha virt. eigenvalues -- 2.60855 2.61720 2.61729 2.61735 2.62010 Alpha virt. eigenvalues -- 2.62027 2.62037 2.62051 2.62196 2.62198 Alpha virt. eigenvalues -- 2.62214 2.62248 2.62256 2.62263 2.62406 Alpha virt. eigenvalues -- 2.62412 2.62420 2.62421 2.62428 2.62699 Alpha virt. eigenvalues -- 2.62703 2.62709 2.62717 2.62722 2.62922 Alpha virt. eigenvalues -- 2.62926 2.62932 2.63028 2.63034 2.63039 Alpha virt. eigenvalues -- 2.63370 2.63387 2.63392 2.63396 2.63912 Alpha virt. eigenvalues -- 2.64953 2.64963 2.64970 2.64973 2.65188 Alpha virt. eigenvalues -- 2.65204 2.65209 2.65218 2.65229 2.65484 Alpha virt. eigenvalues -- 2.65493 2.65502 2.65507 2.65520 2.65721 Alpha virt. eigenvalues -- 2.65724 2.65732 2.65737 2.65742 2.65747 Alpha virt. eigenvalues -- 2.65754 2.65903 2.65908 2.65914 2.65923 Alpha virt. eigenvalues -- 2.66138 2.66142 2.66152 2.67246 2.67256 Alpha virt. eigenvalues -- 2.67259 2.67270 2.67286 2.68042 2.68051 Alpha virt. eigenvalues -- 2.68053 2.68057 2.68070 2.68900 2.68913 Alpha virt. eigenvalues -- 2.68915 2.69079 2.69087 2.69092 2.69104 Alpha virt. eigenvalues -- 2.69115 2.69446 2.69451 2.69474 2.69482 Alpha virt. eigenvalues -- 2.69990 2.70000 2.70002 2.70013 2.70020 Alpha virt. eigenvalues -- 2.70299 2.70302 2.70320 2.71317 2.71318 Alpha virt. eigenvalues -- 2.71321 2.71330 2.71337 2.72773 2.72780 Alpha virt. eigenvalues -- 2.72791 2.72797 2.72874 2.73503 2.73517 Alpha virt. eigenvalues -- 2.73522 2.75103 2.75112 2.75115 2.75117 Alpha virt. eigenvalues -- 2.75492 2.75502 2.75511 2.75513 2.75521 Alpha virt. eigenvalues -- 2.75647 2.75657 2.75659 2.76762 2.76770 Alpha virt. eigenvalues -- 2.76773 2.76859 2.76872 2.76884 2.77106 Alpha virt. eigenvalues -- 2.77110 2.77123 2.77520 2.77529 2.77532 Alpha virt. eigenvalues -- 2.77535 2.77737 2.77745 2.77748 2.77754 Alpha virt. eigenvalues -- 2.77767 2.78863 2.78873 2.78884 2.78888 Alpha virt. eigenvalues -- 2.78893 2.79538 2.79549 2.79555 2.79582 Alpha virt. eigenvalues -- 2.79587 2.79588 2.79599 2.79609 2.79612 Alpha virt. eigenvalues -- 2.79621 2.80582 2.80591 2.80593 2.80603 Alpha virt. eigenvalues -- 2.81960 2.81968 2.81972 2.81976 2.81982 Alpha virt. eigenvalues -- 2.82006 2.82010 2.82013 2.82016 2.82023 Alpha virt. eigenvalues -- 2.82524 2.82527 2.82529 2.82537 2.82712 Alpha virt. eigenvalues -- 2.82714 2.82720 2.82726 2.82732 2.83117 Alpha virt. eigenvalues -- 2.83129 2.83136 2.83150 2.83854 2.83861 Alpha virt. eigenvalues -- 2.83873 2.84648 2.84650 2.84656 2.84667 Alpha virt. eigenvalues -- 2.84672 2.85579 2.85758 2.85772 2.85782 Alpha virt. eigenvalues -- 2.85784 2.85791 2.86575 2.86582 2.86591 Alpha virt. eigenvalues -- 2.86598 2.87189 2.87194 2.87206 2.87313 Alpha virt. eigenvalues -- 2.87316 2.87324 2.88565 2.88578 2.88583 Alpha virt. eigenvalues -- 2.88589 2.88799 2.88802 2.88809 2.89469 Alpha virt. eigenvalues -- 2.89481 2.89495 2.89511 2.91393 2.91397 Alpha virt. eigenvalues -- 2.91398 2.91412 2.91428 2.92574 2.92585 Alpha virt. eigenvalues -- 2.92586 2.92594 2.92790 2.92798 2.92824 Alpha virt. eigenvalues -- 2.93808 2.93814 2.93817 2.93821 2.93824 Alpha virt. eigenvalues -- 2.93892 2.93894 2.93899 2.93908 2.93916 Alpha virt. eigenvalues -- 2.93957 2.93964 2.93970 2.94327 2.94337 Alpha virt. eigenvalues -- 2.94343 2.94348 2.94350 2.95772 2.95808 Alpha virt. eigenvalues -- 2.95818 2.95911 2.95915 2.95924 2.97158 Alpha virt. eigenvalues -- 2.97166 2.97170 2.97185 2.98458 2.98465 Alpha virt. eigenvalues -- 2.98476 2.98489 2.98493 2.99428 2.99462 Alpha virt. eigenvalues -- 2.99474 2.99485 3.01576 3.01597 3.01604 Alpha virt. eigenvalues -- 3.01608 3.01614 3.04417 3.04426 3.04439 Alpha virt. eigenvalues -- 3.04446 3.06462 3.06477 3.06480 3.06659 Alpha virt. eigenvalues -- 3.09417 3.09422 3.09429 3.11086 3.11088 Alpha virt. eigenvalues -- 3.11101 3.11366 3.11371 3.11379 3.11382 Alpha virt. eigenvalues -- 3.11386 3.15102 3.15117 3.15140 3.15516 Alpha virt. eigenvalues -- 3.15525 3.15529 3.15538 3.16878 3.16888 Alpha virt. eigenvalues -- 3.16892 3.16903 3.16905 3.18303 3.18308 Alpha virt. eigenvalues -- 3.18314 3.19425 3.19438 3.19447 3.19664 Alpha virt. eigenvalues -- 3.19676 3.19686 3.19690 3.20486 3.24231 Alpha virt. eigenvalues -- 3.24245 3.24249 3.24256 3.24268 3.25473 Alpha virt. eigenvalues -- 3.25494 3.25499 3.25503 3.25515 3.25518 Alpha virt. eigenvalues -- 3.25523 3.25526 3.26644 3.26649 3.26662 Alpha virt. eigenvalues -- 3.26667 3.29254 3.29256 3.29256 3.32605 Alpha virt. eigenvalues -- 3.32615 3.32624 3.32640 3.36170 3.36181 Alpha virt. eigenvalues -- 3.36188 3.36561 3.36567 3.36578 3.36581 Alpha virt. eigenvalues -- 3.36588 3.37814 3.37819 3.37826 3.37832 Alpha virt. eigenvalues -- 3.37837 3.43878 3.43888 3.43894 3.43901 Alpha virt. eigenvalues -- 3.43908 3.44864 3.44873 3.44883 3.44892 Alpha virt. eigenvalues -- 3.49614 3.49631 3.49640 3.49653 3.52866 Alpha virt. eigenvalues -- 3.52876 3.52884 3.53111 3.53119 3.53134 Alpha virt. eigenvalues -- 3.53147 3.57901 3.57917 3.57923 3.60028 Alpha virt. eigenvalues -- 3.60032 3.60044 3.60056 3.60061 3.60712 Alpha virt. eigenvalues -- 3.60718 3.60735 3.60739 3.62310 3.62320 Alpha virt. eigenvalues -- 3.62339 3.68075 3.68077 3.68096 3.72687 Alpha virt. eigenvalues -- 3.94028 3.94336 3.94338 3.94342 3.94853 Alpha virt. eigenvalues -- 3.94856 3.94859 3.94863 3.94866 3.95320 Alpha virt. eigenvalues -- 3.95329 3.95330 3.95339 3.96325 3.96329 Alpha virt. eigenvalues -- 3.96333 3.96340 3.96344 3.96357 3.96360 Alpha virt. eigenvalues -- 3.97959 3.97965 3.97967 3.97974 3.97975 Alpha virt. eigenvalues -- 3.98279 3.98284 3.98290 3.98293 3.98298 Alpha virt. eigenvalues -- 3.99144 3.99150 3.99156 3.99504 3.99510 Alpha virt. eigenvalues -- 3.99513 4.00022 4.00026 4.00030 4.00248 Alpha virt. eigenvalues -- 4.00248 4.00252 4.00258 4.00853 4.00855 Alpha virt. eigenvalues -- 4.00859 4.00865 4.00868 4.02114 4.02211 Alpha virt. eigenvalues -- 4.02216 4.02223 4.02226 4.02230 4.02450 Alpha virt. eigenvalues -- 4.02452 4.02454 4.02627 4.02632 4.02634 Alpha virt. eigenvalues -- 4.02805 4.02807 4.02813 4.02815 4.03399 Alpha virt. eigenvalues -- 4.03403 4.03406 4.03409 4.03412 4.05415 Alpha virt. eigenvalues -- 4.05418 4.05429 4.05753 4.05758 4.05760 Alpha virt. eigenvalues -- 4.05762 4.05915 4.05921 4.05924 4.05990 Alpha virt. eigenvalues -- 4.05993 4.05994 4.05999 4.06001 4.07357 Alpha virt. eigenvalues -- 4.07361 4.07365 4.07370 4.08919 4.08925 Alpha virt. eigenvalues -- 4.08926 4.09376 4.09378 4.09381 4.09382 Alpha virt. eigenvalues -- 4.09384 4.09542 4.09543 4.09545 4.09549 Alpha virt. eigenvalues -- 4.10361 4.10363 4.10364 4.10366 4.10497 Alpha virt. eigenvalues -- 4.10500 4.10501 4.10504 4.10508 4.10850 Alpha virt. eigenvalues -- 4.10851 4.10856 4.12052 4.12054 4.12056 Alpha virt. eigenvalues -- 4.12923 4.12923 4.12925 4.12925 4.12930 Alpha virt. eigenvalues -- 4.16886 4.16887 4.16888 4.18862 4.18863 Alpha virt. eigenvalues -- 4.18869 4.23277 4.23280 4.23281 4.23282 Alpha virt. eigenvalues -- 4.23284 4.26339 4.26341 4.26342 4.26343 Alpha virt. eigenvalues -- 4.26344 4.26617 4.26618 4.26620 4.26622 Alpha virt. eigenvalues -- 4.26864 4.28663 4.28665 4.28669 4.28965 Alpha virt. eigenvalues -- 4.28967 4.28969 4.28972 4.28973 4.29431 Alpha virt. eigenvalues -- 4.29434 4.29436 4.32724 4.32725 4.32728 Alpha virt. eigenvalues -- 4.33025 4.33027 4.33028 4.33029 4.33879 Alpha virt. eigenvalues -- 4.33881 4.33883 4.33885 4.33887 4.36352 Alpha virt. eigenvalues -- 4.36353 4.36355 4.36361 4.37878 4.37879 Alpha virt. eigenvalues -- 4.37880 4.37884 4.37886 4.41379 4.41379 Alpha virt. eigenvalues -- 4.41382 4.41383 4.41387 4.42712 4.42714 Alpha virt. eigenvalues -- 4.42714 4.42715 4.47400 4.47407 4.47407 Alpha virt. eigenvalues -- 4.51263 4.51270 4.51271 4.54311 4.54315 Alpha virt. eigenvalues -- 4.54319 4.54320 4.54324 4.54425 4.54427 Alpha virt. eigenvalues -- 4.54432 4.55941 4.55944 4.55947 4.55948 Alpha virt. eigenvalues -- 4.62509 4.63728 4.63736 4.63740 4.65968 Alpha virt. eigenvalues -- 4.65969 4.65969 4.65974 4.70659 4.70664 Alpha virt. eigenvalues -- 4.70667 4.70669 4.70672 4.76246 4.76251 Alpha virt. eigenvalues -- 4.76257 4.85923 4.85925 4.85927 4.85935 Alpha virt. eigenvalues -- 4.85936 4.86024 4.86026 4.86031 4.94265 Alpha virt. eigenvalues -- 4.94271 4.94275 4.94280 4.94284 5.00821 Alpha virt. eigenvalues -- 5.00831 5.00836 5.00838 5.14966 5.14968 Alpha virt. eigenvalues -- 5.14977 5.14979 5.17073 5.17078 5.17080 Condensed to atoms (all electrons): Mulliken charges: 1 1 C -0.075318 2 C -0.076034 3 C -0.075329 4 C -0.077473 5 C -0.075688 6 C -0.076544 7 C -0.075652 8 C -0.076500 9 C -0.076146 10 C -0.075884 11 C -0.075125 12 C -0.075934 13 C -0.075111 14 C -0.076200 15 C -0.075867 16 C -0.075698 17 C -0.075619 18 C -0.076417 19 C -0.076131 20 C -0.075982 21 C -0.075009 22 C -0.075819 23 C -0.076472 24 C -0.076346 25 C -0.075934 26 C -0.076008 27 C -0.076182 28 C -0.075929 29 C -0.075946 30 C -0.075787 31 C -0.074899 32 C -0.075709 33 C -0.077209 34 C -0.075216 35 C -0.076680 36 C -0.075729 37 C -0.076143 38 C -0.076808 39 C -0.075353 40 C -0.076591 41 C -0.076188 42 C -0.075952 43 C -0.075936 44 C -0.076166 45 C -0.075587 46 C -0.076485 47 C -0.076159 48 C -0.076372 49 C -0.075364 50 C -0.075317 51 C -0.075833 52 C -0.076137 53 C -0.076463 54 C -0.075688 55 C -0.075665 56 C -0.076050 57 C -0.076224 58 C -0.074870 59 C -0.075956 60 C -0.075661 61 C 0.002891 62 C 0.002749 63 C 0.003370 64 C 0.002610 65 C 0.001733 66 C 0.003077 67 C 0.002343 68 C 0.002926 69 C 0.002002 70 C 0.003071 71 C 0.003697 72 C 0.002620 73 C 0.002681 74 C 0.001916 75 C 0.002818 76 C 0.003048 77 C 0.002839 78 C 0.003252 79 C 0.003322 80 C 0.002236 81 C 0.002937 82 C 0.002015 83 C 0.002968 84 C 0.003065 85 C 0.002995 86 C 0.002769 87 C 0.002590 88 C 0.003125 89 C 0.002973 90 C 0.002348 91 C 0.002219 92 C 0.002955 93 C 0.002874 94 C 0.002937 95 C 0.002649 96 C 0.003265 97 C 0.003118 98 C 0.002949 99 C 0.002485 100 C 0.002560 101 C 0.002269 102 C 0.003333 103 C 0.003249 104 C 0.002834 105 C 0.002941 106 C 0.002913 107 C 0.001981 108 C 0.002616 109 C 0.002347 110 C 0.003969 111 C 0.002914 112 C 0.002459 113 C 0.002789 114 C 0.002348 115 C 0.003133 116 C 0.001857 117 C 0.002200 118 C 0.003497 119 C 0.002743 120 C 0.003216 121 C 0.003371 122 C 0.002383 123 C 0.002465 124 C 0.003875 125 C 0.002407 126 C 0.002833 127 C 0.003162 128 C 0.003333 129 C 0.002360 130 C 0.003519 131 C 0.002292 132 C 0.002204 133 C 0.002361 134 C 0.003476 135 C 0.002619 136 C 0.003269 137 C 0.002376 138 C 0.002307 139 C 0.002240 140 C 0.002371 141 C 0.002429 142 C 0.003390 143 C 0.003624 144 C 0.002523 145 C 0.002322 146 C 0.002690 147 C 0.002946 148 C 0.003535 149 C 0.002066 150 C 0.003937 151 C 0.003846 152 C 0.002422 153 C 0.002516 154 C 0.003237 155 C 0.002687 156 C 0.002614 157 C 0.003096 158 C 0.003309 159 C 0.002706 160 C 0.003796 161 C 0.001761 162 C 0.002680 163 C 0.003405 164 C 0.002583 165 C 0.003071 166 C 0.002526 167 C 0.002082 168 C 0.002642 169 C 0.003467 170 C 0.002379 171 C 0.002409 172 C 0.002179 173 C 0.002545 174 C 0.003670 175 C 0.003960 176 C 0.002134 177 C 0.003358 178 C 0.002582 179 C 0.002859 180 C 0.002469 181 C 0.070662 182 C 0.071523 183 C 0.070448 184 C 0.070442 185 C 0.069502 186 C 0.070205 187 C 0.070783 188 C 0.070979 189 C 0.070040 190 C 0.070419 191 C 0.070095 192 C 0.070162 193 C 0.069852 194 C 0.070032 195 C 0.070288 196 C 0.071082 197 C 0.070033 198 C 0.070560 199 C 0.070087 200 C 0.070898 201 C 0.069890 202 C 0.070694 203 C 0.071269 204 C 0.069647 205 C 0.069412 206 C 0.070289 207 C 0.070424 208 C 0.070243 209 C 0.070616 210 C 0.070006 211 C 0.071198 212 C 0.070119 213 C 0.070617 214 C 0.069799 215 C 0.070482 216 C 0.071540 217 C 0.070348 218 C 0.070696 219 C 0.070239 220 C 0.070208 221 C 0.069601 222 C 0.070385 223 C 0.069330 224 C 0.070363 225 C 0.070217 226 C 0.070070 227 C 0.070916 228 C 0.071641 229 C 0.069627 230 C 0.069666 231 C 0.068731 232 C 0.070929 233 C 0.070630 234 C 0.069437 235 C 0.070153 236 C 0.070547 237 C 0.071788 238 C 0.070872 239 C 0.070075 240 C 0.069407 Sum of Mulliken charges = -0.00000 Mulliken charges with hydrogens summed into heavy atoms: 1 1 C -0.075318 2 C -0.076034 3 C -0.075329 4 C -0.077473 5 C -0.075688 6 C -0.076544 7 C -0.075652 8 C -0.076500 9 C -0.076146 10 C -0.075884 11 C -0.075125 12 C -0.075934 13 C -0.075111 14 C -0.076200 15 C -0.075867 16 C -0.075698 17 C -0.075619 18 C -0.076417 19 C -0.076131 20 C -0.075982 21 C -0.075009 22 C -0.075819 23 C -0.076472 24 C -0.076346 25 C -0.075934 26 C -0.076008 27 C -0.076182 28 C -0.075929 29 C -0.075946 30 C -0.075787 31 C -0.074899 32 C -0.075709 33 C -0.077209 34 C -0.075216 35 C -0.076680 36 C -0.075729 37 C -0.076143 38 C -0.076808 39 C -0.075353 40 C -0.076591 41 C -0.076188 42 C -0.075952 43 C -0.075936 44 C -0.076166 45 C -0.075587 46 C -0.076485 47 C -0.076159 48 C -0.076372 49 C -0.075364 50 C -0.075317 51 C -0.075833 52 C -0.076137 53 C -0.076463 54 C -0.075688 55 C -0.075665 56 C -0.076050 57 C -0.076224 58 C -0.074870 59 C -0.075956 60 C -0.075661 61 C 0.002891 62 C 0.002749 63 C 0.003370 64 C 0.002610 65 C 0.001733 66 C 0.003077 67 C 0.002343 68 C 0.002926 69 C 0.002002 70 C 0.003071 71 C 0.003697 72 C 0.002620 73 C 0.002681 74 C 0.001916 75 C 0.002818 76 C 0.003048 77 C 0.002839 78 C 0.003252 79 C 0.003322 80 C 0.002236 81 C 0.002937 82 C 0.002015 83 C 0.002968 84 C 0.003065 85 C 0.002995 86 C 0.002769 87 C 0.002590 88 C 0.003125 89 C 0.002973 90 C 0.002348 91 C 0.002219 92 C 0.002955 93 C 0.002874 94 C 0.002937 95 C 0.002649 96 C 0.003265 97 C 0.003118 98 C 0.002949 99 C 0.002485 100 C 0.002560 101 C 0.002269 102 C 0.003333 103 C 0.003249 104 C 0.002834 105 C 0.002941 106 C 0.002913 107 C 0.001981 108 C 0.002616 109 C 0.002347 110 C 0.003969 111 C 0.002914 112 C 0.002459 113 C 0.002789 114 C 0.002348 115 C 0.003133 116 C 0.001857 117 C 0.002200 118 C 0.003497 119 C 0.002743 120 C 0.003216 121 C 0.003371 122 C 0.002383 123 C 0.002465 124 C 0.003875 125 C 0.002407 126 C 0.002833 127 C 0.003162 128 C 0.003333 129 C 0.002360 130 C 0.003519 131 C 0.002292 132 C 0.002204 133 C 0.002361 134 C 0.003476 135 C 0.002619 136 C 0.003269 137 C 0.002376 138 C 0.002307 139 C 0.002240 140 C 0.002371 141 C 0.002429 142 C 0.003390 143 C 0.003624 144 C 0.002523 145 C 0.002322 146 C 0.002690 147 C 0.002946 148 C 0.003535 149 C 0.002066 150 C 0.003937 151 C 0.003846 152 C 0.002422 153 C 0.002516 154 C 0.003237 155 C 0.002687 156 C 0.002614 157 C 0.003096 158 C 0.003309 159 C 0.002706 160 C 0.003796 161 C 0.001761 162 C 0.002680 163 C 0.003405 164 C 0.002583 165 C 0.003071 166 C 0.002526 167 C 0.002082 168 C 0.002642 169 C 0.003467 170 C 0.002379 171 C 0.002409 172 C 0.002179 173 C 0.002545 174 C 0.003670 175 C 0.003960 176 C 0.002134 177 C 0.003358 178 C 0.002582 179 C 0.002859 180 C 0.002469 181 C 0.070662 182 C 0.071523 183 C 0.070448 184 C 0.070442 185 C 0.069502 186 C 0.070205 187 C 0.070783 188 C 0.070979 189 C 0.070040 190 C 0.070419 191 C 0.070095 192 C 0.070162 193 C 0.069852 194 C 0.070032 195 C 0.070288 196 C 0.071082 197 C 0.070033 198 C 0.070560 199 C 0.070087 200 C 0.070898 201 C 0.069890 202 C 0.070694 203 C 0.071269 204 C 0.069647 205 C 0.069412 206 C 0.070289 207 C 0.070424 208 C 0.070243 209 C 0.070616 210 C 0.070006 211 C 0.071198 212 C 0.070119 213 C 0.070617 214 C 0.069799 215 C 0.070482 216 C 0.071540 217 C 0.070348 218 C 0.070696 219 C 0.070239 220 C 0.070208 221 C 0.069601 222 C 0.070385 223 C 0.069330 224 C 0.070363 225 C 0.070217 226 C 0.070070 227 C 0.070916 228 C 0.071641 229 C 0.069627 230 C 0.069666 231 C 0.068731 232 C 0.070929 233 C 0.070630 234 C 0.069437 235 C 0.070153 236 C 0.070547 237 C 0.071788 238 C 0.070872 239 C 0.070075 240 C 0.069407 Electronic spatial extent (au): = 258542.9252 Charge= -0.0000 electrons Dipole moment (field-independent basis, Debye): X= -0.0003 Y= -0.0006 Z= -0.0001 Tot= 0.0006 Quadrupole moment (field-independent basis, Debye-Ang): XX= -1278.2462 YY= -1278.2894 ZZ= -1278.3170 XY= 0.0312 XZ= 0.0096 YZ= -0.0114 Traceless Quadrupole moment (field-independent basis, Debye-Ang): XX= 0.0380 YY= -0.0051 ZZ= -0.0328 XY= 0.0312 XZ= 0.0096 YZ= -0.0114 Octapole moment (field-independent basis, Debye-Ang**2): XXX= -0.0708 YYY= 0.0333 ZZZ= 0.0421 XYY= -0.0654 XXY= -0.0115 XXZ= -0.0610 XZZ= 0.0949 YZZ= -0.0513 YYZ= -0.0240 XYZ= 0.0121 Hexadecapole moment (field-independent basis, Debye-Ang**3): XXXX= -128139.3430 YYYY= -128139.2872 ZZZZ= -128139.2349 XXXY= 0.8454 XXXZ= 0.3635 YYYX= 1.0943 YYYZ= -0.6982 ZZZX= 0.3220 ZZZY= -0.3256 XXYY= -42714.0762 XXZZ= -42714.1642 YYZZ= -42713.8778 XXYZ= 0.3822 YYXZ= 0.1332 ZZXY= 0.4075 N-N= 7.244844287875D+04 E-N=-1.660875476743D+05 KE= 9.071345381904D+03 Leave Link 601 at Tue Feb 14 12:54:51 2017, MaxMem= 16106127360 cpu: 149.9 (Enter /root/g09/l9999.exe) 1\1\ WCSS.PL-BEM-CLIENT10\SP\RBLYP\6-31G(d)\C240\ROOT\14-Feb-2017\0\\# p BLYP/6-31G*\\Title Card Required\\0,1\C\C,1,1.38793372\C,2,1.3881894 7,1,108.02583956\C,3,1.3884675,2,107.98575889,1,0.00713125,0\C,1,1.387 97442,2,107.99194944,3,0.02535164,0\C,1,7.28129975,2,111.52023638,3,13 5.81462422,0\C,6,1.38843509,1,32.51523179,2,67.55728171,0\C,7,1.388016 57,6,107.96559919,1,45.83727504,0\C,8,1.38906191,7,108.00842359,6,-0.0 1001844,0\C,6,1.3880317,1,84.54917058,2,-155.65062825,0\C,7,7.28028118 ,6,111.55949042,1,-90.00551486,0\C,11,1.38814589,7,84.55664072,6,155.6 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YOU CANNOT PULL ON ONE END WITHOUT MAKING THE OTHER END MOVE. -- GREG WETTSTEIN Job cpu time: 0 days 16 hours 15 minutes 14.5 seconds. File lengths (MBytes): RWF= 6935 Int= 0 D2E= 0 Chk= 647 Scr= 1 Normal termination of Gaussian 09 at Tue Feb 14 12:54:52 2017. From reza.... at gmail.com Fri Feb 17 17:23:28 2017 From: reza.... at gmail.com (Reza) Date: Fri, 17 Feb 2017 09:23:28 -0800 (PST) Subject: [CP2K:8706] Libinit compilation In-Reply-To: References: <4eb14ada-2833-4cc8-b70e-c0646e2b3426@googlegroups.com> Message-ID: <0e4b2506-154a-4d2c-9f9c-db2bb23fdcfa@googlegroups.com> Very thanks for time devoted to my discussion. But my main question was about parallel compiling of Libint. Is it possible? May be my very bad performance of hybrid method is due to the serial compiling of Libint. -------------- next part -------------- An HTML attachment was scrubbed... URL: From rat... at gmail.com Fri Feb 17 17:27:39 2017 From: rat... at gmail.com (Dominik 'Rathann' Mierzejewski) Date: Fri, 17 Feb 2017 18:27:39 +0100 Subject: [CP2K:8709] Libinit compilation In-Reply-To: <0e4b2506-154a-4d2c-9f9c-db2bb23fdcfa@googlegroups.com> References: <4eb14ada-2833-4cc8-b70e-c0646e2b3426@googlegroups.com> <0e4b2506-154a-4d2c-9f9c-db2bb23fdcfa@googlegroups.com> Message-ID: <20170217172739.GH32559@sakura.greysector.net> Dear Reza, On Friday, 17 February 2017 at 18:21, Reza wrote: > Very thanks for time devoted to my discussion. > > But my main question was about parallel compiling of Libint. Is it > possible? May be my very bad performance of hybrid method is due to the > serial compiling of Libint. libinit-1.1.x (the only one supported by cp2k) doesn't support any kind of parallelization as far as I know. Regards, Dominik -- Fedora http://fedoraproject.org/wiki/User:Rathann RPMFusion http://rpmfusion.org "Faith manages." -- Delenn to Lennier in Babylon 5:"Confessions and Lamentations" From hut... at chem.uzh.ch Fri Feb 17 17:33:21 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Fri, 17 Feb 2017 18:33:21 +0100 Subject: [CP2K:8709] Libinit compilation In-Reply-To: <0e4b2506-154a-4d2c-9f9c-db2bb23fdcfa@googlegroups.com> References: <0e4b2506-154a-4d2c-9f9c-db2bb23fdcfa@googlegroups.com>, <4eb14ada-2833-4cc8-b70e-c0646e2b3426@googlegroups.com>,> Message-ID: Hi integrals are distributed over processors by CP2K. Each processor calls libint to calculate the integrals. (lack of) Parallelization of libint is not causing your problem. regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Reza Sent by: cp... at googlegroups.com Date: 02/17/2017 06:21PM Subject: Re: [CP2K:8709] Libinit compilation Very thanks for time devoted to my discussion. But my main question was about parallel compiling of Libint. Is it possible? May be my very bad performance of hybrid method is due to the serial compiling of Libint. On Friday, February 17, 2017 at 8:47:55 PM UTC+3:30, Reza wrote: Hi again, I have set parameters to obtain the same total energy to the Gaussian, as could as possible. the change of total energy in the last SCF converged in Gaussian is about 5*10(-9) and for CP2K is 8*10(-9). the grid of Gaussian is 75 for radial and 302 for angular point. Setting lower or higher cutoff of grids in CP2K changes total energy in CP2K. total energy of Gaussian is -9143.41735963 and for CP2K is -9142.9538484165. About memory, you are right. I forgot to increase it in CP2K. You can see the output of Gaussian as attached file. On Friday, February 17, 2017 at 2:25:42 PM UTC+3:30, jgh wrote:Hi from your output one can see that your settings (no input to confirm) are far from optimal. I'm also sure you didn't use the same tight settings in your Gaussian calculations. three obvious points: - no screening of integrals (10^-16) - recalculation of almost all integrals (not enough memory allocated) - very tight SCF convergence and non-optimal OT settings (your BLYP ? calculation could converge 10 times faster) regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Reza Sent by: cp... at googlegroups.com Date: 02/17/2017 10:48AM Subject: Re: [CP2K:8706] Libinit compilation Dear Juerg; Thank you for your answer. I calculated nearly the same job for Gaussian09 and CP2K for C240 molecule (contains 240 carbon atom). For BLYP, wall clock times of Gaussian09 and CP2K are similar (about 20min), but for hybrid methods such as PBE0 and B3LYP, the wall clock times are very different. For Gaussian09, PBE0 time is about 40 min, and B3LYP is about 45 min, but? for CP2K, PBE0 two cycles of SCF needs 96 min!!!!. It needs at least 10 cycles to SCF to be converged. Please see the attached files. I think this is because I didn't use parallel compiling for Libint (googling doesn't show any parallel compiling for Libint). Thanks again. On Friday, February 17, 2017 at 12:37:35 PM UTC+3:30, jgh wrote:Hi without more information I will have to guess: this is most likely NOT a libint problem. Doing a basic PBE0 calculation will cost you about 10 times more than a PBE calculation. Now, if you didn't have enough memory (check the output) this will be even longer. The settings of the HFX part are also crucial for performance (screening). regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Reza Sent by: cp... at googlegroups.com Date: 02/17/2017 07:44AM Subject: [CP2K:8704] Libinit compilation Dear Users, I have compile libint and linked it in cp2k ssmp and psmp versions. I used ifort, icc, icpc of intel. speed of GGA BLYP method for fullerene (C240 molecule in 30*30*30 box) is good, but when I use PBE0, a hybrid method, speed is very low. Is it possible to compile libint with mpicc? I think libint should be very fast for HFX, but my performance is very low. I used 6-31G** basis set for C atoms in C240. -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. [attachment "C240_6_31Gxx_SCF_Conv_blyp.inp" removed by J?rg Hutter/at/UZH] [attachment "C240_6_31Gxx_SCF_Conv_blyp_cpu40_psmp_mpirun_Good_Perf.out" removed by J?rg Hutter/at/UZH] [attachment "C240_6_31Gxx_2SCF_40cpu_ssmp_Bad_Perf.out" removed by J?rg Hutter/at/UZH] -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. From hut... at chem.uzh.ch Fri Feb 17 18:02:38 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Fri, 17 Feb 2017 19:02:38 +0100 Subject: [CP2K:8708] Libinit compilation In-Reply-To: References: , <4eb14ada-2833-4cc8-b70e-c0646e2b3426@googlegroups.com>,> Message-ID: Hi the comparison of total energies with such small basis sets can be tricky. You need to tune some of the GAPW specific variables in the input. However, the first thing you have to do, is to use the same basis set in both calculation. In Gaussian you are using the basis with 6d functions, CP2K uses always spherical basis functions (5d). see total number of basis functions 3600 vs 3360. regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Reza Sent by: cp... at googlegroups.com Date: 02/17/2017 06:18PM Subject: Re: [CP2K:8708] Libinit compilation Hi again, I have set parameters to obtain the same total energy to the Gaussian, as could as possible. the change of total energy in the last SCF converged in Gaussian is about 5*10(-9) and for CP2K is 8*10(-9). the grid of Gaussian is 75 for radial and 302 for angular point. Setting lower or higher cutoff of grids in CP2K changes total energy in CP2K. total energy of Gaussian is -9143.41735963 and for CP2K is -9142.9538484165. About memory, you are right. I forgot to increase it in CP2K. You can see the output of Gaussian as attached file. On Friday, February 17, 2017 at 2:25:42 PM UTC+3:30, jgh wrote:Hi from your output one can see that your settings (no input to confirm) are far from optimal. I'm also sure you didn't use the same tight settings in your Gaussian calculations. three obvious points: - no screening of integrals (10^-16) - recalculation of almost all integrals (not enough memory allocated) - very tight SCF convergence and non-optimal OT settings (your BLYP ? calculation could converge 10 times faster) regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Reza Sent by: cp... at googlegroups.com Date: 02/17/2017 10:48AM Subject: Re: [CP2K:8706] Libinit compilation Dear Juerg; Thank you for your answer. I calculated nearly the same job for Gaussian09 and CP2K for C240 molecule (contains 240 carbon atom). For BLYP, wall clock times of Gaussian09 and CP2K are similar (about 20min), but for hybrid methods such as PBE0 and B3LYP, the wall clock times are very different. For Gaussian09, PBE0 time is about 40 min, and B3LYP is about 45 min, but? for CP2K, PBE0 two cycles of SCF needs 96 min!!!!. It needs at least 10 cycles to SCF to be converged. Please see the attached files. I think this is because I didn't use parallel compiling for Libint (googling doesn't show any parallel compiling for Libint). Thanks again. On Friday, February 17, 2017 at 12:37:35 PM UTC+3:30, jgh wrote:Hi without more information I will have to guess: this is most likely NOT a libint problem. Doing a basic PBE0 calculation will cost you about 10 times more than a PBE calculation. Now, if you didn't have enough memory (check the output) this will be even longer. The settings of the HFX part are also crucial for performance (screening). regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Reza Sent by: cp... at googlegroups.com Date: 02/17/2017 07:44AM Subject: [CP2K:8704] Libinit compilation Dear Users, I have compile libint and linked it in cp2k ssmp and psmp versions. I used ifort, icc, icpc of intel. speed of GGA BLYP method for fullerene (C240 molecule in 30*30*30 box) is good, but when I use PBE0, a hybrid method, speed is very low. Is it possible to compile libint with mpicc? I think libint should be very fast for HFX, but my performance is very low. I used 6-31G** basis set for C atoms in C240. -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. [attachment "C240_6_31Gxx_SCF_Conv_blyp.inp" removed by J?rg Hutter/at/UZH] [attachment "C240_6_31Gxx_SCF_Conv_blyp_cpu40_psmp_mpirun_Good_Perf.out" removed by J?rg Hutter/at/UZH] [attachment "C240_6_31Gxx_2SCF_40cpu_ssmp_Bad_Perf.out" removed by J?rg Hutter/at/UZH] -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. [attachment "Fullerene_C240_BLYP.log" removed by J?rg Hutter/at/UZH] From reza.... at gmail.com Fri Feb 17 18:07:22 2017 From: reza.... at gmail.com (Reza) Date: Fri, 17 Feb 2017 10:07:22 -0800 (PST) Subject: Libinit compilation In-Reply-To: References: Message-ID: Dear my friends Thank you very much for your kindness and time to guide me. I tested ORCA, Gamess-US, Gaussian09, NWChem, CP2K, FHI-aims for PBE0 (hybrid) calculation of C240 with nearly similar parameters (same basis sets, grid, ...). The Fastest Code is Gaussian till now. It is welcomed an optimized input to test CP2K speed. total energy of SCF-converged calculation should be the same (-9143 Hartree). -------------- next part -------------- An HTML attachment was scrubbed... URL: From reza.... at gmail.com Fri Feb 17 18:11:03 2017 From: reza.... at gmail.com (Reza) Date: Fri, 17 Feb 2017 10:11:03 -0800 (PST) Subject: [CP2K:8708] Libinit compilation In-Reply-To: References: ,> <4eb14ada-2833-4cc8-b70e-c0646e2b3426@googlegroups.com>,> Message-ID: <42350666-06c0-490b-9843-eda034fd75f7@googlegroups.com> Dear Juerg, Yes, CP2K is similar to Gamess-US which prefers spherical basis sets. But I am a user, and it is difficult to change the source code. I compare the codes as is. the comparison of total energies with such small basis sets > can be tricky. You need to tune some of the GAPW specific > variables in the input. > > However, the first thing you have to do, is to use the same basis > set in both calculation. In Gaussian you are using the basis with > 6d functions, CP2K uses always spherical basis functions (5d). > > see total number of basis functions 3600 vs 3360. > > regards > > Juerg > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From reza.... at gmail.com Fri Feb 17 18:21:48 2017 From: reza.... at gmail.com (Reza) Date: Fri, 17 Feb 2017 10:21:48 -0800 (PST) Subject: [CP2K:8708] Libinit compilation In-Reply-To: <42350666-06c0-490b-9843-eda034fd75f7@googlegroups.com> References: ,> <4eb14ada-2833-4cc8-b70e-c0646e2b3426@googlegroups.com>,> <42350666-06c0-490b-9843-eda034fd75f7@googlegroups.com> Message-ID: How should I increase "MEMORY" to save integrals in RAM? What is the keyword? I uses 40 cpu and 140GB RAM: nearly 4G per core. -------------- next part -------------- An HTML attachment was scrubbed... URL: From manoo... at gmail.com Fri Feb 17 21:18:28 2017 From: manoo... at gmail.com (Babgen Manookian) Date: Fri, 17 Feb 2017 13:18:28 -0800 (PST) Subject: Isolated system Geometry Optimizations In-Reply-To: <1a744090-32fc-4286-a8ff-a32fbcb27c07@googlegroups.com> References: <1a744090-32fc-4286-a8ff-a32fbcb27c07@googlegroups.com> Message-ID: <1c927d4b-0f91-49b5-a976-80b9316e1ccd@googlegroups.com> Hey Juerg, Thank you so much for the reply. I re-converged my cutoff values for the larger cell size and found that 400Ry and 80Ry produce energies which have much less deviation. What I do notice is that there is still the oscillation of the energy as the cell size changes. Is there a reason for this oscillation occurring? My thoughts on this are that the planewaves are being cut at the cell wall at different values as the cell size changes which in turn causes the energy to oscillate. I would imagine if I could force the calculation to set the density equal to zero at the cell wall then there would be no oscillation. I am not sure if this reasoning is correct. Bobby On Tuesday, February 14, 2017 at 1:21:43 PM UTC-5, Babgen Manookian wrote: > > Hey Everyone, > > I am a new cp2k user and have been working on a test system in order to > get a feel for how the program works. My test system is a cyclohexane > molecule and I am interested in determining the energy difference between > boat and chair conformations. I am using a wavelet poisson solver with > periodicity turned off and the molecule centered in the cell. I attached > the template input file which I used to create the different inputs with > varying cells size. > > What I have noticed is that as I increase my cell size the energy does not > converge on a single value, instead it seems to oscillate. The graphs below > show the energies of each conformation and their differences as functions > of cell size. I am very curious as to what is causing these oscillations. > If I have a single cyclohexane molecule centered in my cell, as I increase > my cell size, I would think that the extra vacuum space around the molecule > will not affect the energy. > > If there is anyone out there who could provide any sort of input on this > it would be much appreciated. > > Thanks, > Bobby > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mattwa... at gmail.com Fri Feb 17 21:48:40 2017 From: mattwa... at gmail.com (Matt W) Date: Fri, 17 Feb 2017 13:48:40 -0800 (PST) Subject: Libinit compilation In-Reply-To: References: Message-ID: Hi, just a general note: you do need to be quite careful running performance tests. It can easily be that your test is not representative of the systems you are are going to run in practice. Whilst all these codes will run this C-240 system. It may be that their ability to use symmetry, run 3D periodic systems, scalability to large number of processors and other factors, such as local knowledge to get help, are going to vary a lot. Depending on what you need for the whole of your project, just seeing which one runs this system fastest might not be a very sensible cost function. Matt On Friday, February 17, 2017 at 6:07:22 PM UTC, Reza wrote: > > Dear my friends > Thank you very much for your kindness and time to guide me. > > I tested ORCA, Gamess-US, Gaussian09, NWChem, CP2K, FHI-aims for PBE0 > (hybrid) calculation of C240 with nearly similar parameters (same basis > sets, grid, ...). The Fastest Code is Gaussian till now. It is welcomed an > optimized input to test CP2K speed. total energy of SCF-converged > calculation should be the same (-9143 Hartree). > -------------- next part -------------- An HTML attachment was scrubbed... URL: From reza.... at gmail.com Sat Feb 18 03:54:46 2017 From: reza.... at gmail.com (Reza) Date: Fri, 17 Feb 2017 19:54:46 -0800 (PST) Subject: Libinit compilation In-Reply-To: References: Message-ID: <8c7e8f85-b379-411d-93c9-7ff0884c7bac@googlegroups.com> Dear Matt Yes, Symm can affect performance. I think software in conjunction with hardware is very important. For a big cluster, the best code is different from a SMP. Every one should test what is the best choose for his system/network. I agree that other things are also important in choosing the code, but speed is also very important. Some codes run very fast on SMP, but have very bad performance on big clusters. My test was for 40 core SMP. At first of this discussion,I guessed that the large different time between GGA and Hybrid goes to libint compilation. Note that this difference is very higher than 10 times!!!! See former files for 2scf cycle and optimized scf blyp. From reza.... at gmail.com Sat Feb 18 04:00:41 2017 From: reza.... at gmail.com (Reza) Date: Fri, 17 Feb 2017 20:00:41 -0800 (PST) Subject: Libinit compilation In-Reply-To: <8c7e8f85-b379-411d-93c9-7ff0884c7bac@googlegroups.com> References: <8c7e8f85-b379-411d-93c9-7ff0884c7bac@googlegroups.com> Message-ID: One more thing:Is it possible to retain point group symmetry during geometry optimization for molecular systems in CP2K? From ari.p.s... at gmail.com Sat Feb 18 15:49:30 2017 From: ari.p.s... at gmail.com (Ari Paavo Seitsonen) Date: Sat, 18 Feb 2017 16:49:30 +0100 Subject: [CP2K:8664] Re: Comparison between CP2K and Quantum Espresso In-Reply-To: References: <0ffff976-c924-4c83-ad18-1b2fe2ecbe91@googlegroups.com> Message-ID: Dear Tommaso and David, I would definitely _not_ call using Vanderbilt pseudo potentials as having "minimal basis set", usually the precision is better than with norm-conserving pseudo potentials (due to several reference energies/projectors). The reduction of cut-off is due to a good reason. So lowering the basis set in CP2K would be unfair, as the results are of lower precision. Rather using GAPW (instead of GPW) would have kind-of the same effect, as this would allow a lower cut-off energy being used in the plane wave part of QuickStep. The idea of shifting the k point might refer to the scheme of Baldereschi's special point (I do not know much, I was just told that this is the "best" point if using a single point; since most people do not know it and Monkhorst-Pack is so "black box"-convenient, younger generations have probably not become users of it). Just my guess. Greetings from Paris, apsi 2017-02-08 11:28 GMT+01:00 : > Dear David, > first of all thanks a lot for your very useful comments. > > I will benchmark my system in CP2K with a lower basis sets, in order to > test again the parameters and to have better reference with respect to QE. > > Regarding the compilation of the program in our cluster, I think that it > is the pitfall and that our technician missed something. He told me ( > because I am not allowed to install anything, but only the technician ) > that he compiled the precompiled version of CP2K. But I am pretty sure he > missed some of the libraries you listed above. Indeed I am insisting in a > more "serious" compilation of the program, that we wanna massively exploit > for our dynamics. > > Regarding the single point shift from the gamma point in QE, that was > suggested by one of my old Professors. At that time ( almost three years > ago) he told us that the shift is recommended. > I always used that setting, without honestly taking care too much about > the change in performances. By the way, thanks a lot for the really useful > hints. Now I will re-benchemark the new machine testing several levels of > theory as you suggested. > > Best Regards, > Tommaso Francese > > Il giorno mercoled? 8 febbraio 2017 11:09:16 UTC+1, David T ha scritto: >> >> Hi Tommaso >> >> as you I am more expert on QE and only recently moved on CP2K. >> On my experience CP2K is much more quicker and allows to work with bigger >> systems that planewave code could not afford. On the other hand it is true >> that this is really system depended so the fact that for nano-porous >> material CP2K is more efficient could not be true for other systems. >> After having read the inputs a comment I can give to you is that you are >> probably not making a fair comparison. >> I've see you use ultrasoft pseudo which allows a very low cut-off and can >> be "though" as minimal basis-set. So you should probably use some >> corresponding low basis-set in CP2K (for instance a dobule zera instead of >> triple zeta). >> >> Probably more important another thing I can tell you is that I've seen >> that if CP2K is not properly compiled, its performance can be slow. For >> instance my own version with mpi, mkl, libxsmm and elpa is about 30% faster >> than the standard one I found on our cluster. >> Moreover the speediness of the code can be further boosted if you use >> also GPU and hybrid openMP-MPI. >> >> P.S. a curiosity, in QE why are you using a single point shifted from >> gamma? if there is not a major reason using the gamma algorithm on QE can >> accelerate you calc up to 30% >> > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.S... at iki.fi / http://www.iki.fi/~apsi/ Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jian... at gmail.com Sun Feb 19 02:14:53 2017 From: jian... at gmail.com (jian... at gmail.com) Date: Sat, 18 Feb 2017 18:14:53 -0800 (PST) Subject: Some problems in DFT-MD Message-ID: <472a57f6-705e-41c0-a68b-9552a94ed66c@googlegroups.com> Dear all, When I do a DFT-MD simulation, there are some problems, 1. In NVT ensemble, when I do MD, the simulation stop after 40-90 steps. When I open the output file, the calculation stops at an electronic step, Such as: SCF WAVEFUNCTION OPTIMIZATION Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ 1 Broy./Diag. 0.40E+00 0.7 0.14977302 -2040.1579823603 -2.04E+03 2 Broy./Diag. 0.40E+00 0.8 0.70593320 -2040.2840422664 -1.26E-01 3 Broy./Diag. 0.40E+00 0.8 0.65580185 -2037.4293129009 2.85E+00 4 Broy./Diag. 0.40E+00 0.8 0.37555503 -2040.5915369715 -3.16E+00 5 Broy./Diag. 0.40E+00 0.8 0.47252064 -2040.4903662017 1.01E-01 6 Broy./Diag. 0.40E+00 0.9 0.39094220 -2040.2208346612 2.70E-01 And then the calculation stop at this step. 2. The temperature in the MD simulation (NVT ensemble) cannot be controlled. Such as, the wanted temperature is 2413 K, but deceases in the MD simulation. The input file: &GLOBAL PROJECT 27o2 RUN_TYPE MD PRINT_LEVEL LOW &END GLOBAL &MOTION &PRINT &VELOCITIES &EACH MD 1 &END EACH &END VELOCITIES &STRESS &EACH MD 1 &END EACH &END STRESS &END PRINT &MD ENSEMBLE NVT STEPS 8000 TIMESTEP 0.5 TEMPERATURE 2413 &THERMOSTAT REGION GLOBAL TYPE NOSE &NOSE LENGTH 3 TIMECON 10.0 &END &END &END MD &END MOTION &FORCE_EVAL METHOD Quickstep STRESS_TENSOR ANALYTICAL &DFT BASIS_SET_FILE_NAME ../../cp2k-4.1/data/BASIS_SET POTENTIAL_FILE_NAME ../../cp2k-4.1/data/POTENTIAL MULTIPLICITY 1 &MGRID CUTOFF 300 NGRIDS 4 REL_CUTOFF 40 &END MGRID &PRINT &MO EIGENVALUES OCCUPATION_NUMBERS &EACH QS_SCF 0 &END EACH &END MO &END PRINT &QS EPS_DEFAULT 1.0E-10 EPS_GVG 1.0E-5 EPS_PGF_ORB 1.0E-5 &END QS &SCF #CHOLESKY INVERSE MAX_SCF 200 ADDED_MOS 200 SCF_GUESS atomic EPS_SCF 1.00E-05 &SMEAR ON METHOD FERMI_DIRAC ELECTRONIC_TEMPERATURE 2413 &END SMEAR # &DIAGONALIZATION # ALGORITHM STANDARD # &END DIAGONALIZATION &MIXING METHOD BROYDEN_MIXING ALPHA 0.4 BETA 0.5 NBROYDEN 18 # METHOD PULAY_MIXING # ALPHA 0.4 # BETA 0.5 # NPULAY 8 # PULAY_ALPHA 0.0 &END MIXING &END SCF &XC &XC_FUNCTIONAL PBE &END XC_FUNCTIONAL &END XC &END DFT &SUBSYS &KIND O BASIS_SET DZVP-GTH-PBE POTENTIAL GTH-PBE-q6 &END &CELL ABC 8.30995 8.30995 8.30995 &END CELL &COORD SCALED O 0.20905 0.20905 0.20905 O 0.20905 0.20905 0.54238 O 0.20905 0.20905 0.87571 O 0.20905 0.54238 0.20905 O 0.20905 0.54238 0.54238 O 0.20905 0.54238 0.87571 O 0.20905 0.87571 0.20905 O 0.20905 0.87571 0.54238 O 0.20905 0.87571 0.87571 O 0.54238 0.20905 0.20905 O 0.54238 0.20905 0.54238 O 0.54238 0.20905 0.87571 O 0.54238 0.54238 0.20905 O 0.54238 0.54238 0.54238 O 0.54238 0.54238 0.87571 O 0.54238 0.87571 0.20905 O 0.54238 0.87571 0.54238 O 0.54238 0.87571 0.87571 O 0.87571 0.20905 0.20905 O 0.87571 0.20905 0.54238 O 0.87571 0.20905 0.87571 O 0.87571 0.54238 0.20905 O 0.87571 0.54238 0.54238 O 0.87571 0.54238 0.87571 O 0.87571 0.87571 0.20905 O 0.87571 0.87571 0.54238 O 0.87571 0.87571 0.87571 O 0.12429 0.12429 0.12429 O 0.12429 0.12429 0.45762 O 0.12429 0.12429 0.79095 O 0.12429 0.45762 0.12429 O 0.12429 0.45762 0.45762 O 0.12429 0.45762 0.79095 O 0.12429 0.79095 0.12429 O 0.12429 0.79095 0.45762 O 0.12429 0.79095 0.79095 O 0.45762 0.12429 0.12429 O 0.45762 0.12429 0.45762 O 0.45762 0.12429 0.79095 O 0.45762 0.45762 0.12429 O 0.45762 0.45762 0.45762 O 0.45762 0.45762 0.79095 O 0.45762 0.79095 0.12429 O 0.45762 0.79095 0.45762 O 0.45762 0.79095 0.79095 O 0.79095 0.12429 0.12429 O 0.79095 0.12429 0.45762 O 0.79095 0.12429 0.79095 O 0.79095 0.45762 0.12429 O 0.79095 0.45762 0.45762 O 0.79095 0.45762 0.79095 O 0.79095 0.79095 0.12429 O 0.79095 0.79095 0.45762 O 0.79095 0.79095 0.79095 &END COORD &END SUBSYS &END FORCE_EVAL Could you give me some advice? Best regards, ZJ. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tfran... at gmail.com Sun Feb 19 07:45:07 2017 From: tfran... at gmail.com (Tommaso Francese) Date: Sun, 19 Feb 2017 08:45:07 +0100 Subject: [CP2K:8719] Comparison between CP2K and Quantum Espresso In-Reply-To: References: <0ffff976-c924-4c83-ad18-1b2fe2ecbe91@googlegroups.com> Message-ID: Dear Apsi, thanks for the reply. I will take into considerations also your suggestions! Best, Tommaso > Il giorno 18 feb 2017, alle ore 16:49, Ari Paavo Seitsonen ha scritto: > > Dear Tommaso and David, > > I would definitely _not_ call using Vanderbilt pseudo potentials as having "minimal basis set", usually the precision is better than with norm-conserving pseudo potentials (due to several reference energies/projectors). The reduction of cut-off is due to a good reason. So lowering the basis set in CP2K would be unfair, as the results are of lower precision. Rather using GAPW (instead of GPW) would have kind-of the same effect, as this would allow a lower cut-off energy being used in the plane wave part of QuickStep. > > The idea of shifting the k point might refer to the scheme of Baldereschi's special point (I do not know much, I was just told that this is the "best" point if using a single point; since most people do not know it and Monkhorst-Pack is so "black box"-convenient, younger generations have probably not become users of it). Just my guess. > > Greetings from Paris, > > apsi > > 2017-02-08 11:28 GMT+01:00 >: > Dear David, > first of all thanks a lot for your very useful comments. > > I will benchmark my system in CP2K with a lower basis sets, in order to test again the parameters and to have better reference with respect to QE. > > Regarding the compilation of the program in our cluster, I think that it is the pitfall and that our technician missed something. He told me ( because I am not allowed to install anything, but only the technician ) that he compiled the precompiled version of CP2K. But I am pretty sure he missed some of the libraries you listed above. Indeed I am insisting in a more "serious" compilation of the program, that we wanna massively exploit for our dynamics. > > Regarding the single point shift from the gamma point in QE, that was suggested by one of my old Professors. At that time ( almost three years ago) he told us that the shift is recommended. > I always used that setting, without honestly taking care too much about the change in performances. By the way, thanks a lot for the really useful hints. Now I will re-benchemark the new machine testing several levels of theory as you suggested. > > Best Regards, > Tommaso Francese > > Il giorno mercoled? 8 febbraio 2017 11:09:16 UTC+1, David T ha scritto: > Hi Tommaso > > as you I am more expert on QE and only recently moved on CP2K. > On my experience CP2K is much more quicker and allows to work with bigger systems that planewave code could not afford. On the other hand it is true that this is really system depended so the fact that for nano-porous material CP2K is more efficient could not be true for other systems. > After having read the inputs a comment I can give to you is that you are probably not making a fair comparison. > I've see you use ultrasoft pseudo which allows a very low cut-off and can be "though" as minimal basis-set. So you should probably use some corresponding low basis-set in CP2K (for instance a dobule zera instead of triple zeta). > > Probably more important another thing I can tell you is that I've seen that if CP2K is not properly compiled, its performance can be slow. For instance my own version with mpi, mkl, libxsmm and elpa is about 30% faster than the standard one I found on our cluster. > Moreover the speediness of the code can be further boosted if you use also GPU and hybrid openMP-MPI. > > P.S. a curiosity, in QE why are you using a single point shifted from gamma? if there is not a major reason using the gamma algorithm on QE can accelerate you calc up to 30% > > -- > You received this message because you are subscribed to the Google Groups "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com . > To post to this group, send email to cp... at googlegroups.com . > Visit this group at https://groups.google.com/group/cp2k . > For more options, visit https://groups.google.com/d/optout . > > > > -- > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari Paavo Seitsonen / Ari.P.S... at iki.fi / http://www.iki.fi/~apsi/ > Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris > Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935 > > -- > You received this message because you are subscribed to a topic in the Google Groups "cp2k" group. > To unsubscribe from this topic, visit https://groups.google.com/d/topic/cp2k/YXGli4aI2kw/unsubscribe . > To unsubscribe from this group and all its topics, send an email to cp2k+uns... at googlegroups.com . > To post to this group, send email to cp... at googlegroups.com . > Visit this group at https://groups.google.com/group/cp2k . > For more options, visit https://groups.google.com/d/optout . -------------- next part -------------- An HTML attachment was scrubbed... URL: From ari.p.s... at gmail.com Sun Feb 19 09:57:20 2017 From: ari.p.s... at gmail.com (Ari Paavo Seitsonen) Date: Sun, 19 Feb 2017 10:57:20 +0100 Subject: [CP2K:8721] Some problems in DFT-MD In-Reply-To: <472a57f6-705e-41c0-a68b-9552a94ed66c@googlegroups.com> References: <472a57f6-705e-41c0-a68b-9552a94ed66c@googlegroups.com> Message-ID: Dear Zhifu Jian, I see some problems in your simulation: Why the calculation stops, well could be a problem on your setup; I do not see a reason CP2K to stop otherwise. Is there any other output, for example from the queueing system that could hint the reason for stopping? Does the electronic structure converge? If not, I would go for smaller value of 'ALPHA'. Your basis set is quite small, value for 'EPS_DEFAULT' quite large (usually 1e-14 or so). Are 200 added states enough, with the large broadening that you are using? You do not seem to include spin-polarisation in the calculation, is that intentional? The time constant in the Nos?-Hoover is very short, probably leading to difficulties in keeping the average temperature ('CSVR' is better in cases when asking for very fast equilibration). Greetings from Paris, apsi 2017-02-19 2:46 GMT+01:00 : > Dear all, > > When I do a DFT-MD simulation, there are some problems, > > 1. In NVT ensemble, when I do MD, the simulation stop after 40-50 steps. > When I open the output file, the calculation stops at an electronic step, > > Such as: > > SCF WAVEFUNCTION OPTIMIZATION > > > > Step Update method Time Convergence Total energy > Change > > ------------------------------------------------------------ > ------------------ > > 1 Broy./Diag. 0.40E+00 0.7 0.14977302 -2040.1579823603 > -2.04E+03 > > 2 Broy./Diag. 0.40E+00 0.8 0.70593320 -2040.2840422664 > -1.26E-01 > > 3 Broy./Diag. 0.40E+00 0.8 0.65580185 -2037.4293129009 > 2.85E+00 > > 4 Broy./Diag. 0.40E+00 0.8 0.37555503 -2040.5915369715 > -3.16E+00 > > 5 Broy./Diag. 0.40E+00 0.8 0.47252064 -2040.4903662017 > 1.01E-01 > > 6 Broy./Diag. 0.40E+00 0.9 0.39094220 -2040.2208346612 > 2.70E-01 > > > > And then the calculation stop at this step. > > > > 2. The temperature in the MD simulation (NVT ensemble) cannot be > controlled. Such as, the wanted temperature is 2413 K, but deceases in the > MD simulation. > > > > > > The input file: > > &GLOBAL > > PROJECT 27o2 > > RUN_TYPE MD > > PRINT_LEVEL LOW > > &END GLOBAL > > > > &MOTION > > &PRINT > > &VELOCITIES > > &EACH > > MD 1 > > &END EACH > > &END VELOCITIES > > &STRESS > > &EACH > > MD 1 > > &END EACH > > &END STRESS > > &END PRINT > > &MD > > ENSEMBLE NVT > > STEPS 8000 > > TIMESTEP 0.5 > > TEMPERATURE 2413 > > &THERMOSTAT > > REGION GLOBAL > > TYPE NOSE > > &NOSE > > LENGTH 3 > > TIMECON 10.0 > > &END > > &END > > &END MD > > &END MOTION > > > > &FORCE_EVAL > > METHOD Quickstep > > STRESS_TENSOR ANALYTICAL > > &DFT > > BASIS_SET_FILE_NAME ../../cp2k-4.1/data/BASIS_SET > > POTENTIAL_FILE_NAME ../../cp2k-4.1/data/POTENTIAL > > MULTIPLICITY 1 > > &MGRID > > CUTOFF 300 > > NGRIDS 4 > > REL_CUTOFF 40 > > &END MGRID > > &PRINT > > &MO > > EIGENVALUES > > OCCUPATION_NUMBERS > > &EACH > > QS_SCF 0 > > &END EACH > > &END MO > > &END PRINT > > &QS > > EPS_DEFAULT 1.0E-10 > > EPS_GVG 1.0E-5 > > EPS_PGF_ORB 1.0E-5 > > &END QS > > &SCF > > #CHOLESKY INVERSE > > MAX_SCF 200 > > ADDED_MOS 200 > > SCF_GUESS atomic > > EPS_SCF 1.00E-05 > > &SMEAR ON > > METHOD FERMI_DIRAC > > ELECTRONIC_TEMPERATURE 2413 > > &END SMEAR > > # &DIAGONALIZATION > > # ALGORITHM STANDARD > > # &END DIAGONALIZATION > > &MIXING > > METHOD BROYDEN_MIXING > > ALPHA 0.4 > > BETA 0.5 > > NBROYDEN 18 > > # METHOD PULAY_MIXING > > # ALPHA 0.4 > > # BETA 0.5 > > # NPULAY 8 > > # PULAY_ALPHA 0.0 > > &END MIXING > > &END SCF > > &XC > > &XC_FUNCTIONAL PBE > > &END XC_FUNCTIONAL > > &END XC > > &END DFT > > &SUBSYS > > &KIND O > > BASIS_SET DZVP-GTH-PBE > > POTENTIAL GTH-PBE-q6 > > > &END > > &CELL > > ABC 8.30995 8.30995 8.30995 > > &END CELL > > &COORD > > SCALED > > O 0.20905 0.20905 0.20905 > > O 0.20905 0.20905 0.54238 > > O 0.20905 0.20905 0.87571 > > O 0.20905 0.54238 0.20905 > > O 0.20905 0.54238 0.54238 > > O 0.20905 0.54238 0.87571 > > O 0.20905 0.87571 0.20905 > > O 0.20905 0.87571 0.54238 > > O 0.20905 0.87571 0.87571 > > O 0.54238 0.20905 0.20905 > > O 0.54238 0.20905 0.54238 > > O 0.54238 0.20905 0.87571 > > O 0.54238 0.54238 0.20905 > > O 0.54238 0.54238 0.54238 > > O 0.54238 0.54238 0.87571 > > O 0.54238 0.87571 0.20905 > > O 0.54238 0.87571 0.54238 > > O 0.54238 0.87571 0.87571 > > O 0.87571 0.20905 0.20905 > > O 0.87571 0.20905 0.54238 > > O 0.87571 0.20905 0.87571 > > O 0.87571 0.54238 0.20905 > > O 0.87571 0.54238 0.54238 > > O 0.87571 0.54238 0.87571 > > O 0.87571 0.87571 0.20905 > > O 0.87571 0.87571 0.54238 > > O 0.87571 0.87571 0.87571 > > O 0.12429 0.12429 0.12429 > > O 0.12429 0.12429 0.45762 > > O 0.12429 0.12429 0.79095 > > O 0.12429 0.45762 0.12429 > > O 0.12429 0.45762 0.45762 > > O 0.12429 0.45762 0.79095 > > O 0.12429 0.79095 0.12429 > > O 0.12429 0.79095 0.45762 > > O 0.12429 0.79095 0.79095 > > O 0.45762 0.12429 0.12429 > > O 0.45762 0.12429 0.45762 > > O 0.45762 0.12429 0.79095 > > O 0.45762 0.45762 0.12429 > > O 0.45762 0.45762 0.45762 > > O 0.45762 0.45762 0.79095 > > O 0.45762 0.79095 0.12429 > > O 0.45762 0.79095 0.45762 > > O 0.45762 0.79095 0.79095 > > O 0.79095 0.12429 0.12429 > > O 0.79095 0.12429 0.45762 > > O 0.79095 0.12429 0.79095 > > O 0.79095 0.45762 0.12429 > > O 0.79095 0.45762 0.45762 > > O 0.79095 0.45762 0.79095 > > O 0.79095 0.79095 0.12429 > > O 0.79095 0.79095 0.45762 > > O 0.79095 0.79095 0.79095 > > &END COORD > > &END SUBSYS > > &END FORCE_EVAL > > > Could you give me some advice? > > Best regards, > > ZJ. > > > > > > > > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+uns... at googlegroups.com. > To post to this group, send email to cp... at googlegroups.com. > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.S... at iki.fi / http://www.iki.fi/~apsi/ Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jian... at gmail.com Mon Feb 20 01:42:57 2017 From: jian... at gmail.com (jian... at gmail.com) Date: Sun, 19 Feb 2017 17:42:57 -0800 (PST) Subject: [CP2K:8721] Some problems in DFT-MD In-Reply-To: References: <472a57f6-705e-41c0-a68b-9552a94ed66c@googlegroups.com> Message-ID: Dear Ari Paavo Seitsonen, *Why the calculation stops, well could be a problem on your setup; I do not see a reason CP2K to stop otherwise. Is there any other output, for example from the queueing system that could hint the reason for stopping?* I have some output files (in the attachment), and no queueing system, I use a single machine with 24CPU for calculation. *Does the electronic structure converge? If not, I would go for smaller value of 'ALPHA'. Your basis set is quite small, value for 'EPS_DEFAULT' quite large (usually 1e-14 or so).* The electronic structure converged (I have used the same parameters by VASP, and there is no problem). I have used the small ALPHA=0.1, changed basis set with PADE, EPS_DEFAULT=1E-14, but the CP2K simulations stops at 97 steps. So by CTRL-C terminated the calculation. *Are 200 added states enough, with the large broadening that you are using? You do not seem to include spin-polarisation in the calculation, is that intentional?* Yes, 200 added states are enough by the occupation number output. Yes, I don?t open the spin-polarization in the calculation. *The time constant in the Nos?-Hoover is very short, probably leading to difficulties in keeping the average temperature ('CSVR' is better in cases when asking for very fast equilibration).* CSVR replaced the Nose-Hoover method, and the time constant set 1000, but the calculation still stop at 97 steps and the average temperature is lower than I set. By the way, how to choose an appropriate basis set? From the basis_set file, there are only several basis set. And the basis set can be constructed by myself? Best regards, ZJ. ? 2017?2?19???? UTC+8??5:57:21?Ari Paavo Seitsonen??? > > Dear Zhifu Jian, > > I see some problems in your simulation: Why the calculation stops, well > could be a problem on your setup; I do not see a reason CP2K to stop > otherwise. Is there any other output, for example from the queueing system > that could hint the reason for stopping? > > Does the electronic structure converge? If not, I would go for smaller > value of 'ALPHA'. Your basis set is quite small, value for 'EPS_DEFAULT' > quite large (usually 1e-14 or so). Are 200 added states enough, with the > large broadening that you are using? You do not seem to include > spin-polarisation in the calculation, is that intentional? The time > constant in the Nos?-Hoover is very short, probably leading to difficulties > in keeping the average temperature ('CSVR' is better in cases when asking > for very fast equilibration). > > Greetings from Paris, > > apsi > > 2017-02-19 2:46 GMT+01:00 >: > >> Dear all, >> >> When I do a DFT-MD simulation, there are some problems, >> >> 1. In NVT ensemble, when I do MD, the simulation stop after 40-50 steps. >> When I open the output file, the calculation stops at an electronic step, >> >> Such as: >> >> SCF WAVEFUNCTION OPTIMIZATION >> >> >> >> Step Update method Time Convergence Total energy >> Change >> >> >> ------------------------------------------------------------------------------ >> >> 1 Broy./Diag. 0.40E+00 0.7 0.14977302 -2040.1579823603 >> -2.04E+03 >> >> 2 Broy./Diag. 0.40E+00 0.8 0.70593320 -2040.2840422664 >> -1.26E-01 >> >> 3 Broy./Diag. 0.40E+00 0.8 0.65580185 -2037.4293129009 >> 2.85E+00 >> >> 4 Broy./Diag. 0.40E+00 0.8 0.37555503 -2040.5915369715 >> -3.16E+00 >> >> 5 Broy./Diag. 0.40E+00 0.8 0.47252064 -2040.4903662017 >> 1.01E-01 >> >> 6 Broy./Diag. 0.40E+00 0.9 0.39094220 -2040.2208346612 >> 2.70E-01 >> >> >> >> And then the calculation stop at this step. >> >> >> >> 2. The temperature in the MD simulation (NVT ensemble) cannot be >> controlled. Such as, the wanted temperature is 2413 K, but deceases in the >> MD simulation. >> >> >> >> >> >> The input file: >> >> &GLOBAL >> >> PROJECT 27o2 >> >> RUN_TYPE MD >> >> PRINT_LEVEL LOW >> >> &END GLOBAL >> >> >> >> &MOTION >> >> &PRINT >> >> &VELOCITIES >> >> &EACH >> >> MD 1 >> >> &END EACH >> >> &END VELOCITIES >> >> &STRESS >> >> &EACH >> >> MD 1 >> >> &END EACH >> >> &END STRESS >> >> &END PRINT >> >> &MD >> >> ENSEMBLE NVT >> >> STEPS 8000 >> >> TIMESTEP 0.5 >> >> TEMPERATURE 2413 >> >> &THERMOSTAT >> >> REGION GLOBAL >> >> TYPE NOSE >> >> &NOSE >> >> LENGTH 3 >> >> TIMECON 10.0 >> >> &END >> >> &END >> >> &END MD >> >> &END MOTION >> >> >> >> &FORCE_EVAL >> >> METHOD Quickstep >> >> STRESS_TENSOR ANALYTICAL >> >> &DFT >> >> BASIS_SET_FILE_NAME ../../cp2k-4.1/data/BASIS_SET >> >> POTENTIAL_FILE_NAME ../../cp2k-4.1/data/POTENTIAL >> >> MULTIPLICITY 1 >> >> &MGRID >> >> CUTOFF 300 >> >> NGRIDS 4 >> >> REL_CUTOFF 40 >> >> &END MGRID >> >> &PRINT >> >> &MO >> >> EIGENVALUES >> >> OCCUPATION_NUMBERS >> >> &EACH >> >> QS_SCF 0 >> >> &END EACH >> >> &END MO >> >> &END PRINT >> >> &QS >> >> EPS_DEFAULT 1.0E-10 >> >> EPS_GVG 1.0E-5 >> >> EPS_PGF_ORB 1.0E-5 >> >> &END QS >> >> &SCF >> >> #CHOLESKY INVERSE >> >> MAX_SCF 200 >> >> ADDED_MOS 200 >> >> SCF_GUESS atomic >> >> EPS_SCF 1.00E-05 >> >> &SMEAR ON >> >> METHOD FERMI_DIRAC >> >> ELECTRONIC_TEMPERATURE 2413 >> >> &END SMEAR >> >> # &DIAGONALIZATION >> >> # ALGORITHM STANDARD >> >> # &END DIAGONALIZATION >> >> &MIXING >> >> METHOD BROYDEN_MIXING >> >> ALPHA 0.4 >> >> BETA 0.5 >> >> NBROYDEN 18 >> >> # METHOD PULAY_MIXING >> >> # ALPHA 0.4 >> >> # BETA 0.5 >> >> # NPULAY 8 >> >> # PULAY_ALPHA 0.0 >> >> &END MIXING >> >> &END SCF >> >> &XC >> >> &XC_FUNCTIONAL PBE >> >> &END XC_FUNCTIONAL >> >> &END XC >> >> &END DFT >> >> &SUBSYS >> >> &KIND O >> >> BASIS_SET DZVP-GTH-PBE >> >> POTENTIAL >> GTH-PBE-q6 >> >> &END >> >> &CELL >> >> ABC 8.30995 8.30995 8.30995 >> >> &END CELL >> >> &COORD >> >> SCALED >> >> O 0.20905 0.20905 0.20905 >> >> O 0.20905 0.20905 0.54238 >> >> O 0.20905 0.20905 0.87571 >> >> O 0.20905 0.54238 0.20905 >> >> O 0.20905 0.54238 0.54238 >> >> O 0.20905 0.54238 0.87571 >> >> O 0.20905 0.87571 0.20905 >> >> O 0.20905 0.87571 0.54238 >> >> O 0.20905 0.87571 0.87571 >> >> O 0.54238 0.20905 0.20905 >> >> O 0.54238 0.20905 0.54238 >> >> O 0.54238 0.20905 0.87571 >> >> O 0.54238 0.54238 0.20905 >> >> O 0.54238 0.54238 0.54238 >> >> O 0.54238 0.54238 0.87571 >> >> O 0.54238 0.87571 0.20905 >> >> O 0.54238 0.87571 0.54238 >> >> O 0.54238 0.87571 0.87571 >> >> O 0.87571 0.20905 0.20905 >> >> O 0.87571 0.20905 0.54238 >> >> O 0.87571 0.20905 0.87571 >> >> O 0.87571 0.54238 0.20905 >> >> O 0.87571 0.54238 0.54238 >> >> O 0.87571 0.54238 0.87571 >> >> O 0.87571 0.87571 0.20905 >> >> O 0.87571 0.87571 0.54238 >> >> O 0.87571 0.87571 0.87571 >> >> O 0.12429 0.12429 0.12429 >> >> O 0.12429 0.12429 0.45762 >> >> O 0.12429 0.12429 0.79095 >> >> O 0.12429 0.45762 0.12429 >> >> O 0.12429 0.45762 0.45762 >> >> O 0.12429 0.45762 0.79095 >> >> O 0.12429 0.79095 0.12429 >> >> O 0.12429 0.79095 0.45762 >> >> O 0.12429 0.79095 0.79095 >> >> O 0.45762 0.12429 0.12429 >> >> O 0.45762 0.12429 0.45762 >> >> O 0.45762 0.12429 0.79095 >> >> O 0.45762 0.45762 0.12429 >> >> O 0.45762 0.45762 0.45762 >> >> O 0.45762 0.45762 0.79095 >> >> O 0.45762 0.79095 0.12429 >> >> O 0.45762 0.79095 0.45762 >> >> O 0.45762 0.79095 0.79095 >> >> O 0.79095 0.12429 0.12429 >> >> O 0.79095 0.12429 0.45762 >> >> O 0.79095 0.12429 0.79095 >> >> O 0.79095 0.45762 0.12429 >> >> O 0.79095 0.45762 0.45762 >> >> O 0.79095 0.45762 0.79095 >> >> O 0.79095 0.79095 0.12429 >> >> O 0.79095 0.79095 0.45762 >> >> O 0.79095 0.79095 0.79095 >> >> &END COORD >> >> &END SUBSYS >> >> &END FORCE_EVAL >> >> >> Could you give me some advice? >> >> Best regards, >> >> ZJ. >> >> >> >> >> >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "cp2k" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to cp2k+... at googlegroups.com . >> To post to this group, send email to cp... at googlegroups.com >> . >> Visit this group at https://groups.google.com/group/cp2k. >> For more options, visit https://groups.google.com/d/optout. >> > > > > -- > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari Paavo Seitsonen / Ari.P... at iki.fi / > http://www.iki.fi/~apsi/ > Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris > Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935 > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 27o2_1.tar.gz Type: application/octet-stream Size: 535516 bytes Desc: not available URL: From barak.h... at mail.huji.ac.il Mon Feb 20 09:38:28 2017 From: barak.h... at mail.huji.ac.il (Barak Hirshberg) Date: Mon, 20 Feb 2017 01:38:28 -0800 (PST) Subject: Dispersion energy in different versions of CP2K Message-ID: <5c699144-a795-4001-aab8-4afae79188b4@googlegroups.com> Hello, I want to compare calculations done with different (admittedly old) versions of CP2K. I used an identical input file (attached) for CP2K versions 3.0 and 2.5.1. The simulations are MD runs using the PBE functional with the D3 dispersion correction, the TZV2P basis set and GTH pseudo-potentials. The initial SCF (before taking even one MD step) converges fine and all energy components (Core, Hartree and XC) are very similar between the different versions. The only difference which is significant is dispersion energy term. which is -0.20577238097721 Hartree in the 2.5.1 version and -0.20735192667451 in the 3.0 version. This is despite the fact that I used the exact same parameter file (dftd3.dat attached) for both calculations. I have also attached the relevant parts of the output files. I would really appreciate your help in understanding the origin of the difference. Thanks, Barak -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- DBCSR| Multiplication driver BLAS DBCSR| Multrec recursion limit 512 DBCSR| Multiplication stack size 1000 DBCSR| Maximum elements for images UNLIMITED DBCSR| Randmat seed 12341313 DBCSR| Multiplication size stacks 3 DBCSR| Use MPI memory allocation T DBCSR| Use RMA algorithm F DBCSR| Use Communication thread T DBCSR| Communication thread load 87 **** **** ****** ** PROGRAM STARTED AT 2017-02-14 08:43:08.769 ***** ** *** *** ** PROGRAM STARTED ON comet-18-13.sdsc.edu ** **** ****** PROGRAM STARTED BY barakhi ***** ** ** ** ** PROGRAM PROCESS ID 16791 **** ** ******* ** PROGRAM STARTED IN /scratch/barakhi/7646868 CP2K| version string: CP2K version 3.0 CP2K| source code revision number: svn:16458 CP2K| cp2kflags: libint fftw3 libxc parallel mpi2 scalapack CP2K| is freely available from https://www.cp2k.org/ CP2K| Program compiled at Fri Jun 3 00:46:34 PDT 2016 CP2K| Program compiled on comet-01-65.local CP2K| Program compiled for Linux-x86-64-intel CP2K| Data directory path /state/partition1/git/chemistry-roll/BUILD/sdsc-cp CP2K| Input file name water_slab_N2O5_6A_from_surface_z45A_collision.inp GLOBAL| Force Environment number 1 GLOBAL| Basis set file name GTH_POTENTIALS GLOBAL| MM Potential file name MM_POTENTIAL GLOBAL| Coordinate file name __STD_INPUT__ GLOBAL| Method name CP2K GLOBAL| Project name water GLOBAL| Preferred FFT library FFTW3 GLOBAL| Preferred diagonalization lib. SL GLOBAL| Run type MD GLOBAL| All-to-all communication in single precision F GLOBAL| FFTs using library dependent lengths F GLOBAL| Global print level MEDIUM GLOBAL| Total number of message passing processes 72 GLOBAL| Number of threads for this process 1 GLOBAL| This output is from process 0 GLOBAL| CPU model name : Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz MEMORY| system memory details [Kb] MEMORY| rank 0 min max average MEMORY| MemTotal 132004740 132004740 132004740 132004740 MEMORY| MemFree 128238064 128236788 128351148 128287109 MEMORY| Buffers 14604 11092 14604 12726 MEMORY| Cached 277924 255724 277924 263193 MEMORY| Slab 658000 650244 686032 664758 MEMORY| SReclaimable 17692 16640 36416 23582 MEMORY| MemLikelyFree 128548284 128547008 128655772 128586611 *** Fundamental physical constants (SI units) *** *** Literature: B. J. Mohr and B. N. Taylor, *** CODATA recommended values of the fundamental physical *** constants: 2006, Web Version 5.1 *** http://physics.nist.gov/constants Speed of light in vacuum [m/s] 2.99792458000000E+08 Magnetic constant or permeability of vacuum [N/A**2] 1.25663706143592E-06 Electric constant or permittivity of vacuum [F/m] 8.85418781762039E-12 Planck constant (h) [J*s] 6.62606896000000E-34 Planck constant (h-bar) [J*s] 1.05457162825177E-34 Elementary charge [C] 1.60217648700000E-19 Electron mass [kg] 9.10938215000000E-31 Electron g factor [ ] -2.00231930436220E+00 Proton mass [kg] 1.67262163700000E-27 Fine-structure constant 7.29735253760000E-03 Rydberg constant [1/m] 1.09737315685270E+07 Avogadro constant [1/mol] 6.02214179000000E+23 Boltzmann constant [J/K] 1.38065040000000E-23 Atomic mass unit [kg] 1.66053878200000E-27 Bohr radius [m] 5.29177208590000E-11 *** Conversion factors *** [u] -> [a.u.] 1.82288848426455E+03 [Angstrom] -> [Bohr] = [a.u.] 1.88972613288564E+00 [a.u.] = [Bohr] -> [Angstrom] 5.29177208590000E-01 [a.u.] -> [s] 2.41888432650478E-17 [a.u.] -> [fs] 2.41888432650478E-02 [a.u.] -> [J] 4.35974393937059E-18 [a.u.] -> [N] 8.23872205491840E-08 [a.u.] -> [K] 3.15774647902944E+05 [a.u.] -> [kJ/mol] 2.62549961709828E+03 [a.u.] -> [kcal/mol] 6.27509468713739E+02 [a.u.] -> [Pa] 2.94210107994716E+13 [a.u.] -> [bar] 2.94210107994716E+08 [a.u.] -> [atm] 2.90362800883016E+08 [a.u.] -> [eV] 2.72113838565563E+01 [a.u.] -> [Hz] 6.57968392072181E+15 [a.u.] -> [1/cm] (wave numbers) 2.19474631370540E+05 [a.u./Bohr**2] -> [1/cm] 5.14048714338585E+03 CELL_TOP| Volume [angstrom^3]: 9431.313 CELL_TOP| Vector a [angstrom 13.472 0.000 0.000 |a| = 13.472 CELL_TOP| Vector b [angstrom 0.000 15.557 0.000 |b| = 15.557 CELL_TOP| Vector c [angstrom 0.000 0.000 45.000 |c| = 45.000 CELL_TOP| Angle (b,c), alpha [degree]: 90.000 CELL_TOP| Angle (a,c), beta [degree]: 90.000 CELL_TOP| Angle (a,b), gamma [degree]: 90.000 CELL_TOP| Numerically orthorhombic: YES GENERATE| Preliminary Number of Bonds generated: 0 GENERATE| Achieved consistency in connectivity generation. CELL| Volume [angstrom^3]: 9431.313 CELL| Vector a [angstrom]: 13.472 0.000 0.000 |a| = 13.472 CELL| Vector b [angstrom]: 0.000 15.557 0.000 |b| = 15.557 CELL| Vector c [angstrom]: 0.000 0.000 45.000 |c| = 45.000 CELL| Angle (b,c), alpha [degree]: 90.000 CELL| Angle (a,c), beta [degree]: 90.000 CELL| Angle (a,b), gamma [degree]: 90.000 CELL| Numerically orthorhombic: YES CELL_REF| Volume [angstrom^3]: 9431.313 CELL_REF| Vector a [angstrom 13.472 0.000 0.000 |a| = 13.472 CELL_REF| Vector b [angstrom 0.000 15.557 0.000 |b| = 15.557 CELL_REF| Vector c [angstrom 0.000 0.000 45.000 |c| = 45.000 CELL_REF| Angle (b,c), alpha [degree]: 90.000 CELL_REF| Angle (a,c), beta [degree]: 90.000 CELL_REF| Angle (a,b), gamma [degree]: 90.000 CELL_REF| Numerically orthorhombic: YES ******************************************************************************* ******************************************************************************* ** ** ** ##### ## ## ** ** ## ## ## ## ## ** ** ## ## ## ###### ** ** ## ## ## ## ## ##### ## ## #### ## ##### ##### ** ** ## ## ## ## ## ## ## ## ## ## ## ## ## ## ** ** ## ## ## ## ## ## ## #### ### ## ###### ###### ** ** ## ### ## ## ## ## ## ## ## ## ## ## ** ** ####### ##### ## ##### ## ## #### ## ##### ## ** ** ## ## ** ** ** ** ... make the atoms dance ** ** ** ** Copyright (C) by CP2K Developers Group (2000 - 2015) ** ** ** ******************************************************************************* DFT| Spin restricted Kohn-Sham (RKS) calculation RKS DFT| Multiplicity 1 DFT| Number of spin states 1 DFT| Charge 0 DFT| Self-interaction correction (SIC) NO DFT| Cutoffs: density 1.000000E-10 DFT| gradient 1.000000E-10 DFT| tau 1.000000E-10 DFT| cutoff_smoothing_range 0.000000E+00 DFT| XC density smoothing NN10 DFT| XC derivatives SPLINE2_SMOOTH FUNCTIONAL| ROUTINE=NEW FUNCTIONAL| PBE: FUNCTIONAL| J.P.Perdew, K.Burke, M.Ernzerhof, Phys. Rev. Letter, vol. 77, n 18, FUNCTIONAL| pp. 3865-3868, (1996){spin unpolarized} vdW POTENTIAL| Pair Potential vdW POTENTIAL| DFT-D3 (Version 3.1) vdW POTENTIAL| Potential Form: S. Grimme et al, JCP 132: 154104 (2010) vdW POTENTIAL| Zero Damping vdW POTENTIAL| Cutoff Radius [Bohr]: 28.35 vdW POTENTIAL| s6 Scaling Factor: 1.0000 vdW POTENTIAL| sr6 Scaling Factor: 1.2170 vdW POTENTIAL| s8 Scaling Factor: 0.7220 vdW POTENTIAL| Cutoff for CN calculation: 0.1000E-05 QS| Method: GPW QS| Density plane wave grid type NON-SPHERICAL FULLSPACE QS| Number of grid levels: 4 QS| Density cutoff [a.u.]: 160.0 QS| Multi grid cutoff [a.u.]: 1) grid level 160.0 QS| 2) grid level 53.3 QS| 3) grid level 17.8 QS| 4) grid level 5.9 QS| Grid level progression factor: 3.0 QS| Relative density cutoff [a.u.]: 25.0 QS| Consistent realspace mapping and integration QS| Interaction thresholds: eps_pgf_orb: 1.0E-07 QS| eps_filter_matrix: 0.0E+00 QS| eps_core_charge: 1.0E-16 QS| eps_rho_gspace: 1.0E-14 QS| eps_rho_rspace: 1.0E-14 QS| eps_gvg_rspace: 1.0E-07 QS| eps_ppl: 1.0E-02 QS| eps_ppnl: 1.0E-09 ATOMIC KIND INFORMATION 1. Atomic kind: N Number of atoms: 2 Orbital Basis Set TZV2P-GTH Number of orbital shell sets: 2 Number of orbital shells: 8 Number of primitive Cartesian functions: 7 Number of Cartesian basis functions: 24 Number of spherical basis functions: 22 Norm type: 2 Normalised Cartesian orbitals: Set Shell Orbital Exponent Coefficient 1 1 2s 7.622745 0.321703 2.797061 0.161118 0.990977 -0.264934 0.341731 -0.199987 0.111682 -0.023066 1 2 3s 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.318547 0.111682 0.000000 1 3 4s 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.000000 0.111682 0.137689 1 4 3px 7.622745 -1.014025 2.797061 -0.927144 0.990977 -0.514975 0.341731 -0.158623 0.111682 -0.021774 1 4 3py 7.622745 -1.014025 2.797061 -0.927144 0.990977 -0.514975 0.341731 -0.158623 0.111682 -0.021774 1 4 3pz 7.622745 -1.014025 2.797061 -0.927144 0.990977 -0.514975 0.341731 -0.158623 0.111682 -0.021774 1 5 4px 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.372431 0.111682 0.000000 1 5 4py 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.372431 0.111682 0.000000 1 5 4pz 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.372431 0.111682 0.000000 1 6 5px 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.000000 0.111682 0.092028 1 6 5py 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.000000 0.111682 0.092028 1 6 5pz 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.000000 0.111682 0.092028 2 1 3dx2 1.654000 3.970513 0.469000 0.000000 2 1 3dxy 1.654000 6.877130 0.469000 0.000000 2 1 3dxz 1.654000 6.877130 0.469000 0.000000 2 1 3dy2 1.654000 3.970513 0.469000 0.000000 2 1 3dyz 1.654000 6.877130 0.469000 0.000000 2 1 3dz2 1.654000 3.970513 0.469000 0.000000 2 2 4dx2 1.654000 0.000000 0.469000 0.437484 2 2 4dxy 1.654000 0.000000 0.469000 0.757744 2 2 4dxz 1.654000 0.000000 0.469000 0.757744 2 2 4dy2 1.654000 0.000000 0.469000 0.437484 2 2 4dyz 1.654000 0.000000 0.469000 0.757744 2 2 4dz2 1.654000 0.000000 0.469000 0.437484 Potential information for GTH-PBE-q5 Description: Goedecker-Teter-Hutter pseudopotential Goedecker et al., PRB 54, 1703 (1996) Hartwigsen et al., PRB 58, 3641 (1998) Krack, TCA 114, 145 (2005) Gaussian exponent of the core charge distribution: 6.208322 Electronic configuration (s p d ...): 2 3 Parameters of the local part of the GTH pseudopotential: rloc C1 C2 C3 C4 0.283791 -12.415226 1.868096 Parameters of the non-local part of the GTH pseudopotential: l r(l) h(i,j,l) 0 0.255405 13.630263 1 0.245495 2. Atomic kind: O Number of atoms: 77 Orbital Basis Set TZV2P-GTH Number of orbital shell sets: 2 Number of orbital shells: 8 Number of primitive Cartesian functions: 7 Number of Cartesian basis functions: 24 Number of spherical basis functions: 22 Norm type: 2 Normalised Cartesian orbitals: Set Shell Orbital Exponent Coefficient 1 1 2s 10.267442 0.404544 3.748050 0.199889 1.330834 -0.336302 0.455680 -0.246356 0.146292 -0.028287 1 2 3s 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.395280 0.146292 0.000000 1 3 4s 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.000000 0.146292 0.168588 1 4 3px 10.267442 -1.561025 3.748050 -1.394275 1.330834 -0.754014 0.455680 -0.224400 0.146292 -0.029841 1 4 3py 10.267442 -1.561025 3.748050 -1.394275 1.330834 -0.754014 0.455680 -0.224400 0.146292 -0.029841 1 4 3pz 10.267442 -1.561025 3.748050 -1.394275 1.330834 -0.754014 0.455680 -0.224400 0.146292 -0.029841 1 5 4px 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.533661 0.146292 0.000000 1 5 4py 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.533661 0.146292 0.000000 1 5 4pz 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.533661 0.146292 0.000000 1 6 5px 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.000000 0.146292 0.128963 1 6 5py 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.000000 0.146292 0.128963 1 6 5pz 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.000000 0.146292 0.128963 2 1 3dx2 2.314000 7.145709 0.645000 0.000000 2 1 3dxy 2.314000 12.376731 0.645000 0.000000 2 1 3dxz 2.314000 12.376731 0.645000 0.000000 2 1 3dy2 2.314000 7.145709 0.645000 0.000000 2 1 3dyz 2.314000 12.376731 0.645000 0.000000 2 1 3dz2 2.314000 7.145709 0.645000 0.000000 2 2 4dx2 2.314000 0.000000 0.645000 0.764080 2 2 4dxy 2.314000 0.000000 0.645000 1.323426 2 2 4dxz 2.314000 0.000000 0.645000 1.323426 2 2 4dy2 2.314000 0.000000 0.645000 0.764080 2 2 4dyz 2.314000 0.000000 0.645000 1.323426 2 2 4dz2 2.314000 0.000000 0.645000 0.764080 Potential information for GTH-PBE-q6 Description: Goedecker-Teter-Hutter pseudopotential Goedecker et al., PRB 54, 1703 (1996) Hartwigsen et al., PRB 58, 3641 (1998) Krack, TCA 114, 145 (2005) Gaussian exponent of the core charge distribution: 8.360253 Electronic configuration (s p d ...): 2 4 Parameters of the local part of the GTH pseudopotential: rloc C1 C2 C3 C4 0.244554 -16.667215 2.487311 Parameters of the non-local part of the GTH pseudopotential: l r(l) h(i,j,l) 0 0.220956 18.337458 1 0.211332 3. Atomic kind: H Number of atoms: 144 Orbital Basis Set TZV2P-GTH Number of orbital shell sets: 2 Number of orbital shells: 5 Number of primitive Cartesian functions: 7 Number of Cartesian basis functions: 9 Number of spherical basis functions: 9 Norm type: 2 Normalised Cartesian orbitals: Set Shell Orbital Exponent Coefficient 1 1 1s 10.882724 -0.071340 3.096875 -0.104410 0.987452 -0.135375 0.345069 -0.133923 0.149269 -0.073092 1 2 2s 10.882724 0.000000 3.096875 0.000000 0.987452 0.000000 0.345069 0.320878 0.149269 0.000000 1 3 3s 10.882724 0.000000 3.096875 0.000000 0.987452 0.000000 0.345069 0.000000 0.149269 0.171154 2 1 2px 1.407000 2.184277 0.388000 0.000000 2 1 2py 1.407000 2.184277 0.388000 0.000000 2 1 2pz 1.407000 2.184277 0.388000 0.000000 2 2 3px 1.407000 0.000000 0.388000 0.436495 2 2 3py 1.407000 0.000000 0.388000 0.436495 2 2 3pz 1.407000 0.000000 0.388000 0.436495 Potential information for GTH-PBE-q1 Description: Goedecker-Teter-Hutter pseudopotential Goedecker et al., PRB 54, 1703 (1996) Hartwigsen et al., PRB 58, 3641 (1998) Krack, TCA 114, 145 (2005) Gaussian exponent of the core charge distribution: 12.500000 Electronic configuration (s p d ...): 1 Parameters of the local part of the GTH pseudopotential: rloc C1 C2 C3 C4 0.200000 -4.178900 0.724463 MOLECULE KIND INFORMATION All atoms are their own molecule, skipping detailed information TOTAL NUMBERS AND MAXIMUM NUMBERS Total number of - Atomic kinds: 3 - Atoms: 223 - Shell sets: 446 - Shells: 1352 - Primitive Cartesian functions: 1561 - Cartesian basis functions: 3192 - Spherical basis functions: 3034 Maximum angular momentum of- Orbital basis functions: 2 - Local part of the GTH pseudopotential: 2 - Non-local part of the GTH pseudopotential: 0 MODULE QUICKSTEP: ATOMIC COORDINATES IN angstrom Atom Kind Element X Y Z Z(eff) Mass 1 1 N 7 -19.317260 -5.454080 11.996970 5.00 14.0067 2 2 O 8 -20.190990 -4.825770 11.466250 6.00 15.9994 3 2 O 8 -19.251930 -6.548670 12.479720 6.00 15.9994 4 2 O 8 -18.051260 -4.552420 12.105280 6.00 15.9994 5 1 N 7 -16.691860 -5.287400 12.291490 5.00 14.0067 6 2 O 8 -16.627980 -6.423410 11.915720 6.00 15.9994 7 2 O 8 -15.898220 -4.515540 12.754550 6.00 15.9994 8 2 O 8 -26.566797 5.885766 -4.325634 6.00 15.9994 9 3 H 1 -26.158273 6.043929 -3.435499 1.00 2.0000 10 3 H 1 -26.611093 6.760476 -4.676844 1.00 2.0000 11 2 O 8 -9.468377 -11.270550 0.584346 6.00 15.9994 12 3 H 1 -10.380793 -11.077813 0.081767 1.00 2.0000 13 3 H 1 -8.866036 -10.622268 0.238165 1.00 2.0000 14 2 O 8 -8.515451 -10.716151 -3.124136 6.00 15.9994 15 3 H 1 -8.871918 -9.979485 -2.588685 1.00 2.0000 16 3 H 1 -8.380633 -11.457102 -2.382064 1.00 2.0000 17 2 O 8 -15.407322 -9.706175 1.152142 6.00 15.9994 18 3 H 1 -15.919904 -9.502920 0.300948 1.00 2.0000 19 3 H 1 -15.479816 -10.654609 1.318487 1.00 2.0000 20 2 O 8 -18.657623 -5.954755 -2.906634 6.00 15.9994 21 3 H 1 -18.715786 -6.841698 -2.495810 1.00 2.0000 22 3 H 1 -18.292159 -5.343766 -2.163856 1.00 2.0000 23 2 O 8 -25.874532 -3.300482 -0.518665 6.00 15.9994 24 3 H 1 -26.443879 -2.645222 -1.028018 1.00 2.0000 25 3 H 1 -25.048064 -3.565552 -1.000270 1.00 2.0000 26 2 O 8 -22.004939 -2.394582 -2.702908 6.00 15.9994 27 3 H 1 -22.646176 -3.086506 -2.375252 1.00 2.0000 28 3 H 1 -22.411575 -1.495636 -2.610173 1.00 2.0000 29 2 O 8 -21.674779 2.782972 -1.222029 6.00 15.9994 30 3 H 1 -23.495427 0.179908 0.934808 1.00 2.0000 31 3 H 1 -20.754022 2.413233 -1.036063 1.00 2.0000 32 2 O 8 -15.563999 -10.587243 -3.389380 6.00 15.9994 33 3 H 1 -15.439484 -11.500275 -3.083774 1.00 2.0000 34 3 H 1 -14.670989 -10.314392 -3.695421 1.00 2.0000 35 2 O 8 -17.706802 -10.778740 -5.423265 6.00 15.9994 36 3 H 1 -16.831766 -10.692388 -4.960214 1.00 2.0000 37 3 H 1 -17.500550 -10.795254 -6.319638 1.00 2.0000 38 2 O 8 -18.858603 -8.475688 -1.800109 6.00 15.9994 39 3 H 1 -19.051286 -9.008189 -2.658335 1.00 2.0000 40 3 H 1 -19.404077 -8.869064 -1.134524 1.00 2.0000 41 2 O 8 -20.894408 -6.579352 -4.602279 6.00 15.9994 42 3 H 1 -20.681870 -7.528857 -4.572102 1.00 2.0000 43 3 H 1 -24.700569 -10.987772 -4.682408 1.00 2.0000 44 3 H 1 -20.123229 -6.279792 -4.080849 1.00 2.0000 45 2 O 8 -23.201780 -6.377694 -3.271665 6.00 15.9994 46 3 H 1 -23.876723 -6.186120 -3.916763 1.00 2.0000 47 3 H 1 -22.317574 -6.405702 -3.801122 1.00 2.0000 48 2 O 8 -24.221224 -11.797515 -4.388924 6.00 15.9994 49 3 H 1 -17.368477 -3.492455 -0.943834 1.00 2.0000 50 3 H 1 -23.447534 -11.427342 -3.904331 1.00 2.0000 51 2 O 8 -18.073531 -0.792565 -2.310338 6.00 15.9994 52 3 H 1 -18.728938 -1.465594 -2.611348 1.00 2.0000 53 3 H 1 -18.508357 0.060532 -2.008636 1.00 2.0000 54 2 O 8 -16.797841 0.709889 -4.703266 6.00 15.9994 55 3 H 1 -16.899250 0.114493 -3.912154 1.00 2.0000 56 3 H 1 -17.656753 1.189617 -4.657401 1.00 2.0000 57 2 O 8 -21.482986 -13.917292 -5.277215 6.00 15.9994 58 3 H 1 -22.136925 -13.238744 -5.030117 1.00 2.0000 59 3 H 1 -21.647726 -14.611729 -4.625745 1.00 2.0000 60 2 O 8 -19.677349 -9.326342 -4.258990 6.00 15.9994 61 3 H 1 -20.340685 -9.992412 -3.856958 1.00 2.0000 62 3 H 1 -18.972774 -9.829239 -4.677509 1.00 2.0000 63 2 O 8 -19.089924 -13.830752 -1.653956 6.00 15.9994 64 3 H 1 -18.814470 -13.259645 -0.879613 1.00 2.0000 65 3 H 1 -19.024421 -13.119411 -2.379935 1.00 2.0000 66 2 O 8 -9.428566 -15.031955 -2.722401 6.00 15.9994 67 3 H 1 -8.901382 -14.306282 -2.318582 1.00 2.0000 68 3 H 1 -10.377049 -14.646092 -2.879623 1.00 2.0000 69 2 O 8 -13.895594 -7.297004 -1.388427 6.00 15.9994 70 3 H 1 -13.936919 -6.509339 -1.923312 1.00 2.0000 71 3 H 1 -14.748502 -7.794839 -1.462674 1.00 2.0000 72 2 O 8 -17.966888 -4.239045 -0.879390 6.00 15.9994 73 3 H 1 -19.567288 -3.431965 -0.544106 1.00 2.0000 74 3 H 1 -17.807612 -4.685849 0.001510 1.00 2.0000 75 2 O 8 -19.624155 -2.328222 -4.075912 6.00 15.9994 76 3 H 1 -20.573860 -2.399433 -3.675120 1.00 2.0000 77 3 H 1 -19.743270 -2.380261 -5.030232 1.00 2.0000 78 2 O 8 -15.002983 2.083462 -3.065194 6.00 15.9994 79 3 H 1 -15.540876 1.655779 -3.769307 1.00 2.0000 80 3 H 1 -14.075486 1.886847 -3.154348 1.00 2.0000 81 2 O 8 -18.223527 -5.241135 1.642568 6.00 15.9994 82 3 H 1 -17.360065 -5.223620 2.196571 1.00 2.0000 83 3 H 1 -18.737953 -4.554903 2.060801 1.00 2.0000 84 2 O 8 -22.646206 -10.794753 3.331511 6.00 15.9994 85 3 H 1 -22.893050 -10.889629 2.344531 1.00 2.0000 86 3 H 1 -22.344034 -9.826444 3.419465 1.00 2.0000 87 2 O 8 -23.714704 -4.404961 -1.556718 6.00 15.9994 88 3 H 1 -23.473307 -5.108142 -2.176332 1.00 2.0000 89 3 H 1 -23.409404 -4.706244 -0.637705 1.00 2.0000 90 2 O 8 -13.771982 -5.449281 0.637008 6.00 15.9994 91 3 H 1 -17.183103 -8.762858 -1.601220 1.00 2.0000 92 3 H 1 -13.472219 -4.682816 0.140979 1.00 2.0000 93 2 O 8 -21.880436 -1.686751 3.348032 6.00 15.9994 94 3 H 1 -22.184305 -1.109689 2.591359 1.00 2.0000 95 3 H 1 -22.627295 -2.351101 3.406321 1.00 2.0000 96 2 O 8 -20.540597 1.537957 1.959986 6.00 15.9994 97 3 H 1 -20.927105 2.029535 2.847357 1.00 2.0000 98 3 H 1 -19.270027 0.589953 2.523492 1.00 2.0000 99 2 O 8 -20.326170 5.963779 0.218818 6.00 15.9994 100 3 H 1 -19.983560 6.667843 0.825409 1.00 2.0000 101 3 H 1 -19.835202 5.122233 0.405881 1.00 2.0000 102 2 O 8 -16.132213 -1.186959 1.600520 6.00 15.9994 103 3 H 1 -16.900188 -0.669734 1.853686 1.00 2.0000 104 3 H 1 -15.786008 -1.568446 2.426499 1.00 2.0000 105 2 O 8 -16.192760 -8.849836 -1.493114 6.00 15.9994 106 3 H 1 -15.894972 -9.537712 -2.228412 1.00 2.0000 107 2 O 8 -18.991261 -12.101906 0.816505 6.00 15.9994 108 3 H 1 -18.076233 -12.044519 1.165194 1.00 2.0000 109 3 H 1 -19.537269 -12.761394 1.332216 1.00 2.0000 110 2 O 8 -19.017293 -13.002493 -4.487816 6.00 15.9994 111 3 H 1 -18.779227 -12.153080 -4.875275 1.00 2.0000 112 3 H 1 -19.914257 -13.300164 -4.846476 1.00 2.0000 113 2 O 8 -13.846862 -4.814880 -2.803914 6.00 15.9994 114 3 H 1 -13.860347 -3.836424 -2.790102 1.00 2.0000 115 3 H 1 -14.748879 -5.055615 -3.226935 1.00 2.0000 116 3 H 1 -22.069708 3.078929 -0.381905 1.00 2.0000 117 2 O 8 -19.511457 -2.744666 2.375729 6.00 15.9994 118 3 H 1 -20.402986 -2.718301 2.797179 1.00 2.0000 119 3 H 1 -19.747674 -2.678196 1.447195 1.00 2.0000 120 2 O 8 -22.480097 0.004721 0.938894 6.00 15.9994 121 3 H 1 -21.269751 1.045936 1.458934 1.00 2.0000 122 3 H 1 -22.187954 -0.377403 0.081361 1.00 2.0000 123 2 O 8 -15.755094 -5.007273 2.467645 6.00 15.9994 124 3 H 1 -16.136059 -1.679623 0.123637 1.00 2.0000 125 3 H 1 -15.118985 -5.245440 1.752973 1.00 2.0000 126 2 O 8 -18.857446 2.650958 5.234485 6.00 15.9994 127 3 H 1 -18.074428 2.498889 4.619720 1.00 2.0000 128 3 H 1 -15.280924 -4.285893 2.897510 1.00 2.0000 129 2 O 8 -12.717663 -13.621686 -0.636682 6.00 15.9994 130 3 H 1 -13.680469 -13.707198 -0.454507 1.00 2.0000 131 3 H 1 -12.494374 -12.679151 -0.361702 1.00 2.0000 132 2 O 8 -12.428020 -6.395508 -4.415771 6.00 15.9994 133 3 H 1 -12.829547 -6.380702 -5.304294 1.00 2.0000 134 3 H 1 -12.928783 -5.727527 -3.849016 1.00 2.0000 135 2 O 8 -16.039597 -5.763793 -3.963596 6.00 15.9994 136 3 H 1 -16.205472 -5.004378 -4.461053 1.00 2.0000 137 3 H 1 -16.951564 -5.873893 -3.468604 1.00 2.0000 138 2 O 8 -13.291901 -0.490104 -4.449387 6.00 15.9994 139 3 H 1 -14.153992 -0.118816 -4.774740 1.00 2.0000 140 3 H 1 -12.898323 0.313194 -4.217093 1.00 2.0000 141 2 O 8 -12.251318 -9.304754 -1.895463 6.00 15.9994 142 3 H 1 -11.334116 -9.069043 -1.691476 1.00 2.0000 143 3 H 1 -12.777418 -8.459122 -1.912379 1.00 2.0000 144 2 O 8 -12.538787 -2.214523 2.040255 6.00 15.9994 145 3 H 1 -12.369178 -2.613381 1.099113 1.00 2.0000 146 3 H 1 -12.248015 -1.271585 2.003711 1.00 2.0000 147 2 O 8 -14.068003 -2.123963 -2.243486 6.00 15.9994 148 3 H 1 -13.813298 -1.495347 -2.930916 1.00 2.0000 149 3 H 1 -14.959036 -1.985449 -1.911796 1.00 2.0000 150 2 O 8 -14.775496 -2.407665 3.641523 6.00 15.9994 151 3 H 1 -14.905539 -1.632921 4.239437 1.00 2.0000 152 3 H 1 -13.931729 -2.312820 3.181967 1.00 2.0000 153 2 O 8 -25.206690 -11.476252 4.458583 6.00 15.9994 154 3 H 1 -24.285875 -11.317999 4.156750 1.00 2.0000 155 3 H 1 -25.709107 -11.068033 3.752467 1.00 2.0000 156 2 O 8 -19.301988 -7.789603 2.042123 6.00 15.9994 157 3 H 1 -18.496147 -8.177613 2.490654 1.00 2.0000 158 3 H 1 -19.089680 -6.889051 1.801584 1.00 2.0000 159 2 O 8 -21.831161 -8.058387 3.045820 6.00 15.9994 160 3 H 1 -20.853247 -7.907769 2.832747 1.00 2.0000 161 3 H 1 -22.250421 -7.388211 3.604301 1.00 2.0000 162 2 O 8 -20.434261 -3.043875 -0.310618 6.00 15.9994 163 3 H 1 -21.489035 -4.434524 0.508345 1.00 2.0000 164 3 H 1 -20.836437 -2.644857 -1.072504 1.00 2.0000 165 2 O 8 -18.573340 -0.072650 2.760800 6.00 15.9994 166 3 H 1 -19.083061 -0.963371 2.750164 1.00 2.0000 167 3 H 1 -15.812579 2.542741 1.038339 1.00 2.0000 168 2 O 8 -15.530893 1.766859 -0.377216 6.00 15.9994 169 3 H 1 -15.503136 1.905309 -1.364685 1.00 2.0000 170 3 H 1 -15.655849 0.809544 -0.185183 1.00 2.0000 171 2 O 8 -14.409749 0.536390 4.679163 6.00 15.9994 172 3 H 1 -13.536822 0.952036 4.246160 1.00 2.0000 173 3 H 1 -14.279840 1.028143 5.522151 1.00 2.0000 174 2 O 8 -11.645959 0.365713 1.489198 6.00 15.9994 175 3 H 1 -12.221505 0.848396 0.832955 1.00 2.0000 176 3 H 1 -11.871981 0.835631 2.304797 1.00 2.0000 177 2 O 8 -21.196535 2.693631 4.145587 6.00 15.9994 178 3 H 1 -21.617510 3.610657 3.884948 1.00 2.0000 179 3 H 1 -20.374241 2.850574 4.612551 1.00 2.0000 180 2 O 8 -12.872565 -9.732182 1.978547 6.00 15.9994 181 3 H 1 -12.575848 -8.821493 2.008513 1.00 2.0000 182 3 H 1 -13.813360 -9.530351 1.661305 1.00 2.0000 183 2 O 8 -10.349500 -3.790132 3.010216 6.00 15.9994 184 3 H 1 -9.775833 -3.895205 2.234065 1.00 2.0000 185 3 H 1 -11.185013 -3.442374 2.611073 1.00 2.0000 186 2 O 8 -16.276429 -1.940542 -0.869248 6.00 15.9994 187 3 H 1 -13.809971 -6.176607 -0.037799 1.00 2.0000 188 3 H 1 -17.113336 -1.434139 -1.253808 1.00 2.0000 189 2 O 8 -16.193239 3.171433 1.736967 6.00 15.9994 190 3 H 1 -18.897790 1.772168 5.702941 1.00 2.0000 191 3 H 1 -16.256299 2.561079 2.543264 1.00 2.0000 192 2 O 8 -22.380535 -4.879305 0.844050 6.00 15.9994 193 3 H 1 -22.417352 -5.842135 0.700576 1.00 2.0000 194 2 O 8 -25.304787 1.372816 3.871868 6.00 15.9994 195 3 H 1 -25.135555 2.356491 3.936286 1.00 2.0000 196 3 H 1 -24.602092 0.972833 4.561711 1.00 2.0000 197 2 O 8 -16.807799 1.544227 3.792630 6.00 15.9994 198 3 H 1 -17.350683 0.722039 3.517363 1.00 2.0000 199 3 H 1 -16.110488 1.221447 4.364994 1.00 2.0000 200 2 O 8 -11.970991 -7.078546 2.092407 6.00 15.9994 201 3 H 1 -12.527926 -6.347959 1.724283 1.00 2.0000 202 3 H 1 -11.397552 -6.689802 2.819160 1.00 2.0000 203 2 O 8 -23.102235 -7.610124 0.807482 6.00 15.9994 204 3 H 1 -22.770015 -7.909488 1.647301 1.00 2.0000 205 3 H 1 -24.112868 -7.381948 1.074874 1.00 2.0000 206 2 O 8 -12.147379 -13.823098 -3.277745 6.00 15.9994 207 3 H 1 -12.271951 -13.831658 -2.261772 1.00 2.0000 208 3 H 1 -11.836342 -12.855485 -3.567627 1.00 2.0000 209 2 O 8 -23.137640 0.614020 5.152014 6.00 15.9994 210 3 H 1 -22.699821 1.479447 4.900930 1.00 2.0000 211 3 H 1 -22.619008 -0.138851 4.781627 1.00 2.0000 212 2 O 8 -9.706923 -8.713400 -1.675297 6.00 15.9994 213 3 H 1 -9.537835 -7.840829 -2.248215 1.00 2.0000 214 3 H 1 -9.568580 -8.468381 -0.694682 1.00 2.0000 215 2 O 8 -17.078435 6.913749 3.148262 6.00 15.9994 216 3 H 1 -16.597300 7.570803 3.665547 1.00 2.0000 217 3 H 1 -16.516880 6.913325 2.300982 1.00 2.0000 218 2 O 8 -10.429598 -6.118336 4.133162 6.00 15.9994 219 3 H 1 -10.976353 -6.244853 4.915371 1.00 2.0000 220 3 H 1 -10.371174 -5.179569 3.833850 1.00 2.0000 221 2 O 8 -12.000043 -11.150965 0.013566 6.00 15.9994 222 3 H 1 -12.328514 -10.664902 -0.857592 1.00 2.0000 223 3 H 1 -12.321550 -10.613832 0.835245 1.00 2.0000 SCF PARAMETERS Density guess: ATOMIC -------------------------------------------------------- max_scf: 50 max_scf_history: 0 max_diis: 4 -------------------------------------------------------- eps_scf: 1.00E-07 eps_scf_history: 0.00E+00 eps_diis: 1.00E-01 eps_eigval: 1.00E-05 -------------------------------------------------------- level_shift [a.u.]: 0.00 -------------------------------------------------------- Outer loop SCF in use No variables optimised in outer loop eps_scf 1.00E-07 max_scf 50 No outer loop optimization step_size 5.00E-01 PW_GRID| Information for grid number 1 PW_GRID| Grid distributed over 72 processors PW_GRID| Real space group dimensions 72 1 PW_GRID| the grid is blocked: NO PW_GRID| Cutoff [a.u.] 320.0 PW_GRID| spherical cutoff: NO PW_GRID| Bounds 1 -108 107 Points: 216 PW_GRID| Bounds 2 -120 119 Points: 240 PW_GRID| Bounds 3 -360 359 Points: 720 PW_GRID| Volume element (a.u.^3) 0.1705E-02 Volume (a.u.^3) 63645.6571 PW_GRID| Grid span FULLSPACE PW_GRID| Distribution Average Max Min PW_GRID| G-Vectors 518400.0 518400 518400 PW_GRID| G-Rays 2400.0 2400 2400 PW_GRID| Real Space Points 518400.0 518400 518400 PW_GRID| Information for grid number 2 PW_GRID| Grid distributed over 72 processors PW_GRID| Real space group dimensions 72 1 PW_GRID| the grid is blocked: NO PW_GRID| Cutoff [a.u.] 160.0 PW_GRID| spherical cutoff: NO PW_GRID| Bounds 1 -75 74 Points: 150 PW_GRID| Bounds 2 -90 89 Points: 180 PW_GRID| Bounds 3 -243 242 Points: 486 PW_GRID| Volume element (a.u.^3) 0.4850E-02 Volume (a.u.^3) 63645.6571 PW_GRID| Grid span FULLSPACE PW_GRID| Distribution Average Max Min PW_GRID| G-Vectors 182250.0 189150 163200 PW_GRID| G-Rays 1215.0 1261 1088 PW_GRID| Real Space Points 182250.0 262440 174960 PW_GRID| Information for grid number 3 PW_GRID| Grid distributed over 72 processors PW_GRID| Real space group dimensions 72 1 PW_GRID| the grid is blocked: NO PW_GRID| Cutoff [a.u.] 53.3 PW_GRID| spherical cutoff: NO PW_GRID| Bounds 1 -45 44 Points: 90 PW_GRID| Bounds 2 -50 49 Points: 100 PW_GRID| Bounds 3 -144 143 Points: 288 PW_GRID| Volume element (a.u.^3) 0.2455E-01 Volume (a.u.^3) 63645.6571 PW_GRID| Grid span FULLSPACE PW_GRID| Distribution Average Max Min PW_GRID| G-Vectors 36000.0 39060 35190 PW_GRID| G-Rays 400.0 434 391 PW_GRID| Real Space Points 36000.0 57600 28800 PW_GRID| Information for grid number 4 PW_GRID| Grid distributed over 72 processors PW_GRID| Real space group dimensions 72 1 PW_GRID| the grid is blocked: NO PW_GRID| Cutoff [a.u.] 17.8 PW_GRID| spherical cutoff: NO PW_GRID| Bounds 1 -27 26 Points: 54 PW_GRID| Bounds 2 -30 29 Points: 60 PW_GRID| Bounds 3 -81 80 Points: 162 PW_GRID| Volume element (a.u.^3) 0.1213 Volume (a.u.^3) 63645.6571 PW_GRID| Grid span FULLSPACE PW_GRID| Distribution Average Max Min PW_GRID| G-Vectors 7290.0 7938 6480 PW_GRID| G-Rays 135.0 147 120 PW_GRID| Real Space Points 7290.0 9720 0 PW_GRID| Information for grid number 5 PW_GRID| Grid distributed over 72 processors PW_GRID| Real space group dimensions 72 1 PW_GRID| the grid is blocked: NO PW_GRID| Cutoff [a.u.] 5.9 PW_GRID| spherical cutoff: NO PW_GRID| Bounds 1 -13 13 Points: 27 PW_GRID| Bounds 2 -18 17 Points: 36 PW_GRID| Bounds 3 -48 47 Points: 96 PW_GRID| Volume element (a.u.^3) 0.6821 Volume (a.u.^3) 63645.6571 PW_GRID| Grid span FULLSPACE PW_GRID| Distribution Average Max Min PW_GRID| G-Vectors 1296.0 1404 1188 PW_GRID| G-Rays 48.0 52 44 PW_GRID| Real Space Points 1296.0 3456 0 POISSON| Solver Martyna-Tuckerman (MT) POISSON| MT| Alpha 7.000 POISSON| MT| Relative cutoff 2.0 POISSON| Periodicity XY RS_GRID| Information for grid number 2 RS_GRID| Bounds 1 -75 74 Points: 150 RS_GRID| Bounds 2 -90 89 Points: 180 RS_GRID| Bounds 3 -243 242 Points: 486 RS_GRID| Real space distribution over 6 groups RS_GRID| Real space distribution along direction 2 RS_GRID| Border size 27 RS_GRID| Real space distribution over 12 groups RS_GRID| Real space distribution along direction 3 RS_GRID| Border size 27 RS_GRID| Distribution Average Max Min RS_GRID| Planes 84.0 84 84 RS_GRID| Distribution Average Max Min RS_GRID| Planes 94.5 95 94 RS_GRID| Information for grid number 3 RS_GRID| Bounds 1 -45 44 Points: 90 RS_GRID| Bounds 2 -50 49 Points: 100 RS_GRID| Bounds 3 -144 143 Points: 288 RS_GRID| Real space distribution over 6 groups RS_GRID| Real space distribution along direction 2 RS_GRID| Border size 27 RS_GRID| Real space distribution over 12 groups RS_GRID| Real space distribution along direction 3 RS_GRID| Border size 27 RS_GRID| Distribution Average Max Min RS_GRID| Planes 70.7 71 70 RS_GRID| Distribution Average Max Min RS_GRID| Planes 78.0 78 78 RS_GRID| Information for grid number 4 RS_GRID| Bounds 1 -27 26 Points: 54 RS_GRID| Bounds 2 -30 29 Points: 60 RS_GRID| Bounds 3 -81 80 Points: 162 RS_GRID| Real space fully replicated RS_GRID| Group size 1 RS_GRID| Information for grid number 5 RS_GRID| Bounds 1 -13 13 Points: 27 RS_GRID| Bounds 2 -18 17 Points: 36 RS_GRID| Bounds 3 -48 47 Points: 96 RS_GRID| Real space fully replicated RS_GRID| Group size 1 DISTRIBUTION OF THE PARTICLES (ROWS) Process row Number of particles Number of matrix rows 0 39 -1 1 36 -1 2 36 -1 3 39 -1 4 37 -1 5 36 -1 Sum 223 -1 DISTRIBUTION OF THE PARTICLES (COLUMNS) Process col Number of particles Number of matrix columns 0 19 -1 1 20 -1 2 18 -1 3 18 -1 4 18 -1 5 18 -1 6 19 -1 7 20 -1 8 18 -1 9 19 -1 10 18 -1 11 18 -1 Sum 223 -1 MD| Molecular Dynamics Protocol MD| Ensemble Type NVE MD| Number of Time Steps 50000 MD| Time Step [fs] 0.50 MD| Temperature [K] 300.00 MD| Temperature tolerance [K] 0.00 MD| Print MD information every 1 step(s) MD| File type Print frequency[steps] File names MD| Coordinates 1 water-pos-1.xyz MD| Velocities 1 water-vel-1.xyz MD| Energies 1 water-1.ener MD| Dump 20 water-1.restart ROT| Rotational Analysis Info ROT| Principal axes and moments of inertia in atomic units: ROT| 1 2 3 ROT| EIGENVALUES 0.333392366E+09 0.473188005E+09 0.491315243E+09 ROT| X 0.376526826 -0.673919443 -0.635657246 ROT| Y -0.869031069 -0.019223038 -0.494383936 ROT| Z -0.320955683 -0.738554710 0.592894923 ROT| Numer of Rotovibrational vectors: 6 Calculation of degrees of freedom Number of atoms: 223 Number of Intramolecular constraints: 0 Number of Intermolecular constraints: 0 Invariants(translation + rotations): 4 Degrees of freedom: 665 Restraints Information Number of Intramolecular restraints: 0 Number of Intermolecular restraints: 0 ************************** Velocities initialization ************************** Initial Temperature 298.35 K COM velocity: -0.000020451803 -0.000014845920 -0.000010029888 ******************************************************************************* DISTRIBUTION OF THE NEIGHBOR LISTS Total number of particle pairs: 33914 Total number of matrix elements: 6332759 Average number of particle pairs: 472 Maximum number of particle pairs: 579 Average number of matrix element: 87955 Maximum number of matrix elements: 103965 DISTRIBUTION OF THE OVERLAP MATRIX Number of non-zero blocks: 22761 Percentage non-zero blocks: 91.13 Average number of blocks per CPU: 317 Maximum number of blocks per CPU: 401 Average number of matrix elements per CPU: 57376 Maximum number of matrix elements per CPU: 68459 Number of electrons: 616 Number of occupied orbitals: 308 Number of molecular orbitals: 308 Number of orbital functions: 3034 Number of independent orbital functions: 3034 Extrapolation method: initial_guess Atomic guess: The first density matrix is obtained in terms of atomic orbitals and electronic configurations assigned to each atomic kind Guess for atomic kind: N Electronic structure Total number of core electrons 2.00 Total number of valence electrons 5.00 Total number of electrons 7.00 Multiplicity not specified S [ 2.00] 2.00 P 3.00 ******************************************************************************* Iteration Convergence Energy [au] ******************************************************************************* 1 1.15283 -9.106557061822 2 0.871956 -9.149783991284 3 0.963150E-01 -9.540592510391 4 0.266247E-02 -9.546174590474 5 0.308219E-03 -9.546178123327 6 0.232633E-04 -9.546178176652 7 0.287731E-08 -9.546178176959 Energy components [Hartree] Total Energy :: -9.546178176959 Band Energy :: -2.056052179060 Kinetic Energy :: 6.750514597613 Potential Energy :: -16.296692774573 Virial (-V/T) :: 2.414140809404 Core Energy :: -15.541752719680 XC Energy :: -2.162895802006 Coulomb Energy :: 8.158470344727 Total Pseudopotential Energy :: -22.329540629779 Local Pseudopotential Energy :: -23.278432419853 Nonlocal Pseudopotential Energy :: 0.948891790074 Confinement :: 0.372733124857 Orbital energies State L Occupation Energy[a.u.] Energy[eV] 1 0 2.000 -0.663798 -18.062863 1 1 3.000 -0.242819 -6.607433 Guess for atomic kind: O Electronic structure Total number of core electrons 2.00 Total number of valence electrons 6.00 Total number of electrons 8.00 Multiplicity not specified S [ 2.00] 2.00 P 4.00 ******************************************************************************* Iteration Convergence Energy [au] ******************************************************************************* 1 2.51497 -14.566691316144 2 2.35806 -14.184114409661 3 0.313328 -15.624381918049 4 0.277189E-01 -15.656178317323 5 0.123634E-02 -15.656397040537 6 0.593196E-04 -15.656397458397 7 0.437058E-05 -15.656397459367 8 0.556571E-07 -15.656397459370 Energy components [Hartree] Total Energy :: -15.656397459370 Band Energy :: -3.001887330005 Kinetic Energy :: 11.780461874254 Potential Energy :: -27.436859333624 Virial (-V/T) :: 2.329013889819 Core Energy :: -26.138301090847 XC Energy :: -3.153767334965 Coulomb Energy :: 13.635670966443 Total Pseudopotential Energy :: -37.953933650738 Local Pseudopotential Energy :: -39.253304888308 Nonlocal Pseudopotential Energy :: 1.299371237570 Confinement :: 0.351706856372 Orbital energies State L Occupation Energy[a.u.] Energy[eV] 1 0 2.000 -0.864888 -23.534802 1 1 4.000 -0.318028 -8.653976 Guess for atomic kind: H Electronic structure Total number of core electrons 0.00 Total number of valence electrons 1.00 Total number of electrons 1.00 Multiplicity not specified S 1.00 ******************************************************************************* Iteration Convergence Energy [au] ******************************************************************************* 1 0.440266E-02 -0.423513531970 2 0.325828E-03 -0.423525175186 3 0.252148E-04 -0.423525335541 4 0.637775E-08 -0.423525336420 Energy components [Hartree] Total Energy :: -0.423525336420 Band Energy :: -0.195262559383 Kinetic Energy :: 0.470173284674 Potential Energy :: -0.893698621094 Virial (-V/T) :: 1.900785625696 Core Energy :: -0.479699819139 XC Energy :: -0.247097449670 Coulomb Energy :: 0.303271932388 Total Pseudopotential Energy :: -0.967738859557 Local Pseudopotential Energy :: -0.967738859557 Nonlocal Pseudopotential Energy :: 0.000000000000 Confinement :: 0.178657557441 Orbital energies State L Occupation Energy[a.u.] Energy[eV] 1 0 1.000 -0.195263 -5.313364 Re-scaling the density matrix to get the right number of electrons # Electrons Trace(P) Scaling factor 616 616.000 1.000 SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Minimizer : DIIS : direct inversion in the iterative subspace using 7 DIIS vectors safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.00100000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999997875 0.0000002125 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000002125 Total charge density g-space grids: 0.0000002125 1 OT DIIS 0.15E+00 4.7 0.02393040 -1291.7605291911 -1.29E+03 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998271 0.0000001729 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001729 Total charge density g-space grids: 0.0000001729 2 OT DIIS 0.15E+00 2.5 0.06132715 -1305.2872481753 -1.35E+01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998299 0.0000001701 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001701 Total charge density g-space grids: 0.0000001701 3 OT DIIS 0.15E+00 1.9 0.02135565 -1323.6155572222 -1.83E+01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998018 0.0000001982 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001982 Total charge density g-space grids: 0.0000001982 4 OT DIIS 0.15E+00 1.5 0.05205544 -1319.1232903420 4.49E+00 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998073 0.0000001927 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001927 Total charge density g-space grids: 0.0000001927 5 OT DIIS 0.15E+00 1.5 0.01171200 -1333.0028949194 -1.39E+01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998204 0.0000001796 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001796 Total charge density g-space grids: 0.0000001796 6 OT DIIS 0.15E+00 1.4 0.00870872 -1334.7858056646 -1.78E+00 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998168 0.0000001832 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001832 Total charge density g-space grids: 0.0000001832 7 OT DIIS 0.15E+00 1.4 0.00617422 -1337.2510818332 -2.47E+00 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998177 0.0000001823 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001823 Total charge density g-space grids: 0.0000001823 8 OT DIIS 0.15E+00 1.4 0.00386415 -1338.0049792750 -7.54E-01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998186 0.0000001814 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001814 Total charge density g-space grids: 0.0000001814 9 OT DIIS 0.15E+00 1.3 0.00261330 -1338.6834870217 -6.79E-01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998169 0.0000001831 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001830 Total charge density g-space grids: 0.0000001830 10 OT DIIS 0.15E+00 1.4 0.00214265 -1338.9315341589 -2.48E-01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998186 0.0000001814 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001814 Total charge density g-space grids: 0.0000001814 11 OT DIIS 0.15E+00 1.3 0.00163172 -1339.1058903025 -1.74E-01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998186 0.0000001814 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001814 Total charge density g-space grids: 0.0000001814 12 OT DIIS 0.15E+00 1.3 0.00101528 -1339.1950968755 -8.92E-02 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998185 0.0000001815 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001815 Total charge density g-space grids: 0.0000001815 13 OT DIIS 0.15E+00 1.3 0.00069191 -1339.2288030645 -3.37E-02 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998192 0.0000001808 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001808 Total charge density g-space grids: 0.0000001808 14 OT DIIS 0.15E+00 1.3 0.00053991 -1339.2460263171 -1.72E-02 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998180 0.0000001820 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001820 Total charge density g-space grids: 0.0000001820 15 OT DIIS 0.15E+00 1.3 0.00037388 -1339.2592672900 -1.32E-02 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998193 0.0000001807 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001807 Total charge density g-space grids: 0.0000001807 16 OT DIIS 0.15E+00 1.3 0.00025303 -1339.2671085655 -7.84E-03 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998188 0.0000001812 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001812 Total charge density g-space grids: 0.0000001812 17 OT DIIS 0.15E+00 1.3 0.00017866 -1339.2710065976 -3.90E-03 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998188 0.0000001812 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001812 Total charge density g-space grids: 0.0000001812 18 OT DIIS 0.15E+00 1.3 0.00012866 -1339.2733770779 -2.37E-03 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998189 0.0000001811 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 19 OT DIIS 0.15E+00 1.3 0.00010342 -1339.2752098252 -1.83E-03 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998189 0.0000001811 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 20 OT DIIS 0.15E+00 1.3 0.00009566 -1339.2768138970 -1.60E-03 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998189 0.0000001811 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001811 Total charge density g-space grids: 0.0000001811 21 OT DIIS 0.15E+00 1.3 0.00008626 -1339.2776444134 -8.31E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 22 OT DIIS 0.15E+00 1.3 0.00007696 -1339.2786279609 -9.84E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998189 0.0000001811 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001811 Total charge density g-space grids: 0.0000001811 23 OT DIIS 0.15E+00 1.3 0.00006828 -1339.2791828642 -5.55E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 24 OT DIIS 0.15E+00 1.3 0.00005829 -1339.2797968326 -6.14E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998189 0.0000001811 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 25 OT DIIS 0.15E+00 1.3 0.00005340 -1339.2803148355 -5.18E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 26 OT DIIS 0.15E+00 1.3 0.00004663 -1339.2807947361 -4.80E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 27 OT DIIS 0.15E+00 1.3 0.00004123 -1339.2812323249 -4.38E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 28 OT DIIS 0.15E+00 1.3 0.00003925 -1339.2816508605 -4.19E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 29 OT DIIS 0.15E+00 1.3 0.00003696 -1339.2818878875 -2.37E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 30 OT DIIS 0.15E+00 1.3 0.00003409 -1339.2822037556 -3.16E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 31 OT DIIS 0.15E+00 1.3 0.00003500 -1339.2824303466 -2.27E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 32 OT DIIS 0.15E+00 1.3 0.00003018 -1339.2826401247 -2.10E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 33 OT DIIS 0.15E+00 1.3 0.00002786 -1339.2828291441 -1.89E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 34 OT DIIS 0.15E+00 1.3 0.00002537 -1339.2830048335 -1.76E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 35 OT DIIS 0.15E+00 1.3 0.00002332 -1339.2831615324 -1.57E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 36 OT DIIS 0.15E+00 1.3 0.00002243 -1339.2833254303 -1.64E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 37 OT DIIS 0.15E+00 1.3 0.00002175 -1339.2834328942 -1.07E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 38 OT DIIS 0.15E+00 1.3 0.00002010 -1339.2835665203 -1.34E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 39 OT DIIS 0.15E+00 1.3 0.00002028 -1339.2836673049 -1.01E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 40 OT DIIS 0.15E+00 1.3 0.00001871 -1339.2837498539 -8.25E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 41 OT DIIS 0.15E+00 1.3 0.00001763 -1339.2838361626 -8.63E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 42 OT DIIS 0.15E+00 1.3 0.00001643 -1339.2839198270 -8.37E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 43 OT DIIS 0.15E+00 1.3 0.00001537 -1339.2839954785 -7.57E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 44 OT DIIS 0.15E+00 1.3 0.00001479 -1339.2840738970 -7.84E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 45 OT DIIS 0.15E+00 1.3 0.00001416 -1339.2841269395 -5.30E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 46 OT DIIS 0.15E+00 1.3 0.00001320 -1339.2841911967 -6.43E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 47 OT DIIS 0.15E+00 1.3 0.00001379 -1339.2842470177 -5.58E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 48 OT DIIS 0.15E+00 1.3 0.00001258 -1339.2842876474 -4.06E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 49 OT DIIS 0.15E+00 1.3 0.00001168 -1339.2843279550 -4.03E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 50 OT DIIS 0.15E+00 1.3 0.00001090 -1339.2843630073 -3.51E-05 Leaving inner SCF loop after reaching 50 steps. Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 Overlap energy of the core charge distribution: 0.00000233573955 Self energy of the core charge distribution: -3450.32743283959644 Core Hamiltonian energy: 1001.78258927866443 Hartree energy: 1434.68307657161949 Exchange-correlation energy: -325.21524642709443 Dispersion energy: -0.20735192667451 Total energy: -1339.28436300734165 outer SCF iter = 1 RMS gradient = 0.11E-04 energy = -1339.2843630073 ----------------------------------- OT --------------------------------------- Minimizer : DIIS : direct inversion in the iterative subspace using 7 DIIS vectors safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.00100000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 1 OT DIIS 0.15E+00 5.5 0.00004504 -1339.2843919277 -2.89E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 2 OT DIIS 0.15E+00 1.5 0.00001853 -1339.2845896369 -1.98E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 3 OT DIIS 0.15E+00 1.3 0.00001816 -1339.2846203374 -3.07E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 4 OT DIIS 0.15E+00 1.2 0.00000232 -1339.2846275388 -7.20E-06 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 5 OT DIIS 0.15E+00 1.3 0.00000052 -1339.2846276860 -1.47E-07 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 6 OT DIIS 0.15E+00 1.3 0.00000039 -1339.2846276895 -3.46E-09 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 7 OT DIIS 0.15E+00 1.2 0.00000008 -1339.2846276928 -3.26E-09 *** SCF run converged in 7 steps *** Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 Overlap energy of the core charge distribution: 0.00000233573955 Self energy of the core charge distribution: -3450.32743283959644 Core Hamiltonian energy: 1001.78139775306806 Hartree energy: 1434.68384135493488 Exchange-correlation energy: -325.21508437023346 Dispersion energy: -0.20735192667451 Total energy: -1339.28462769276166 outer SCF iter = 2 RMS gradient = 0.79E-07 energy = -1339.2846276928 outer SCF loop converged in 2 iterations or 57 steps !-----------------------------------------------------------------------------! Mulliken Population Analysis # Atom Element Kind Atomic population Net charge 1 N 1 4.442456 0.557544 2 O 2 6.228768 -0.228768 3 O 2 6.244548 -0.244548 4 O 2 6.166640 -0.166640 5 N 1 4.443326 0.556674 6 O 2 6.245334 -0.245334 7 O 2 6.228928 -0.228928 8 O 2 6.793280 -0.793280 9 H 3 0.598050 0.401950 10 H 3 0.643892 0.356108 11 O 2 6.814090 -0.814090 12 H 3 0.574471 0.425529 13 H 3 0.608056 0.391944 14 O 2 6.864887 -0.864887 15 H 3 0.575360 0.424640 16 H 3 0.591990 0.408010 17 O 2 6.761264 -0.761264 18 H 3 0.617218 0.382782 19 H 3 0.593730 0.406270 20 O 2 6.855376 -0.855376 21 H 3 0.571867 0.428133 22 H 3 0.565649 0.434351 23 O 2 6.837388 -0.837388 24 H 3 0.585540 0.414460 25 H 3 0.585536 0.414464 26 O 2 6.825778 -0.825778 27 H 3 0.580586 0.419414 28 H 3 0.585953 0.414047 29 O 2 6.793141 -0.793141 30 H 3 0.573482 0.426518 31 H 3 0.614575 0.385425 32 O 2 6.792325 -0.792325 33 H 3 0.595145 0.404855 34 H 3 0.581797 0.418203 35 O 2 6.720144 -0.720144 36 H 3 0.605942 0.394058 37 H 3 0.650187 0.349813 38 O 2 6.815195 -0.815195 39 H 3 0.625585 0.374415 40 H 3 0.590571 0.409429 41 O 2 6.751008 -0.751008 42 H 3 0.615100 0.384900 43 H 3 0.648935 0.351065 44 H 3 0.582477 0.417523 45 O 2 6.793062 -0.793062 46 H 3 0.619556 0.380444 47 H 3 0.585546 0.414454 48 O 2 6.728920 -0.728920 49 H 3 0.594334 0.405666 50 H 3 0.611397 0.388603 51 O 2 6.774955 -0.774955 52 H 3 0.599641 0.400359 53 H 3 0.581589 0.418411 54 O 2 6.756151 -0.756151 55 H 3 0.626457 0.373543 56 H 3 0.594178 0.405822 57 O 2 6.715446 -0.715446 58 H 3 0.623021 0.376979 59 H 3 0.624500 0.375500 60 O 2 6.821649 -0.821649 61 H 3 0.589736 0.410264 62 H 3 0.564719 0.435281 63 O 2 6.750860 -0.750860 64 H 3 0.626480 0.373520 65 H 3 0.610361 0.389639 66 O 2 6.805753 -0.805753 67 H 3 0.620309 0.379691 68 H 3 0.606934 0.393066 69 O 2 6.829976 -0.829976 70 H 3 0.587196 0.412804 71 H 3 0.557362 0.442638 72 O 2 6.829204 -0.829204 73 H 3 0.591298 0.408702 74 H 3 0.574772 0.425228 75 O 2 6.727542 -0.727542 76 H 3 0.606648 0.393352 77 H 3 0.674930 0.325070 78 O 2 6.799257 -0.799257 79 H 3 0.607972 0.392028 80 H 3 0.642164 0.357836 81 O 2 6.813495 -0.813495 82 H 3 0.581717 0.418283 83 H 3 0.624031 0.375969 84 O 2 6.799275 -0.799275 85 H 3 0.585826 0.414174 86 H 3 0.595793 0.404207 87 O 2 6.802196 -0.802196 88 H 3 0.584772 0.415228 89 H 3 0.614712 0.385288 90 O 2 6.828238 -0.828238 91 H 3 0.597760 0.402240 92 H 3 0.575841 0.424159 93 O 2 6.799806 -0.799806 94 H 3 0.594956 0.405044 95 H 3 0.614356 0.385644 96 O 2 6.880615 -0.880615 97 H 3 0.570822 0.429178 98 H 3 0.593791 0.406209 99 O 2 6.862041 -0.862041 100 H 3 0.573372 0.426628 101 H 3 0.572980 0.427020 102 O 2 6.716327 -0.716327 103 H 3 0.644191 0.355809 104 H 3 0.628768 0.371232 105 O 2 6.858519 -0.858519 106 H 3 0.585563 0.414437 107 O 2 6.859932 -0.859932 108 H 3 0.585605 0.414395 109 H 3 0.575734 0.424266 110 O 2 6.819606 -0.819606 111 H 3 0.621240 0.378760 112 H 3 0.587395 0.412605 113 O 2 6.799287 -0.799287 114 H 3 0.601722 0.398278 115 H 3 0.631983 0.368017 116 H 3 0.584341 0.415659 117 O 2 6.784675 -0.784675 118 H 3 0.599791 0.400209 119 H 3 0.603217 0.396783 120 O 2 6.769099 -0.769099 121 H 3 0.589394 0.410606 122 H 3 0.648837 0.351163 123 O 2 6.748839 -0.748839 124 H 3 0.559803 0.440197 125 H 3 0.605193 0.394807 126 O 2 6.711878 -0.711878 127 H 3 0.597521 0.402479 128 H 3 0.625706 0.374294 129 O 2 6.846025 -0.846025 130 H 3 0.618042 0.381958 131 H 3 0.566011 0.433989 132 O 2 6.758061 -0.758061 133 H 3 0.686736 0.313264 134 H 3 0.585422 0.414578 135 O 2 6.694818 -0.694818 136 H 3 0.688891 0.311109 137 H 3 0.602629 0.397371 138 O 2 6.706613 -0.706613 139 H 3 0.665678 0.334322 140 H 3 0.618074 0.381926 141 O 2 6.789185 -0.789185 142 H 3 0.585877 0.414123 143 H 3 0.591429 0.408571 144 O 2 6.831533 -0.831533 145 H 3 0.606166 0.393834 146 H 3 0.588262 0.411738 147 O 2 6.818962 -0.818962 148 H 3 0.598339 0.401661 149 H 3 0.586482 0.413518 150 O 2 6.805866 -0.805866 151 H 3 0.623589 0.376411 152 H 3 0.552390 0.447610 153 O 2 6.751969 -0.751969 154 H 3 0.605798 0.394202 155 H 3 0.613957 0.386043 156 O 2 6.844967 -0.844967 157 H 3 0.562690 0.437310 158 H 3 0.592377 0.407623 159 O 2 6.807630 -0.807630 160 H 3 0.579315 0.420685 161 H 3 0.608697 0.391303 162 O 2 6.787147 -0.787147 163 H 3 0.592313 0.407687 164 H 3 0.632851 0.367149 165 O 2 6.802682 -0.802682 166 H 3 0.600362 0.399638 167 H 3 0.599957 0.400043 168 O 2 6.786333 -0.786333 169 H 3 0.567235 0.432765 170 H 3 0.613718 0.386282 171 O 2 6.733174 -0.733174 172 H 3 0.601872 0.398128 173 H 3 0.680396 0.319604 174 O 2 6.782534 -0.782534 175 H 3 0.617298 0.382702 176 H 3 0.608032 0.391968 177 O 2 6.808692 -0.808692 178 H 3 0.596627 0.403373 179 H 3 0.587280 0.412720 180 O 2 6.780578 -0.780578 181 H 3 0.595236 0.404764 182 H 3 0.611397 0.388603 183 O 2 6.777532 -0.777532 184 H 3 0.599938 0.400062 185 H 3 0.596970 0.403030 186 O 2 6.879066 -0.879066 187 H 3 0.582099 0.417901 188 H 3 0.621375 0.378625 189 O 2 6.847122 -0.847122 190 H 3 0.673053 0.326947 191 H 3 0.597837 0.402163 192 O 2 6.822634 -0.822634 193 H 3 0.587021 0.412979 194 O 2 6.804794 -0.804794 195 H 3 0.631006 0.368994 196 H 3 0.594681 0.405319 197 O 2 6.782924 -0.782924 198 H 3 0.611988 0.388012 199 H 3 0.631614 0.368386 200 O 2 6.812491 -0.812491 201 H 3 0.599651 0.400349 202 H 3 0.586517 0.413483 203 O 2 6.835718 -0.835718 204 H 3 0.583873 0.416127 205 H 3 0.605445 0.394555 206 O 2 6.876144 -0.876144 207 H 3 0.565962 0.434038 208 H 3 0.560947 0.439053 209 O 2 6.707006 -0.707006 210 H 3 0.620323 0.379677 211 H 3 0.622067 0.377933 212 O 2 6.829965 -0.829965 213 H 3 0.595247 0.404753 214 H 3 0.573257 0.426743 215 O 2 6.674826 -0.674826 216 H 3 0.656130 0.343870 217 H 3 0.637647 0.362353 218 O 2 6.816675 -0.816675 219 H 3 0.629934 0.370066 220 H 3 0.552490 0.447510 221 O 2 6.832954 -0.832954 222 H 3 0.615465 0.384535 223 H 3 0.549416 0.450584 # Total charge 616.000000 0.000000 !-----------------------------------------------------------------------------! !-----------------------------------------------------------------------------! Hirshfeld Charges #Atom Element Kind Ref Charge Population Net charge 1 N 1 5.000 4.524 0.476 2 O 2 6.000 6.172 -0.172 3 O 2 6.000 6.180 -0.180 4 O 2 6.000 6.245 -0.245 5 N 1 5.000 4.525 0.475 6 O 2 6.000 6.181 -0.181 7 O 2 6.000 6.173 -0.173 8 O 2 6.000 6.515 -0.515 9 H 3 1.000 0.762 0.238 10 H 3 1.000 0.747 0.253 11 O 2 6.000 6.494 -0.494 12 H 3 1.000 0.747 0.253 13 H 3 1.000 0.751 0.249 14 O 2 6.000 6.517 -0.517 15 H 3 1.000 0.761 0.239 16 H 3 1.000 0.747 0.253 17 O 2 6.000 6.488 -0.488 18 H 3 1.000 0.744 0.256 19 H 3 1.000 0.747 0.253 20 O 2 6.000 6.516 -0.516 21 H 3 1.000 0.757 0.243 22 H 3 1.000 0.746 0.254 23 O 2 6.000 6.508 -0.508 24 H 3 1.000 0.748 0.252 25 H 3 1.000 0.754 0.246 26 O 2 6.000 6.495 -0.495 27 H 3 1.000 0.744 0.256 28 H 3 1.000 0.740 0.260 29 O 2 6.000 6.507 -0.507 30 H 3 1.000 0.739 0.261 31 H 3 1.000 0.745 0.255 32 O 2 6.000 6.471 -0.471 33 H 3 1.000 0.744 0.256 34 H 3 1.000 0.749 0.251 35 O 2 6.000 6.448 -0.448 36 H 3 1.000 0.733 0.267 37 H 3 1.000 0.724 0.276 38 O 2 6.000 6.496 -0.496 39 H 3 1.000 0.751 0.249 40 H 3 1.000 0.766 0.234 41 O 2 6.000 6.494 -0.494 42 H 3 1.000 0.744 0.256 43 H 3 1.000 0.737 0.263 44 H 3 1.000 0.745 0.255 45 O 2 6.000 6.484 -0.484 46 H 3 1.000 0.745 0.255 47 H 3 1.000 0.748 0.252 48 O 2 6.000 6.510 -0.510 49 H 3 1.000 0.757 0.243 50 H 3 1.000 0.758 0.242 51 O 2 6.000 6.485 -0.485 52 H 3 1.000 0.735 0.265 53 H 3 1.000 0.742 0.258 54 O 2 6.000 6.523 -0.523 55 H 3 1.000 0.745 0.255 56 H 3 1.000 0.750 0.250 57 O 2 6.000 6.484 -0.484 58 H 3 1.000 0.731 0.269 59 H 3 1.000 0.738 0.262 60 O 2 6.000 6.504 -0.504 61 H 3 1.000 0.745 0.255 62 H 3 1.000 0.757 0.243 63 O 2 6.000 6.487 -0.487 64 H 3 1.000 0.748 0.252 65 H 3 1.000 0.737 0.263 66 O 2 6.000 6.540 -0.540 67 H 3 1.000 0.753 0.247 68 H 3 1.000 0.741 0.259 69 O 2 6.000 6.469 -0.469 70 H 3 1.000 0.745 0.255 71 H 3 1.000 0.745 0.255 72 O 2 6.000 6.485 -0.485 73 H 3 1.000 0.753 0.247 74 H 3 1.000 0.745 0.255 75 O 2 6.000 6.545 -0.545 76 H 3 1.000 0.748 0.252 77 H 3 1.000 0.731 0.269 78 O 2 6.000 6.504 -0.504 79 H 3 1.000 0.752 0.248 80 H 3 1.000 0.759 0.241 81 O 2 6.000 6.496 -0.496 82 H 3 1.000 0.744 0.256 83 H 3 1.000 0.757 0.243 84 O 2 6.000 6.490 -0.490 85 H 3 1.000 0.745 0.255 86 H 3 1.000 0.742 0.258 87 O 2 6.000 6.501 -0.501 88 H 3 1.000 0.760 0.240 89 H 3 1.000 0.749 0.251 90 O 2 6.000 6.494 -0.494 91 H 3 1.000 0.762 0.238 92 H 3 1.000 0.754 0.246 93 O 2 6.000 6.512 -0.512 94 H 3 1.000 0.749 0.251 95 H 3 1.000 0.750 0.250 96 O 2 6.000 6.530 -0.530 97 H 3 1.000 0.754 0.246 98 H 3 1.000 0.762 0.238 99 O 2 6.000 6.526 -0.526 100 H 3 1.000 0.752 0.248 101 H 3 1.000 0.754 0.246 102 O 2 6.000 6.507 -0.507 103 H 3 1.000 0.753 0.247 104 H 3 1.000 0.754 0.246 105 O 2 6.000 6.538 -0.538 106 H 3 1.000 0.756 0.244 107 O 2 6.000 6.527 -0.527 108 H 3 1.000 0.752 0.248 109 H 3 1.000 0.756 0.244 110 O 2 6.000 6.530 -0.530 111 H 3 1.000 0.760 0.240 112 H 3 1.000 0.752 0.248 113 O 2 6.000 6.513 -0.513 114 H 3 1.000 0.754 0.246 115 H 3 1.000 0.758 0.242 116 H 3 1.000 0.754 0.246 117 O 2 6.000 6.494 -0.494 118 H 3 1.000 0.748 0.252 119 H 3 1.000 0.754 0.246 120 O 2 6.000 6.487 -0.487 121 H 3 1.000 0.756 0.244 122 H 3 1.000 0.732 0.268 123 O 2 6.000 6.517 -0.517 124 H 3 1.000 0.756 0.244 125 H 3 1.000 0.755 0.245 126 O 2 6.000 6.507 -0.507 127 H 3 1.000 0.746 0.254 128 H 3 1.000 0.743 0.257 129 O 2 6.000 6.502 -0.502 130 H 3 1.000 0.757 0.243 131 H 3 1.000 0.757 0.243 132 O 2 6.000 6.545 -0.545 133 H 3 1.000 0.738 0.262 134 H 3 1.000 0.757 0.243 135 O 2 6.000 6.510 -0.510 136 H 3 1.000 0.742 0.258 137 H 3 1.000 0.742 0.258 138 O 2 6.000 6.501 -0.501 139 H 3 1.000 0.733 0.267 140 H 3 1.000 0.765 0.235 141 O 2 6.000 6.491 -0.491 142 H 3 1.000 0.762 0.238 143 H 3 1.000 0.750 0.250 144 O 2 6.000 6.522 -0.522 145 H 3 1.000 0.750 0.250 146 H 3 1.000 0.755 0.245 147 O 2 6.000 6.488 -0.488 148 H 3 1.000 0.755 0.245 149 H 3 1.000 0.764 0.236 150 O 2 6.000 6.499 -0.499 151 H 3 1.000 0.730 0.270 152 H 3 1.000 0.752 0.248 153 O 2 6.000 6.513 -0.513 154 H 3 1.000 0.753 0.247 155 H 3 1.000 0.746 0.254 156 O 2 6.000 6.492 -0.492 157 H 3 1.000 0.752 0.248 158 H 3 1.000 0.758 0.242 159 O 2 6.000 6.485 -0.485 160 H 3 1.000 0.743 0.257 161 H 3 1.000 0.741 0.259 162 O 2 6.000 6.511 -0.511 163 H 3 1.000 0.735 0.265 164 H 3 1.000 0.753 0.247 165 O 2 6.000 6.525 -0.525 166 H 3 1.000 0.743 0.257 167 H 3 1.000 0.760 0.240 168 O 2 6.000 6.472 -0.472 169 H 3 1.000 0.744 0.256 170 H 3 1.000 0.729 0.271 171 O 2 6.000 6.520 -0.520 172 H 3 1.000 0.744 0.256 173 H 3 1.000 0.734 0.266 174 O 2 6.000 6.486 -0.486 175 H 3 1.000 0.750 0.250 176 H 3 1.000 0.762 0.238 177 O 2 6.000 6.492 -0.492 178 H 3 1.000 0.746 0.254 179 H 3 1.000 0.761 0.239 180 O 2 6.000 6.491 -0.491 181 H 3 1.000 0.757 0.243 182 H 3 1.000 0.748 0.252 183 O 2 6.000 6.470 -0.470 184 H 3 1.000 0.747 0.253 185 H 3 1.000 0.745 0.255 186 O 2 6.000 6.536 -0.536 187 H 3 1.000 0.750 0.250 188 H 3 1.000 0.762 0.238 189 O 2 6.000 6.538 -0.538 190 H 3 1.000 0.729 0.271 191 H 3 1.000 0.757 0.243 192 O 2 6.000 6.513 -0.513 193 H 3 1.000 0.754 0.246 194 O 2 6.000 6.507 -0.507 195 H 3 1.000 0.757 0.243 196 H 3 1.000 0.741 0.259 197 O 2 6.000 6.487 -0.487 198 H 3 1.000 0.748 0.252 199 H 3 1.000 0.757 0.243 200 O 2 6.000 6.497 -0.497 201 H 3 1.000 0.751 0.249 202 H 3 1.000 0.753 0.247 203 O 2 6.000 6.514 -0.514 204 H 3 1.000 0.768 0.232 205 H 3 1.000 0.746 0.254 206 O 2 6.000 6.511 -0.511 207 H 3 1.000 0.753 0.247 208 H 3 1.000 0.743 0.257 209 O 2 6.000 6.501 -0.501 210 H 3 1.000 0.735 0.265 211 H 3 1.000 0.736 0.264 212 O 2 6.000 6.500 -0.500 213 H 3 1.000 0.737 0.263 214 H 3 1.000 0.747 0.253 215 O 2 6.000 6.484 -0.484 216 H 3 1.000 0.729 0.271 217 H 3 1.000 0.739 0.261 218 O 2 6.000 6.493 -0.493 219 H 3 1.000 0.720 0.280 220 H 3 1.000 0.753 0.247 221 O 2 6.000 6.495 -0.495 222 H 3 1.000 0.742 0.258 223 H 3 1.000 0.752 0.248 Total Charge 0.000 !-----------------------------------------------------------------------------! Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -1339.284627692954928 MD_ENERGIES| Initialization proceeding ******************************** GO CP2K GO! ********************************** INITIAL POTENTIAL ENERGY[hartree] = -0.133928462769E+04 INITIAL KINETIC ENERGY[hartree] = 0.315198655887E+00 INITIAL TEMPERATURE[K] = 299.344 INITIAL VOLUME[bohr^3] = 0.636456570504E+05 INITIAL CELL LNTHS[bohr] = 0.2545915E+02 0.2939771E+02 0.8503768E+02 INITIAL CELL ANGLS[deg] = 0.9000000E+02 0.9000000E+02 0.9000000E+02 ******************************** GO CP2K GO! ********************************** -------------- next part -------------- TACC: Starting up job 8242055 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... DBCSR| Multiplication driver SMM DBCSR| Multrec recursion limit 512 DBCSR| Multiplication stack size 1000 DBCSR| Multiplication size stacks 3 DBCSR| Use subcommunicators T DBCSR| Use MPI combined types F DBCSR| Use MPI memory allocation T DBCSR| Use Communication thread T DBCSR| Communication thread load 87 **** **** ****** ** PROGRAM STARTED AT 2017-02-09 15:25:07.706 ***** ** *** *** ** PROGRAM STARTED ON c453-902.stampede.tacc.utexas. ** **** ****** PROGRAM STARTED BY tg838439 ***** ** ** ** ** PROGRAM PROCESS ID 130777 **** ** ******* ** PROGRAM STARTED IN /work/04544/tg838439/traj1.20170209_1 50201 CP2K| version string: CP2K version 2.5.1 CP2K| source code revision number: svn:13632 CP2K| is freely available from http://www.cp2k.org/ CP2K| Program compiled at Tue Sep 29 14:13:49 CDT 2015 CP2K| Program compiled on c560-901.stampede.tacc.utexas.edu CP2K| Program compiled for Linux-x86-64-intel CP2K| Input file name water_slab_N2O5_6A_from_surface_z45A_collision.inp GLOBAL| Force Environment number 1 GLOBAL| Basis set file name GTH_BASIS_SETS GLOBAL| Geminal file name BASIS_GEMINAL GLOBAL| Potential file name GTH_POTENTIALS GLOBAL| MM Potential file name MM_POTENTIAL GLOBAL| Coordinate file name __STD_INPUT__ GLOBAL| Method name CP2K GLOBAL| Project name water GLOBAL| Preferred FFT library FFTW3 GLOBAL| Preferred diagonalization lib. SL GLOBAL| Run type MD GLOBAL| All-to-all communication in single precision F GLOBAL| FFTs using library dependent lengths F GLOBAL| Global print level MEDIUM GLOBAL| Total number of message passing processes 64 GLOBAL| Number of threads for this process 1 GLOBAL| This output is from process 0 MEMORY| system memory details [Kb] MEMORY| rank 0 min max average MEMORY| MemTotal 32815324 32815324 32815324 32815324 MEMORY| MemFree 27887184 27887184 28096004 28041864 MEMORY| Buffers 6568 2696 6568 4565 MEMORY| Cached 387296 212096 387296 256118 MEMORY| Slab 536140 517104 536140 523418 MEMORY| SReclaimable 15872 12872 15872 13804 MEMORY| MemLikelyFree 28296920 28296920 28324060 28316351 *** Fundamental physical constants (SI units) *** *** Literature: B. J. Mohr and B. N. Taylor, *** CODATA recommended values of the fundamental physical *** constants: 2006, Web Version 5.1 *** http://physics.nist.gov/constants Speed of light in vacuum [m/s] 2.99792458000000E+08 Magnetic constant or permeability of vacuum [N/A**2] 1.25663706143592E-06 Electric constant or permittivity of vacuum [F/m] 8.85418781762039E-12 Planck constant (h) [J*s] 6.62606896000000E-34 Planck constant (h-bar) [J*s] 1.05457162825177E-34 Elementary charge [C] 1.60217648700000E-19 Electron mass [kg] 9.10938215000000E-31 Electron g factor [ ] -2.00231930436220E+00 Proton mass [kg] 1.67262163700000E-27 Fine-structure constant 7.29735253760000E-03 Rydberg constant [1/m] 1.09737315685270E+07 Avogadro constant [1/mol] 6.02214179000000E+23 Boltzmann constant [J/K] 1.38065040000000E-23 Atomic mass unit [kg] 1.66053878200000E-27 Bohr radius [m] 5.29177208590000E-11 *** Conversion factors *** [u] -> [a.u.] 1.82288848426455E+03 [Angstrom] -> [Bohr] = [a.u.] 1.88972613288564E+00 [a.u.] = [Bohr] -> [Angstrom] 5.29177208590000E-01 [a.u.] -> [s] 2.41888432650478E-17 [a.u.] -> [fs] 2.41888432650478E-02 [a.u.] -> [J] 4.35974393937059E-18 [a.u.] -> [N] 8.23872205491840E-08 [a.u.] -> [K] 3.15774647902944E+05 [a.u.] -> [kJ/mol] 2.62549961709828E+03 [a.u.] -> [kcal/mol] 6.27509468713739E+02 [a.u.] -> [Pa] 2.94210107994716E+13 [a.u.] -> [bar] 2.94210107994716E+08 [a.u.] -> [atm] 2.90362800883016E+08 [a.u.] -> [eV] 2.72113838565563E+01 [a.u.] -> [Hz] 6.57968392072181E+15 [a.u.] -> [1/cm] (wave numbers) 2.19474631370540E+05 [a.u./Bohr**2] -> [1/cm] 5.14048714338585E+03 CELL| Volume [angstrom^3]: 9431.313 CELL| Vector a [angstrom]: 13.472 0.000 0.000 |a| = 13.472 CELL| Vector b [angstrom]: 0.000 15.557 0.000 |b| = 15.557 CELL| Vector c [angstrom]: 0.000 0.000 45.000 |c| = 45.000 CELL| Angle (b,c), alpha [degree]: 90.000 CELL| Angle (a,c), beta [degree]: 90.000 CELL| Angle (a,b), gamma [degree]: 90.000 CELL| Numerically orthorhombic: YES CELL_REF| Volume [angstrom^3]: 9431.313 CELL_REF| Vector a [angstrom 13.472 0.000 0.000 |a| = 13.472 CELL_REF| Vector b [angstrom 0.000 15.557 0.000 |b| = 15.557 CELL_REF| Vector c [angstrom 0.000 0.000 45.000 |c| = 45.000 CELL_REF| Angle (b,c), alpha [degree]: 90.000 CELL_REF| Angle (a,c), beta [degree]: 90.000 CELL_REF| Angle (a,b), gamma [degree]: 90.000 CELL_REF| Numerically orthorhombic: YES CELL_TOP| Volume [angstrom^3]: 9431.313 CELL_TOP| Vector a [angstrom 13.472 0.000 0.000 |a| = 13.472 CELL_TOP| Vector b [angstrom 0.000 15.557 0.000 |b| = 15.557 CELL_TOP| Vector c [angstrom 0.000 0.000 45.000 |c| = 45.000 CELL_TOP| Angle (b,c), alpha [degree]: 90.000 CELL_TOP| Angle (a,c), beta [degree]: 90.000 CELL_TOP| Angle (a,b), gamma [degree]: 90.000 CELL_TOP| Numerically orthorhombic: YES GENERATE| Preliminary Number of Bonds generated: 0 GENERATE| Achieved consistency in connectivity generation. ******************************************************************************* ******************************************************************************* ** ** ** ##### ## ## ** ** ## ## ## ## ## ** ** ## ## ## ###### ** ** ## ## ## ## ## ##### ## ## #### ## ##### ##### ** ** ## ## ## ## ## ## ## ## ## ## ## ## ## ## ** ** ## ## ## ## ## ## ## #### ### ## ###### ###### ** ** ## ### ## ## ## ## ## ## ## ## ## ## ** ** ####### ##### ## ##### ## ## #### ## ##### ## ** ** ## ## ** ** ** ** ... make the atoms dance ** ** ** ** Copyright (C) by CP2K Developers Group (2000 - 2014) ** ** ** ******************************************************************************* DFT| Spin restricted Kohn-Sham (RKS) calculation RKS DFT| Multiplicity 1 DFT| Number of spin states 1 DFT| Charge 0 DFT| Self-interaction correction (SIC) NO DFT| Cutoffs: density 1.000000E-10 DFT| gradient 1.000000E-10 DFT| tau 1.000000E-10 DFT| cutoff_smoothing_range 0.000000E+00 DFT| XC density smoothing NN10 DFT| XC derivatives SPLINE2_SMOOTH FUNCTIONAL| ROUTINE=NEW FUNCTIONAL| PBE: FUNCTIONAL| J.P.Perdew, K.Burke, M.Ernzerhof, Phys. Rev. Letter, vol. 77, n 18, FUNCTIONAL| pp. 3865-3868, (1996){spin unpolarized} vdW POTENTIAL| Pair Potential vdW POTENTIAL| Potential Form: S. Grimme et al, JCP 132: 154104 (2010) vdW POTENTIAL| Cutoff Radius [Bohr]: 28.35 vdW POTENTIAL| s6 Scaling Factor: 1.0000 vdW POTENTIAL| sr6 Scaling Factor: 1.2170 vdW POTENTIAL| s8 Scaling Factor: 0.7220 vdW POTENTIAL| Cutoff for CN calculation: 0.1000E-05 QS| Method: GPW QS| Density plane wave grid type NON-SPHERICAL FULLSPACE QS| Number of grid levels: 4 QS| Density cutoff [a.u.]: 160.0 QS| Multi grid cutoff [a.u.]: 1) grid level 160.0 QS| 2) grid level 53.3 QS| 3) grid level 17.8 QS| 4) grid level 5.9 QS| Grid level progression factor: 3.0 QS| Relative density cutoff [a.u.]: 25.0 QS| Consistent realspace mapping and integration QS| Interaction thresholds: eps_pgf_orb: 1.0E-07 QS| eps_filter_matrix: 0.0E+00 QS| eps_core_charge: 1.0E-16 QS| eps_rho_gspace: 1.0E-14 QS| eps_rho_rspace: 1.0E-14 QS| eps_gvg_rspace: 1.0E-07 QS| eps_ppl: 1.0E-02 QS| eps_ppnl: 1.0E-09 ATOMIC KIND INFORMATION 1. Atomic kind: N Number of atoms: 2 Orbital Basis Set TZV2P-GTH Number of orbital shell sets: 2 Number of orbital shells: 8 Number of primitive Cartesian functions: 7 Number of Cartesian basis functions: 24 Number of spherical basis functions: 22 Norm type: 2 Normalised Cartesian orbitals: Set Shell Orbital Exponent Coefficient 1 1 2s 7.622745 0.321703 2.797061 0.161118 0.990977 -0.264934 0.341731 -0.199987 0.111682 -0.023066 1 2 3s 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.318547 0.111682 0.000000 1 3 4s 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.000000 0.111682 0.137689 1 4 3px 7.622745 -1.014025 2.797061 -0.927144 0.990977 -0.514975 0.341731 -0.158623 0.111682 -0.021774 1 4 3py 7.622745 -1.014025 2.797061 -0.927144 0.990977 -0.514975 0.341731 -0.158623 0.111682 -0.021774 1 4 3pz 7.622745 -1.014025 2.797061 -0.927144 0.990977 -0.514975 0.341731 -0.158623 0.111682 -0.021774 1 5 4px 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.372431 0.111682 0.000000 1 5 4py 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.372431 0.111682 0.000000 1 5 4pz 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.372431 0.111682 0.000000 1 6 5px 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.000000 0.111682 0.092028 1 6 5py 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.000000 0.111682 0.092028 1 6 5pz 7.622745 0.000000 2.797061 0.000000 0.990977 0.000000 0.341731 0.000000 0.111682 0.092028 2 1 3dx2 1.654000 3.970513 0.469000 0.000000 2 1 3dxy 1.654000 6.877130 0.469000 0.000000 2 1 3dxz 1.654000 6.877130 0.469000 0.000000 2 1 3dy2 1.654000 3.970513 0.469000 0.000000 2 1 3dyz 1.654000 6.877130 0.469000 0.000000 2 1 3dz2 1.654000 3.970513 0.469000 0.000000 2 2 4dx2 1.654000 0.000000 0.469000 0.437484 2 2 4dxy 1.654000 0.000000 0.469000 0.757744 2 2 4dxz 1.654000 0.000000 0.469000 0.757744 2 2 4dy2 1.654000 0.000000 0.469000 0.437484 2 2 4dyz 1.654000 0.000000 0.469000 0.757744 2 2 4dz2 1.654000 0.000000 0.469000 0.437484 Potential information for GTH-PBE-q5 Description: Goedecker-Teter-Hutter pseudopotential Goedecker et al., PRB 54, 1703 (1996) Hartwigsen et al., PRB 58, 3641 (1998) Krack, TCA 114, 145 (2005) Gaussian exponent of the core charge distribution: 6.208322 Electronic configuration (s p d ...): 2 3 Parameters of the local part of the GTH pseudopotential: rloc C1 C2 C3 C4 0.283791 -12.415226 1.868096 Parameters of the non-local part of the GTH pseudopotential: l r(l) h(i,j,l) 0 0.255405 13.630263 1 0.245495 2. Atomic kind: O Number of atoms: 77 Orbital Basis Set TZV2P-GTH Number of orbital shell sets: 2 Number of orbital shells: 8 Number of primitive Cartesian functions: 7 Number of Cartesian basis functions: 24 Number of spherical basis functions: 22 Norm type: 2 Normalised Cartesian orbitals: Set Shell Orbital Exponent Coefficient 1 1 2s 10.267442 0.404544 3.748050 0.199889 1.330834 -0.336302 0.455680 -0.246356 0.146292 -0.028287 1 2 3s 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.395280 0.146292 0.000000 1 3 4s 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.000000 0.146292 0.168588 1 4 3px 10.267442 -1.561025 3.748050 -1.394275 1.330834 -0.754014 0.455680 -0.224400 0.146292 -0.029841 1 4 3py 10.267442 -1.561025 3.748050 -1.394275 1.330834 -0.754014 0.455680 -0.224400 0.146292 -0.029841 1 4 3pz 10.267442 -1.561025 3.748050 -1.394275 1.330834 -0.754014 0.455680 -0.224400 0.146292 -0.029841 1 5 4px 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.533661 0.146292 0.000000 1 5 4py 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.533661 0.146292 0.000000 1 5 4pz 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.533661 0.146292 0.000000 1 6 5px 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.000000 0.146292 0.128963 1 6 5py 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.000000 0.146292 0.128963 1 6 5pz 10.267442 0.000000 3.748050 0.000000 1.330834 0.000000 0.455680 0.000000 0.146292 0.128963 2 1 3dx2 2.314000 7.145709 0.645000 0.000000 2 1 3dxy 2.314000 12.376731 0.645000 0.000000 2 1 3dxz 2.314000 12.376731 0.645000 0.000000 2 1 3dy2 2.314000 7.145709 0.645000 0.000000 2 1 3dyz 2.314000 12.376731 0.645000 0.000000 2 1 3dz2 2.314000 7.145709 0.645000 0.000000 2 2 4dx2 2.314000 0.000000 0.645000 0.764080 2 2 4dxy 2.314000 0.000000 0.645000 1.323426 2 2 4dxz 2.314000 0.000000 0.645000 1.323426 2 2 4dy2 2.314000 0.000000 0.645000 0.764080 2 2 4dyz 2.314000 0.000000 0.645000 1.323426 2 2 4dz2 2.314000 0.000000 0.645000 0.764080 Potential information for GTH-PBE-q6 Description: Goedecker-Teter-Hutter pseudopotential Goedecker et al., PRB 54, 1703 (1996) Hartwigsen et al., PRB 58, 3641 (1998) Krack, TCA 114, 145 (2005) Gaussian exponent of the core charge distribution: 8.360253 Electronic configuration (s p d ...): 2 4 Parameters of the local part of the GTH pseudopotential: rloc C1 C2 C3 C4 0.244554 -16.667215 2.487311 Parameters of the non-local part of the GTH pseudopotential: l r(l) h(i,j,l) 0 0.220956 18.337458 1 0.211332 3. Atomic kind: H Number of atoms: 144 Orbital Basis Set TZV2P-GTH Number of orbital shell sets: 2 Number of orbital shells: 5 Number of primitive Cartesian functions: 7 Number of Cartesian basis functions: 9 Number of spherical basis functions: 9 Norm type: 2 Normalised Cartesian orbitals: Set Shell Orbital Exponent Coefficient 1 1 1s 10.882724 -0.071340 3.096875 -0.104410 0.987452 -0.135375 0.345069 -0.133923 0.149269 -0.073092 1 2 2s 10.882724 0.000000 3.096875 0.000000 0.987452 0.000000 0.345069 0.320878 0.149269 0.000000 1 3 3s 10.882724 0.000000 3.096875 0.000000 0.987452 0.000000 0.345069 0.000000 0.149269 0.171154 2 1 2px 1.407000 2.184277 0.388000 0.000000 2 1 2py 1.407000 2.184277 0.388000 0.000000 2 1 2pz 1.407000 2.184277 0.388000 0.000000 2 2 3px 1.407000 0.000000 0.388000 0.436495 2 2 3py 1.407000 0.000000 0.388000 0.436495 2 2 3pz 1.407000 0.000000 0.388000 0.436495 Potential information for GTH-PBE-q1 Description: Goedecker-Teter-Hutter pseudopotential Goedecker et al., PRB 54, 1703 (1996) Hartwigsen et al., PRB 58, 3641 (1998) Krack, TCA 114, 145 (2005) Gaussian exponent of the core charge distribution: 12.500000 Electronic configuration (s p d ...): 1 Parameters of the local part of the GTH pseudopotential: rloc C1 C2 C3 C4 0.200000 -4.178900 0.724463 MOLECULE KIND INFORMATION All atoms are their own molecule, skipping detailed information TOTAL NUMBERS AND MAXIMUM NUMBERS Total number of - Atomic kinds: 3 - Atoms: 223 - Shell sets: 446 - Shells: 1352 - Primitive Cartesian functions: 1561 - Cartesian basis functions: 3192 - Spherical basis functions: 3034 Maximum angular momentum of- Orbital basis functions: 2 - Local part of the GTH pseudopotential: 2 - Non-local part of the GTH pseudopotential: 0 MODULE QUICKSTEP: ATOMIC COORDINATES IN angstrom Atom Kind Element X Y Z Z(eff) Mass 1 1 N 7 -19.317260 -5.454080 11.996970 5.00 14.0067 2 2 O 8 -20.190990 -4.825770 11.466250 6.00 15.9994 3 2 O 8 -19.251930 -6.548670 12.479720 6.00 15.9994 4 2 O 8 -18.051260 -4.552420 12.105280 6.00 15.9994 5 1 N 7 -16.691860 -5.287400 12.291490 5.00 14.0067 6 2 O 8 -16.627980 -6.423410 11.915720 6.00 15.9994 7 2 O 8 -15.898220 -4.515540 12.754550 6.00 15.9994 8 2 O 8 -26.566797 5.885766 -4.325634 6.00 15.9994 9 3 H 1 -26.158273 6.043929 -3.435499 1.00 2.0000 10 3 H 1 -26.611093 6.760476 -4.676844 1.00 2.0000 11 2 O 8 -9.468377 -11.270550 0.584346 6.00 15.9994 12 3 H 1 -10.380793 -11.077813 0.081767 1.00 2.0000 13 3 H 1 -8.866036 -10.622268 0.238165 1.00 2.0000 14 2 O 8 -8.515451 -10.716151 -3.124136 6.00 15.9994 15 3 H 1 -8.871918 -9.979485 -2.588685 1.00 2.0000 16 3 H 1 -8.380633 -11.457102 -2.382064 1.00 2.0000 17 2 O 8 -15.407322 -9.706175 1.152142 6.00 15.9994 18 3 H 1 -15.919904 -9.502920 0.300948 1.00 2.0000 19 3 H 1 -15.479816 -10.654609 1.318487 1.00 2.0000 20 2 O 8 -18.657623 -5.954755 -2.906634 6.00 15.9994 21 3 H 1 -18.715786 -6.841698 -2.495810 1.00 2.0000 22 3 H 1 -18.292159 -5.343766 -2.163856 1.00 2.0000 23 2 O 8 -25.874532 -3.300482 -0.518665 6.00 15.9994 24 3 H 1 -26.443879 -2.645222 -1.028018 1.00 2.0000 25 3 H 1 -25.048064 -3.565552 -1.000270 1.00 2.0000 26 2 O 8 -22.004939 -2.394582 -2.702908 6.00 15.9994 27 3 H 1 -22.646176 -3.086506 -2.375252 1.00 2.0000 28 3 H 1 -22.411575 -1.495636 -2.610173 1.00 2.0000 29 2 O 8 -21.674779 2.782972 -1.222029 6.00 15.9994 30 3 H 1 -23.495427 0.179908 0.934808 1.00 2.0000 31 3 H 1 -20.754022 2.413233 -1.036063 1.00 2.0000 32 2 O 8 -15.563999 -10.587243 -3.389380 6.00 15.9994 33 3 H 1 -15.439484 -11.500275 -3.083774 1.00 2.0000 34 3 H 1 -14.670989 -10.314392 -3.695421 1.00 2.0000 35 2 O 8 -17.706802 -10.778740 -5.423265 6.00 15.9994 36 3 H 1 -16.831766 -10.692388 -4.960214 1.00 2.0000 37 3 H 1 -17.500550 -10.795254 -6.319638 1.00 2.0000 38 2 O 8 -18.858603 -8.475688 -1.800109 6.00 15.9994 39 3 H 1 -19.051286 -9.008189 -2.658335 1.00 2.0000 40 3 H 1 -19.404077 -8.869064 -1.134524 1.00 2.0000 41 2 O 8 -20.894408 -6.579352 -4.602279 6.00 15.9994 42 3 H 1 -20.681870 -7.528857 -4.572102 1.00 2.0000 43 3 H 1 -24.700569 -10.987772 -4.682408 1.00 2.0000 44 3 H 1 -20.123229 -6.279792 -4.080849 1.00 2.0000 45 2 O 8 -23.201780 -6.377694 -3.271665 6.00 15.9994 46 3 H 1 -23.876723 -6.186120 -3.916763 1.00 2.0000 47 3 H 1 -22.317574 -6.405702 -3.801122 1.00 2.0000 48 2 O 8 -24.221224 -11.797515 -4.388924 6.00 15.9994 49 3 H 1 -17.368477 -3.492455 -0.943834 1.00 2.0000 50 3 H 1 -23.447534 -11.427342 -3.904331 1.00 2.0000 51 2 O 8 -18.073531 -0.792565 -2.310338 6.00 15.9994 52 3 H 1 -18.728938 -1.465594 -2.611348 1.00 2.0000 53 3 H 1 -18.508357 0.060532 -2.008636 1.00 2.0000 54 2 O 8 -16.797841 0.709889 -4.703266 6.00 15.9994 55 3 H 1 -16.899250 0.114493 -3.912154 1.00 2.0000 56 3 H 1 -17.656753 1.189617 -4.657401 1.00 2.0000 57 2 O 8 -21.482986 -13.917292 -5.277215 6.00 15.9994 58 3 H 1 -22.136925 -13.238744 -5.030117 1.00 2.0000 59 3 H 1 -21.647726 -14.611729 -4.625745 1.00 2.0000 60 2 O 8 -19.677349 -9.326342 -4.258990 6.00 15.9994 61 3 H 1 -20.340685 -9.992412 -3.856958 1.00 2.0000 62 3 H 1 -18.972774 -9.829239 -4.677509 1.00 2.0000 63 2 O 8 -19.089924 -13.830752 -1.653956 6.00 15.9994 64 3 H 1 -18.814470 -13.259645 -0.879613 1.00 2.0000 65 3 H 1 -19.024421 -13.119411 -2.379935 1.00 2.0000 66 2 O 8 -9.428566 -15.031955 -2.722401 6.00 15.9994 67 3 H 1 -8.901382 -14.306282 -2.318582 1.00 2.0000 68 3 H 1 -10.377049 -14.646092 -2.879623 1.00 2.0000 69 2 O 8 -13.895594 -7.297004 -1.388427 6.00 15.9994 70 3 H 1 -13.936919 -6.509339 -1.923312 1.00 2.0000 71 3 H 1 -14.748502 -7.794839 -1.462674 1.00 2.0000 72 2 O 8 -17.966888 -4.239045 -0.879390 6.00 15.9994 73 3 H 1 -19.567288 -3.431965 -0.544106 1.00 2.0000 74 3 H 1 -17.807612 -4.685849 0.001510 1.00 2.0000 75 2 O 8 -19.624155 -2.328222 -4.075912 6.00 15.9994 76 3 H 1 -20.573860 -2.399433 -3.675120 1.00 2.0000 77 3 H 1 -19.743270 -2.380261 -5.030232 1.00 2.0000 78 2 O 8 -15.002983 2.083462 -3.065194 6.00 15.9994 79 3 H 1 -15.540876 1.655779 -3.769307 1.00 2.0000 80 3 H 1 -14.075486 1.886847 -3.154348 1.00 2.0000 81 2 O 8 -18.223527 -5.241135 1.642568 6.00 15.9994 82 3 H 1 -17.360065 -5.223620 2.196571 1.00 2.0000 83 3 H 1 -18.737953 -4.554903 2.060801 1.00 2.0000 84 2 O 8 -22.646206 -10.794753 3.331511 6.00 15.9994 85 3 H 1 -22.893050 -10.889629 2.344531 1.00 2.0000 86 3 H 1 -22.344034 -9.826444 3.419465 1.00 2.0000 87 2 O 8 -23.714704 -4.404961 -1.556718 6.00 15.9994 88 3 H 1 -23.473307 -5.108142 -2.176332 1.00 2.0000 89 3 H 1 -23.409404 -4.706244 -0.637705 1.00 2.0000 90 2 O 8 -13.771982 -5.449281 0.637008 6.00 15.9994 91 3 H 1 -17.183103 -8.762858 -1.601220 1.00 2.0000 92 3 H 1 -13.472219 -4.682816 0.140979 1.00 2.0000 93 2 O 8 -21.880436 -1.686751 3.348032 6.00 15.9994 94 3 H 1 -22.184305 -1.109689 2.591359 1.00 2.0000 95 3 H 1 -22.627295 -2.351101 3.406321 1.00 2.0000 96 2 O 8 -20.540597 1.537957 1.959986 6.00 15.9994 97 3 H 1 -20.927105 2.029535 2.847357 1.00 2.0000 98 3 H 1 -19.270027 0.589953 2.523492 1.00 2.0000 99 2 O 8 -20.326170 5.963779 0.218818 6.00 15.9994 100 3 H 1 -19.983560 6.667843 0.825409 1.00 2.0000 101 3 H 1 -19.835202 5.122233 0.405881 1.00 2.0000 102 2 O 8 -16.132213 -1.186959 1.600520 6.00 15.9994 103 3 H 1 -16.900188 -0.669734 1.853686 1.00 2.0000 104 3 H 1 -15.786008 -1.568446 2.426499 1.00 2.0000 105 2 O 8 -16.192760 -8.849836 -1.493114 6.00 15.9994 106 3 H 1 -15.894972 -9.537712 -2.228412 1.00 2.0000 107 2 O 8 -18.991261 -12.101906 0.816505 6.00 15.9994 108 3 H 1 -18.076233 -12.044519 1.165194 1.00 2.0000 109 3 H 1 -19.537269 -12.761394 1.332216 1.00 2.0000 110 2 O 8 -19.017293 -13.002493 -4.487816 6.00 15.9994 111 3 H 1 -18.779227 -12.153080 -4.875275 1.00 2.0000 112 3 H 1 -19.914257 -13.300164 -4.846476 1.00 2.0000 113 2 O 8 -13.846862 -4.814880 -2.803914 6.00 15.9994 114 3 H 1 -13.860347 -3.836424 -2.790102 1.00 2.0000 115 3 H 1 -14.748879 -5.055615 -3.226935 1.00 2.0000 116 3 H 1 -22.069708 3.078929 -0.381905 1.00 2.0000 117 2 O 8 -19.511457 -2.744666 2.375729 6.00 15.9994 118 3 H 1 -20.402986 -2.718301 2.797179 1.00 2.0000 119 3 H 1 -19.747674 -2.678196 1.447195 1.00 2.0000 120 2 O 8 -22.480097 0.004721 0.938894 6.00 15.9994 121 3 H 1 -21.269751 1.045936 1.458934 1.00 2.0000 122 3 H 1 -22.187954 -0.377403 0.081361 1.00 2.0000 123 2 O 8 -15.755094 -5.007273 2.467645 6.00 15.9994 124 3 H 1 -16.136059 -1.679623 0.123637 1.00 2.0000 125 3 H 1 -15.118985 -5.245440 1.752973 1.00 2.0000 126 2 O 8 -18.857446 2.650958 5.234485 6.00 15.9994 127 3 H 1 -18.074428 2.498889 4.619720 1.00 2.0000 128 3 H 1 -15.280924 -4.285893 2.897510 1.00 2.0000 129 2 O 8 -12.717663 -13.621686 -0.636682 6.00 15.9994 130 3 H 1 -13.680469 -13.707198 -0.454507 1.00 2.0000 131 3 H 1 -12.494374 -12.679151 -0.361702 1.00 2.0000 132 2 O 8 -12.428020 -6.395508 -4.415771 6.00 15.9994 133 3 H 1 -12.829547 -6.380702 -5.304294 1.00 2.0000 134 3 H 1 -12.928783 -5.727527 -3.849016 1.00 2.0000 135 2 O 8 -16.039597 -5.763793 -3.963596 6.00 15.9994 136 3 H 1 -16.205472 -5.004378 -4.461053 1.00 2.0000 137 3 H 1 -16.951564 -5.873893 -3.468604 1.00 2.0000 138 2 O 8 -13.291901 -0.490104 -4.449387 6.00 15.9994 139 3 H 1 -14.153992 -0.118816 -4.774740 1.00 2.0000 140 3 H 1 -12.898323 0.313194 -4.217093 1.00 2.0000 141 2 O 8 -12.251318 -9.304754 -1.895463 6.00 15.9994 142 3 H 1 -11.334116 -9.069043 -1.691476 1.00 2.0000 143 3 H 1 -12.777418 -8.459122 -1.912379 1.00 2.0000 144 2 O 8 -12.538787 -2.214523 2.040255 6.00 15.9994 145 3 H 1 -12.369178 -2.613381 1.099113 1.00 2.0000 146 3 H 1 -12.248015 -1.271585 2.003711 1.00 2.0000 147 2 O 8 -14.068003 -2.123963 -2.243486 6.00 15.9994 148 3 H 1 -13.813298 -1.495347 -2.930916 1.00 2.0000 149 3 H 1 -14.959036 -1.985449 -1.911796 1.00 2.0000 150 2 O 8 -14.775496 -2.407665 3.641523 6.00 15.9994 151 3 H 1 -14.905539 -1.632921 4.239437 1.00 2.0000 152 3 H 1 -13.931729 -2.312820 3.181967 1.00 2.0000 153 2 O 8 -25.206690 -11.476252 4.458583 6.00 15.9994 154 3 H 1 -24.285875 -11.317999 4.156750 1.00 2.0000 155 3 H 1 -25.709107 -11.068033 3.752467 1.00 2.0000 156 2 O 8 -19.301988 -7.789603 2.042123 6.00 15.9994 157 3 H 1 -18.496147 -8.177613 2.490654 1.00 2.0000 158 3 H 1 -19.089680 -6.889051 1.801584 1.00 2.0000 159 2 O 8 -21.831161 -8.058387 3.045820 6.00 15.9994 160 3 H 1 -20.853247 -7.907769 2.832747 1.00 2.0000 161 3 H 1 -22.250421 -7.388211 3.604301 1.00 2.0000 162 2 O 8 -20.434261 -3.043875 -0.310618 6.00 15.9994 163 3 H 1 -21.489035 -4.434524 0.508345 1.00 2.0000 164 3 H 1 -20.836437 -2.644857 -1.072504 1.00 2.0000 165 2 O 8 -18.573340 -0.072650 2.760800 6.00 15.9994 166 3 H 1 -19.083061 -0.963371 2.750164 1.00 2.0000 167 3 H 1 -15.812579 2.542741 1.038339 1.00 2.0000 168 2 O 8 -15.530893 1.766859 -0.377216 6.00 15.9994 169 3 H 1 -15.503136 1.905309 -1.364685 1.00 2.0000 170 3 H 1 -15.655849 0.809544 -0.185183 1.00 2.0000 171 2 O 8 -14.409749 0.536390 4.679163 6.00 15.9994 172 3 H 1 -13.536822 0.952036 4.246160 1.00 2.0000 173 3 H 1 -14.279840 1.028143 5.522151 1.00 2.0000 174 2 O 8 -11.645959 0.365713 1.489198 6.00 15.9994 175 3 H 1 -12.221505 0.848396 0.832955 1.00 2.0000 176 3 H 1 -11.871981 0.835631 2.304797 1.00 2.0000 177 2 O 8 -21.196535 2.693631 4.145587 6.00 15.9994 178 3 H 1 -21.617510 3.610657 3.884948 1.00 2.0000 179 3 H 1 -20.374241 2.850574 4.612551 1.00 2.0000 180 2 O 8 -12.872565 -9.732182 1.978547 6.00 15.9994 181 3 H 1 -12.575848 -8.821493 2.008513 1.00 2.0000 182 3 H 1 -13.813360 -9.530351 1.661305 1.00 2.0000 183 2 O 8 -10.349500 -3.790132 3.010216 6.00 15.9994 184 3 H 1 -9.775833 -3.895205 2.234065 1.00 2.0000 185 3 H 1 -11.185013 -3.442374 2.611073 1.00 2.0000 186 2 O 8 -16.276429 -1.940542 -0.869248 6.00 15.9994 187 3 H 1 -13.809971 -6.176607 -0.037799 1.00 2.0000 188 3 H 1 -17.113336 -1.434139 -1.253808 1.00 2.0000 189 2 O 8 -16.193239 3.171433 1.736967 6.00 15.9994 190 3 H 1 -18.897790 1.772168 5.702941 1.00 2.0000 191 3 H 1 -16.256299 2.561079 2.543264 1.00 2.0000 192 2 O 8 -22.380535 -4.879305 0.844050 6.00 15.9994 193 3 H 1 -22.417352 -5.842135 0.700576 1.00 2.0000 194 2 O 8 -25.304787 1.372816 3.871868 6.00 15.9994 195 3 H 1 -25.135555 2.356491 3.936286 1.00 2.0000 196 3 H 1 -24.602092 0.972833 4.561711 1.00 2.0000 197 2 O 8 -16.807799 1.544227 3.792630 6.00 15.9994 198 3 H 1 -17.350683 0.722039 3.517363 1.00 2.0000 199 3 H 1 -16.110488 1.221447 4.364994 1.00 2.0000 200 2 O 8 -11.970991 -7.078546 2.092407 6.00 15.9994 201 3 H 1 -12.527926 -6.347959 1.724283 1.00 2.0000 202 3 H 1 -11.397552 -6.689802 2.819160 1.00 2.0000 203 2 O 8 -23.102235 -7.610124 0.807482 6.00 15.9994 204 3 H 1 -22.770015 -7.909488 1.647301 1.00 2.0000 205 3 H 1 -24.112868 -7.381948 1.074874 1.00 2.0000 206 2 O 8 -12.147379 -13.823098 -3.277745 6.00 15.9994 207 3 H 1 -12.271951 -13.831658 -2.261772 1.00 2.0000 208 3 H 1 -11.836342 -12.855485 -3.567627 1.00 2.0000 209 2 O 8 -23.137640 0.614020 5.152014 6.00 15.9994 210 3 H 1 -22.699821 1.479447 4.900930 1.00 2.0000 211 3 H 1 -22.619008 -0.138851 4.781627 1.00 2.0000 212 2 O 8 -9.706923 -8.713400 -1.675297 6.00 15.9994 213 3 H 1 -9.537835 -7.840829 -2.248215 1.00 2.0000 214 3 H 1 -9.568580 -8.468381 -0.694682 1.00 2.0000 215 2 O 8 -17.078435 6.913749 3.148262 6.00 15.9994 216 3 H 1 -16.597300 7.570803 3.665547 1.00 2.0000 217 3 H 1 -16.516880 6.913325 2.300982 1.00 2.0000 218 2 O 8 -10.429598 -6.118336 4.133162 6.00 15.9994 219 3 H 1 -10.976353 -6.244853 4.915371 1.00 2.0000 220 3 H 1 -10.371174 -5.179569 3.833850 1.00 2.0000 221 2 O 8 -12.000043 -11.150965 0.013566 6.00 15.9994 222 3 H 1 -12.328514 -10.664902 -0.857592 1.00 2.0000 223 3 H 1 -12.321550 -10.613832 0.835245 1.00 2.0000 SCF PARAMETERS Density guess: ATOMIC -------------------------------------------------------- max_scf: 50 max_scf_history: 0 max_diis: 4 -------------------------------------------------------- eps_scf: 1.00E-07 eps_scf_history: 0.00E+00 eps_diis: 1.00E-01 eps_eigval: 1.00E-05 -------------------------------------------------------- level_shift [a.u.]: 0.00 -------------------------------------------------------- Outer loop SCF in use No variables optimised in outer loop eps_scf 1.00E-07 max_scf 50 No outer loop optimization step_size 5.00E-01 PW_GRID: Information for grid number 1 PW_GRID: Grid distributed over 64 processors PW_GRID: Real space group dimensions 64 1 PW_GRID: the grid is blocked: NO PW_GRID: Cutoff [a.u.] 320.0 PW_GRID: spherical cutoff: NO PW_GRID: Bounds 1 -108 107 Points: 216 PW_GRID: Bounds 2 -120 119 Points: 240 PW_GRID: Bounds 3 -360 359 Points: 720 PW_GRID: Volume element (a.u.^3) 0.1705E-02 Volume (a.u.^3) 63645.6571 PW_GRID: Grid span FULLSPACE PW_GRID: Distribution Average Max Min PW_GRID: G-Vectors 583200.0 583200 583200 PW_GRID: G-Rays 2700.0 2700 2700 PW_GRID: Real Space Points 583200.0 691200 518400 PW_GRID: Information for grid number 2 PW_GRID: Grid distributed over 64 processors PW_GRID: Real space group dimensions 64 1 PW_GRID: the grid is blocked: NO PW_GRID: Cutoff [a.u.] 160.0 PW_GRID: spherical cutoff: NO PW_GRID: Bounds 1 -75 74 Points: 150 PW_GRID: Bounds 2 -90 89 Points: 180 PW_GRID: Bounds 3 -243 242 Points: 486 PW_GRID: Volume element (a.u.^3) 0.4850E-02 Volume (a.u.^3) 63645.6571 PW_GRID: Grid span FULLSPACE PW_GRID: Distribution Average Max Min PW_GRID: G-Vectors 205031.2 212700 201750 PW_GRID: G-Rays 1366.9 1418 1345 PW_GRID: Real Space Points 205031.2 262440 174960 PW_GRID: Information for grid number 3 PW_GRID: Grid distributed over 64 processors PW_GRID: Real space group dimensions 64 1 PW_GRID: the grid is blocked: NO PW_GRID: Cutoff [a.u.] 53.3 PW_GRID: spherical cutoff: NO PW_GRID: Bounds 1 -45 44 Points: 90 PW_GRID: Bounds 2 -50 49 Points: 100 PW_GRID: Bounds 3 -144 143 Points: 288 PW_GRID: Volume element (a.u.^3) 0.2455E-01 Volume (a.u.^3) 63645.6571 PW_GRID: Grid span FULLSPACE PW_GRID: Distribution Average Max Min PW_GRID: G-Vectors 40500.0 41580 39690 PW_GRID: G-Rays 450.0 462 441 PW_GRID: Real Space Points 40500.0 57600 28800 PW_GRID: Information for grid number 4 PW_GRID: Grid distributed over 64 processors PW_GRID: Real space group dimensions 64 1 PW_GRID: the grid is blocked: NO PW_GRID: Cutoff [a.u.] 17.8 PW_GRID: spherical cutoff: NO PW_GRID: Bounds 1 -27 26 Points: 54 PW_GRID: Bounds 2 -30 29 Points: 60 PW_GRID: Bounds 3 -81 80 Points: 162 PW_GRID: Volume element (a.u.^3) 0.1213 Volume (a.u.^3) 63645.6571 PW_GRID: Grid span FULLSPACE PW_GRID: Distribution Average Max Min PW_GRID: G-Vectors 8201.2 8694 7668 PW_GRID: G-Rays 151.9 161 142 PW_GRID: Real Space Points 8201.2 9720 0 PW_GRID: Information for grid number 5 PW_GRID: Grid distributed over 64 processors PW_GRID: Real space group dimensions 64 1 PW_GRID: the grid is blocked: NO PW_GRID: Cutoff [a.u.] 5.9 PW_GRID: spherical cutoff: NO PW_GRID: Bounds 1 -13 13 Points: 27 PW_GRID: Bounds 2 -18 17 Points: 36 PW_GRID: Bounds 3 -48 47 Points: 96 PW_GRID: Volume element (a.u.^3) 0.6821 Volume (a.u.^3) 63645.6571 PW_GRID: Grid span FULLSPACE PW_GRID: Distribution Average Max Min PW_GRID: G-Vectors 1458.0 1593 1323 PW_GRID: G-Rays 54.0 59 49 PW_GRID: Real Space Points 1458.0 3456 0 RS_GRID: Information for grid number 2 RS_GRID: Bounds 1 -75 74 Points: 150 RS_GRID: Bounds 2 -90 89 Points: 180 RS_GRID: Bounds 3 -243 242 Points: 486 RS_GRID: Real space distribution over 4 groups RS_GRID: Real space distribution along direction 2 RS_GRID: Border size 27 RS_GRID: Real space distribution over 16 groups RS_GRID: Real space distribution along direction 3 RS_GRID: Border size 27 RS_GRID: Distribution Average Max Min RS_GRID: Planes 99.0 99 99 RS_GRID: Distribution Average Max Min RS_GRID: Planes 84.4 85 84 RS_GRID: Information for grid number 3 RS_GRID: Bounds 1 -45 44 Points: 90 RS_GRID: Bounds 2 -50 49 Points: 100 RS_GRID: Bounds 3 -144 143 Points: 288 RS_GRID: Real space distribution over 4 groups RS_GRID: Real space distribution along direction 2 RS_GRID: Border size 27 RS_GRID: Real space distribution over 16 groups RS_GRID: Real space distribution along direction 3 RS_GRID: Border size 27 RS_GRID: Distribution Average Max Min RS_GRID: Planes 79.0 79 79 RS_GRID: Distribution Average Max Min RS_GRID: Planes 72.0 72 72 RS_GRID: Information for grid number 4 RS_GRID: Bounds 1 -27 26 Points: 54 RS_GRID: Bounds 2 -30 29 Points: 60 RS_GRID: Bounds 3 -81 80 Points: 162 RS_GRID: Real space fully replicated RS_GRID: Group size 1 RS_GRID: Information for grid number 5 RS_GRID: Bounds 1 -13 13 Points: 27 RS_GRID: Bounds 2 -18 17 Points: 36 RS_GRID: Bounds 3 -48 47 Points: 96 RS_GRID: Real space fully replicated RS_GRID: Group size 1 DISTRIBUTION OF THE PARTICLES (ROWS) Process row Number of particles Number of matrix rows 0 28 -1 1 27 -1 2 29 -1 3 28 -1 4 28 -1 5 28 -1 6 27 -1 7 28 -1 Sum 223 -1 DISTRIBUTION OF THE PARTICLES (COLUMNS) Process col Number of particles Number of matrix columns 0 28 -1 1 27 -1 2 29 -1 3 28 -1 4 28 -1 5 28 -1 6 27 -1 7 28 -1 Sum 223 -1 MD| Molecular Dynamics Protocol MD| Ensemble Type NVE MD| Number of Time Steps 50000 MD| Time Step [fs] 0.50 MD| Temperature [K] 300.00 MD| Temperature tolerance [K] 0.00 MD| Print MD information every 1 step(s) MD| File type Print frequency[steps] File names MD| Coordinates 1 water-pos-1.xyz MD| Velocities 1 water-vel-1.xyz MD| Energies 1 water-1.ener MD| Dump 20 water-1.restart ROT| Rotational Analysis Info ROT| Principal axes and moments of inertia in atomic units: ROT| 1 2 3 ROT| EIGENVALUES 0.333392366E+09 0.473188005E+09 0.491315243E+09 ROT| X 0.376526826 -0.673919443 -0.635657246 ROT| Y -0.869031069 -0.019223038 -0.494383936 ROT| Z -0.320955683 -0.738554710 0.592894923 ROT| Numer of Rotovibrational vectors: 6 Calculation of degrees of freedom Number of atoms: 223 Number of Intramolecular constraints: 0 Number of Intermolecular constraints: 0 Invariants(translation + rotations): 4 Degrees of freedom: 665 Restraints Information Number of Intramolecular restraints: 0 Number of Intermolecular restraints: 0 ************************** Velocities initialization ************************** Initial Temperature 298.35 K COM velocity: -0.000020451803 -0.000014845920 -0.000010029888 ******************************************************************************* DISTRIBUTION OF THE NEIGHBOR LISTS Total number of particle pairs: 33914 Total number of matrix elements: 6332759 Average number of particle pairs: 530 Maximum number of particle pairs: 621 Average number of matrix element: 98950 Maximum number of matrix elements: 110514 DISTRIBUTION OF THE OVERLAP MATRIX Number of non-zero blocks: 22761 Percentage non-zero blocks: 91.13 Average number of blocks per CPU: 356 Maximum number of blocks per CPU: 421 Average number of matrix elements per CPU: 64546 Maximum number of matrix elements per CPU: 72604 Number of electrons: 616 Number of occupied orbitals: 308 Number of molecular orbitals: 308 Number of orbital functions: 3034 Number of independent orbital functions: 3034 Extrapolation method: initial_guess Atomic guess: The first density matrix is obtained in terms of atomic orbitals and electronic configurations assigned to each atomic kind Guess for atomic kind: N Electronic structure Total number of core electrons 2.00 Total number of valence electrons 5.00 Total number of electrons 7.00 Multiplicity not specified S [ 2.00] 2.00 P 3.00 ******************************************************************************* Iteration Convergence Energy [au] ******************************************************************************* 1 1.15283 -9.106557061822 2 0.871956 -9.149783991284 3 0.963150E-01 -9.540592510391 4 0.266247E-02 -9.546174590474 5 0.308219E-03 -9.546178123327 6 0.232633E-04 -9.546178176652 7 0.287728E-08 -9.546178176959 Energy components [Hartree] Total Energy :: -9.546178176959 Band Energy :: -2.056052179060 Kinetic Energy :: 6.750514597613 Potential Energy :: -16.296692774573 Virial (-V/T) :: 2.414140809404 Core Energy :: -15.541752719680 XC Energy :: -2.162895802006 Coulomb Energy :: 8.158470344727 Total Pseudopotential Energy :: -22.329540629779 Local Pseudopotential Energy :: -23.278432419853 Nonlocal Pseudopotential Energy :: 0.948891790074 Confinement :: 0.372733124857 Orbital energies State L Occupation Energy[a.u.] Energy[eV] 1 0 2.000 -0.663798 -18.062863 1 1 3.000 -0.242819 -6.607433 Guess for atomic kind: O Electronic structure Total number of core electrons 2.00 Total number of valence electrons 6.00 Total number of electrons 8.00 Multiplicity not specified S [ 2.00] 2.00 P 4.00 ******************************************************************************* Iteration Convergence Energy [au] ******************************************************************************* 1 2.51497 -14.566691316144 2 2.35806 -14.184114409661 3 0.313328 -15.624381918049 4 0.277189E-01 -15.656178317323 5 0.123634E-02 -15.656397040537 6 0.593196E-04 -15.656397458397 7 0.437058E-05 -15.656397459367 8 0.556572E-07 -15.656397459370 Energy components [Hartree] Total Energy :: -15.656397459370 Band Energy :: -3.001887330005 Kinetic Energy :: 11.780461874254 Potential Energy :: -27.436859333624 Virial (-V/T) :: 2.329013889819 Core Energy :: -26.138301090847 XC Energy :: -3.153767334965 Coulomb Energy :: 13.635670966443 Total Pseudopotential Energy :: -37.953933650738 Local Pseudopotential Energy :: -39.253304888308 Nonlocal Pseudopotential Energy :: 1.299371237570 Confinement :: 0.351706856372 Orbital energies State L Occupation Energy[a.u.] Energy[eV] 1 0 2.000 -0.864888 -23.534802 1 1 4.000 -0.318028 -8.653976 Guess for atomic kind: H Electronic structure Total number of core electrons 0.00 Total number of valence electrons 1.00 Total number of electrons 1.00 Multiplicity not specified S 1.00 ******************************************************************************* Iteration Convergence Energy [au] ******************************************************************************* 1 0.440266E-02 -0.423513531970 2 0.325828E-03 -0.423525175186 3 0.252148E-04 -0.423525335541 4 0.637776E-08 -0.423525336420 Energy components [Hartree] Total Energy :: -0.423525336420 Band Energy :: -0.195262559383 Kinetic Energy :: 0.470173284674 Potential Energy :: -0.893698621094 Virial (-V/T) :: 1.900785625696 Core Energy :: -0.479699819139 XC Energy :: -0.247097449670 Coulomb Energy :: 0.303271932388 Total Pseudopotential Energy :: -0.967738859557 Local Pseudopotential Energy :: -0.967738859557 Nonlocal Pseudopotential Energy :: 0.000000000000 Confinement :: 0.178657557441 Orbital energies State L Occupation Energy[a.u.] Energy[eV] 1 0 1.000 -0.195263 -5.313364 Re-scaling the density matrix to get the right number of electrons # Electrons Trace(P) Scaling factor 616 616.000 1.000 SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Allowing for rotations: F Optimizing orbital energies: F Minimizer : DIIS : direct inversion in the iterative subspace using : - 7 DIIS vectors - safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.00100000 eps_taylor : 0.10000E-15 max_taylor : 4 mixed_precision : F ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999997875 0.0000002125 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000002125 Total charge density g-space grids: 0.0000002125 1 OT DIIS 0.15E+00 3.4 0.02393040 -1291.7589495728 -1.29E+03 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998271 0.0000001729 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001729 Total charge density g-space grids: 0.0000001729 2 OT DIIS 0.15E+00 1.3 0.06132715 -1305.2856686637 -1.35E+01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998299 0.0000001701 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001701 Total charge density g-space grids: 0.0000001701 3 OT DIIS 0.15E+00 1.3 0.02135565 -1323.6139775279 -1.83E+01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998018 0.0000001982 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001982 Total charge density g-space grids: 0.0000001982 4 OT DIIS 0.15E+00 1.3 0.05205544 -1319.1217102818 4.49E+00 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998073 0.0000001927 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001927 Total charge density g-space grids: 0.0000001927 5 OT DIIS 0.15E+00 1.3 0.01171200 -1333.0013153786 -1.39E+01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998204 0.0000001796 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001796 Total charge density g-space grids: 0.0000001796 6 OT DIIS 0.15E+00 1.3 0.00870872 -1334.7842261264 -1.78E+00 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998168 0.0000001832 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001832 Total charge density g-space grids: 0.0000001832 7 OT DIIS 0.15E+00 1.3 0.00617422 -1337.2495022820 -2.47E+00 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998177 0.0000001823 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001823 Total charge density g-space grids: 0.0000001823 8 OT DIIS 0.15E+00 1.3 0.00386415 -1338.0033997127 -7.54E-01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998186 0.0000001814 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001814 Total charge density g-space grids: 0.0000001814 9 OT DIIS 0.15E+00 1.3 0.00261330 -1338.6819074404 -6.79E-01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998169 0.0000001831 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001830 Total charge density g-space grids: 0.0000001830 10 OT DIIS 0.15E+00 1.3 0.00214265 -1338.9299545725 -2.48E-01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998186 0.0000001814 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001814 Total charge density g-space grids: 0.0000001814 11 OT DIIS 0.15E+00 1.3 0.00163172 -1339.1043107079 -1.74E-01 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998186 0.0000001814 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001814 Total charge density g-space grids: 0.0000001814 12 OT DIIS 0.15E+00 1.3 0.00101528 -1339.1935172755 -8.92E-02 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998185 0.0000001815 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001815 Total charge density g-space grids: 0.0000001815 13 OT DIIS 0.15E+00 1.3 0.00069191 -1339.2272234635 -3.37E-02 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998192 0.0000001808 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001808 Total charge density g-space grids: 0.0000001808 14 OT DIIS 0.15E+00 1.3 0.00053991 -1339.2444467143 -1.72E-02 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998180 0.0000001820 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001820 Total charge density g-space grids: 0.0000001820 15 OT DIIS 0.15E+00 1.3 0.00037388 -1339.2576876865 -1.32E-02 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998193 0.0000001807 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001807 Total charge density g-space grids: 0.0000001807 16 OT DIIS 0.15E+00 1.3 0.00025303 -1339.2655289616 -7.84E-03 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998188 0.0000001812 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001812 Total charge density g-space grids: 0.0000001812 17 OT DIIS 0.15E+00 1.3 0.00017866 -1339.2694269934 -3.90E-03 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998188 0.0000001812 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001812 Total charge density g-space grids: 0.0000001812 18 OT DIIS 0.15E+00 1.3 0.00012866 -1339.2717974736 -2.37E-03 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998189 0.0000001811 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 19 OT DIIS 0.15E+00 1.3 0.00010342 -1339.2736302209 -1.83E-03 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998189 0.0000001811 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 20 OT DIIS 0.15E+00 1.3 0.00009566 -1339.2752342927 -1.60E-03 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998189 0.0000001811 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001811 Total charge density g-space grids: 0.0000001811 21 OT DIIS 0.15E+00 1.3 0.00008626 -1339.2760648090 -8.31E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 22 OT DIIS 0.15E+00 1.3 0.00007696 -1339.2770483564 -9.84E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998189 0.0000001811 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001811 Total charge density g-space grids: 0.0000001811 23 OT DIIS 0.15E+00 1.3 0.00006828 -1339.2776032597 -5.55E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 24 OT DIIS 0.15E+00 1.3 0.00005829 -1339.2782172281 -6.14E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998189 0.0000001811 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001811 Total charge density g-space grids: 0.0000001811 25 OT DIIS 0.15E+00 1.3 0.00005340 -1339.2787352310 -5.18E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 26 OT DIIS 0.15E+00 1.3 0.00004663 -1339.2792151315 -4.80E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 27 OT DIIS 0.15E+00 1.3 0.00004123 -1339.2796527203 -4.38E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 28 OT DIIS 0.15E+00 1.3 0.00003925 -1339.2800712559 -4.19E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 29 OT DIIS 0.15E+00 1.3 0.00003696 -1339.2803082829 -2.37E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 30 OT DIIS 0.15E+00 1.3 0.00003409 -1339.2806241510 -3.16E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 31 OT DIIS 0.15E+00 1.3 0.00003500 -1339.2808507420 -2.27E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 32 OT DIIS 0.15E+00 1.3 0.00003018 -1339.2810605201 -2.10E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 33 OT DIIS 0.15E+00 1.3 0.00002786 -1339.2812495394 -1.89E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 34 OT DIIS 0.15E+00 1.3 0.00002537 -1339.2814252289 -1.76E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 35 OT DIIS 0.15E+00 1.3 0.00002332 -1339.2815819277 -1.57E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 36 OT DIIS 0.15E+00 1.3 0.00002243 -1339.2817458256 -1.64E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 37 OT DIIS 0.15E+00 1.3 0.00002175 -1339.2818532895 -1.07E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 38 OT DIIS 0.15E+00 1.3 0.00002010 -1339.2819869156 -1.34E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 39 OT DIIS 0.15E+00 1.3 0.00002028 -1339.2820877003 -1.01E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 40 OT DIIS 0.15E+00 1.3 0.00001871 -1339.2821702492 -8.25E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 41 OT DIIS 0.15E+00 1.3 0.00001763 -1339.2822565579 -8.63E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 42 OT DIIS 0.15E+00 1.3 0.00001643 -1339.2823402223 -8.37E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 43 OT DIIS 0.15E+00 1.3 0.00001537 -1339.2824158738 -7.57E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 44 OT DIIS 0.15E+00 1.3 0.00001479 -1339.2824942923 -7.84E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 45 OT DIIS 0.15E+00 1.3 0.00001416 -1339.2825473348 -5.30E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 46 OT DIIS 0.15E+00 1.3 0.00001320 -1339.2826115920 -6.43E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 47 OT DIIS 0.15E+00 1.3 0.00001379 -1339.2826674130 -5.58E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 48 OT DIIS 0.15E+00 1.3 0.00001258 -1339.2827080427 -4.06E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001810 Total charge density g-space grids: 0.0000001810 49 OT DIIS 0.15E+00 1.3 0.00001168 -1339.2827483503 -4.03E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 50 OT DIIS 0.15E+00 1.3 0.00001090 -1339.2827834026 -3.51E-05 *** SCF run NOT converged *** Electronic density on regular grids: -615.9999998190 0.0000001810 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 Overlap energy of the core charge distribution: 0.00000233573955 Self energy of the core charge distribution: -3450.32743283959644 Core Hamiltonian energy: 1001.78258932011363 Hartree energy: 1434.68307659353263 Exchange-correlation energy: -325.21524643144960 Dispersion energy: -0.20577238097721 Total energy: -1339.28278340263751 outer SCF iter = 1 RMS gradient = 0.11E-04 energy = -1339.2827834026 ----------------------------------- OT --------------------------------------- Allowing for rotations: F Optimizing orbital energies: F Minimizer : DIIS : direct inversion in the iterative subspace using : - 7 DIIS vectors - safer DIIS on Preconditioner : FULL_ALL : diagonalization, state selective Precond_solver : DEFAULT stepsize : 0.15000000 energy_gap : 0.00100000 eps_taylor : 0.10000E-15 max_taylor : 4 mixed_precision : F ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 1 OT DIIS 0.15E+00 5.0 0.00004504 -1339.2828123230 -2.89E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 2 OT DIIS 0.15E+00 1.2 0.00001853 -1339.2830100322 -1.98E-04 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 3 OT DIIS 0.15E+00 1.2 0.00001816 -1339.2830407327 -3.07E-05 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 4 OT DIIS 0.15E+00 1.2 0.00000232 -1339.2830479341 -7.20E-06 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 5 OT DIIS 0.15E+00 1.2 0.00000052 -1339.2830480814 -1.47E-07 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 6 OT DIIS 0.15E+00 1.2 0.00000039 -1339.2830480848 -3.46E-09 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 7 OT DIIS 0.15E+00 1.2 0.00000008 -1339.2830480881 -3.27E-09 *** SCF run converged in 7 steps *** Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 Overlap energy of the core charge distribution: 0.00000233573955 Self energy of the core charge distribution: -3450.32743283959644 Core Hamiltonian energy: 1001.78139780526021 Hartree energy: 1434.68384136669920 Exchange-correlation energy: -325.21508437521578 Dispersion energy: -0.20577238097721 Total energy: -1339.28304808809048 outer SCF iter = 2 RMS gradient = 0.79E-07 energy = -1339.2830480881 outer SCF loop converged in 2 iterations or 57 steps MULLIKEN POPULATION ANALYSIS # Atom Element Kind Atomic population Net charge 1 N 1 4.442456 0.557544 2 O 2 6.228768 -0.228768 3 O 2 6.244548 -0.244548 4 O 2 6.166640 -0.166640 5 N 1 4.443326 0.556674 6 O 2 6.245334 -0.245334 7 O 2 6.228928 -0.228928 8 O 2 6.793280 -0.793280 9 H 3 0.598050 0.401950 10 H 3 0.643892 0.356108 11 O 2 6.814090 -0.814090 12 H 3 0.574471 0.425529 13 H 3 0.608056 0.391944 14 O 2 6.864887 -0.864887 15 H 3 0.575360 0.424640 16 H 3 0.591990 0.408010 17 O 2 6.761264 -0.761264 18 H 3 0.617218 0.382782 19 H 3 0.593730 0.406270 20 O 2 6.855376 -0.855376 21 H 3 0.571867 0.428133 22 H 3 0.565649 0.434351 23 O 2 6.837388 -0.837388 24 H 3 0.585540 0.414460 25 H 3 0.585536 0.414464 26 O 2 6.825778 -0.825778 27 H 3 0.580586 0.419414 28 H 3 0.585953 0.414047 29 O 2 6.793141 -0.793141 30 H 3 0.573482 0.426518 31 H 3 0.614575 0.385425 32 O 2 6.792325 -0.792325 33 H 3 0.595145 0.404855 34 H 3 0.581797 0.418203 35 O 2 6.720144 -0.720144 36 H 3 0.605942 0.394058 37 H 3 0.650187 0.349813 38 O 2 6.815195 -0.815195 39 H 3 0.625585 0.374415 40 H 3 0.590571 0.409429 41 O 2 6.751008 -0.751008 42 H 3 0.615100 0.384900 43 H 3 0.648935 0.351065 44 H 3 0.582477 0.417523 45 O 2 6.793062 -0.793062 46 H 3 0.619556 0.380444 47 H 3 0.585546 0.414454 48 O 2 6.728920 -0.728920 49 H 3 0.594334 0.405666 50 H 3 0.611397 0.388603 51 O 2 6.774955 -0.774955 52 H 3 0.599641 0.400359 53 H 3 0.581589 0.418411 54 O 2 6.756151 -0.756151 55 H 3 0.626457 0.373543 56 H 3 0.594178 0.405822 57 O 2 6.715446 -0.715446 58 H 3 0.623021 0.376979 59 H 3 0.624500 0.375500 60 O 2 6.821649 -0.821649 61 H 3 0.589736 0.410264 62 H 3 0.564719 0.435281 63 O 2 6.750860 -0.750860 64 H 3 0.626480 0.373520 65 H 3 0.610361 0.389639 66 O 2 6.805753 -0.805753 67 H 3 0.620309 0.379691 68 H 3 0.606934 0.393066 69 O 2 6.829976 -0.829976 70 H 3 0.587196 0.412804 71 H 3 0.557362 0.442638 72 O 2 6.829204 -0.829204 73 H 3 0.591298 0.408702 74 H 3 0.574772 0.425228 75 O 2 6.727542 -0.727542 76 H 3 0.606648 0.393352 77 H 3 0.674930 0.325070 78 O 2 6.799257 -0.799257 79 H 3 0.607972 0.392028 80 H 3 0.642164 0.357836 81 O 2 6.813495 -0.813495 82 H 3 0.581717 0.418283 83 H 3 0.624031 0.375969 84 O 2 6.799275 -0.799275 85 H 3 0.585826 0.414174 86 H 3 0.595793 0.404207 87 O 2 6.802196 -0.802196 88 H 3 0.584772 0.415228 89 H 3 0.614712 0.385288 90 O 2 6.828238 -0.828238 91 H 3 0.597760 0.402240 92 H 3 0.575841 0.424159 93 O 2 6.799806 -0.799806 94 H 3 0.594956 0.405044 95 H 3 0.614356 0.385644 96 O 2 6.880615 -0.880615 97 H 3 0.570822 0.429178 98 H 3 0.593791 0.406209 99 O 2 6.862041 -0.862041 100 H 3 0.573372 0.426628 101 H 3 0.572980 0.427020 102 O 2 6.716327 -0.716327 103 H 3 0.644191 0.355809 104 H 3 0.628768 0.371232 105 O 2 6.858519 -0.858519 106 H 3 0.585563 0.414437 107 O 2 6.859932 -0.859932 108 H 3 0.585605 0.414395 109 H 3 0.575734 0.424266 110 O 2 6.819606 -0.819606 111 H 3 0.621240 0.378760 112 H 3 0.587395 0.412605 113 O 2 6.799287 -0.799287 114 H 3 0.601722 0.398278 115 H 3 0.631983 0.368017 116 H 3 0.584341 0.415659 117 O 2 6.784675 -0.784675 118 H 3 0.599791 0.400209 119 H 3 0.603217 0.396783 120 O 2 6.769099 -0.769099 121 H 3 0.589394 0.410606 122 H 3 0.648837 0.351163 123 O 2 6.748839 -0.748839 124 H 3 0.559803 0.440197 125 H 3 0.605193 0.394807 126 O 2 6.711878 -0.711878 127 H 3 0.597521 0.402479 128 H 3 0.625706 0.374294 129 O 2 6.846025 -0.846025 130 H 3 0.618042 0.381958 131 H 3 0.566011 0.433989 132 O 2 6.758061 -0.758061 133 H 3 0.686736 0.313264 134 H 3 0.585422 0.414578 135 O 2 6.694818 -0.694818 136 H 3 0.688891 0.311109 137 H 3 0.602629 0.397371 138 O 2 6.706613 -0.706613 139 H 3 0.665678 0.334322 140 H 3 0.618074 0.381926 141 O 2 6.789185 -0.789185 142 H 3 0.585877 0.414123 143 H 3 0.591429 0.408571 144 O 2 6.831533 -0.831533 145 H 3 0.606166 0.393834 146 H 3 0.588262 0.411738 147 O 2 6.818962 -0.818962 148 H 3 0.598339 0.401661 149 H 3 0.586482 0.413518 150 O 2 6.805866 -0.805866 151 H 3 0.623589 0.376411 152 H 3 0.552390 0.447610 153 O 2 6.751969 -0.751969 154 H 3 0.605798 0.394202 155 H 3 0.613957 0.386043 156 O 2 6.844967 -0.844967 157 H 3 0.562690 0.437310 158 H 3 0.592377 0.407623 159 O 2 6.807630 -0.807630 160 H 3 0.579315 0.420685 161 H 3 0.608697 0.391303 162 O 2 6.787147 -0.787147 163 H 3 0.592313 0.407687 164 H 3 0.632851 0.367149 165 O 2 6.802682 -0.802682 166 H 3 0.600362 0.399638 167 H 3 0.599957 0.400043 168 O 2 6.786333 -0.786333 169 H 3 0.567235 0.432765 170 H 3 0.613718 0.386282 171 O 2 6.733174 -0.733174 172 H 3 0.601872 0.398128 173 H 3 0.680396 0.319604 174 O 2 6.782534 -0.782534 175 H 3 0.617298 0.382702 176 H 3 0.608032 0.391968 177 O 2 6.808692 -0.808692 178 H 3 0.596627 0.403373 179 H 3 0.587280 0.412720 180 O 2 6.780578 -0.780578 181 H 3 0.595236 0.404764 182 H 3 0.611397 0.388603 183 O 2 6.777532 -0.777532 184 H 3 0.599938 0.400062 185 H 3 0.596970 0.403030 186 O 2 6.879066 -0.879066 187 H 3 0.582099 0.417901 188 H 3 0.621375 0.378625 189 O 2 6.847122 -0.847122 190 H 3 0.673053 0.326947 191 H 3 0.597837 0.402163 192 O 2 6.822634 -0.822634 193 H 3 0.587021 0.412979 194 O 2 6.804794 -0.804794 195 H 3 0.631006 0.368994 196 H 3 0.594681 0.405319 197 O 2 6.782924 -0.782924 198 H 3 0.611988 0.388012 199 H 3 0.631614 0.368386 200 O 2 6.812491 -0.812491 201 H 3 0.599651 0.400349 202 H 3 0.586517 0.413483 203 O 2 6.835718 -0.835718 204 H 3 0.583873 0.416127 205 H 3 0.605445 0.394555 206 O 2 6.876144 -0.876144 207 H 3 0.565962 0.434038 208 H 3 0.560947 0.439053 209 O 2 6.707006 -0.707006 210 H 3 0.620323 0.379677 211 H 3 0.622067 0.377933 212 O 2 6.829965 -0.829965 213 H 3 0.595247 0.404753 214 H 3 0.573257 0.426743 215 O 2 6.674826 -0.674826 216 H 3 0.656130 0.343870 217 H 3 0.637647 0.362353 218 O 2 6.816675 -0.816675 219 H 3 0.629934 0.370066 220 H 3 0.552490 0.447510 221 O 2 6.832954 -0.832954 222 H 3 0.615465 0.384535 223 H 3 0.549416 0.450584 # Total charge 616.000000 -0.000000 Trace(PS): 616.0000000000 Electronic density on regular grids: -615.9999998191 0.0000001809 Core density on regular grids: 616.0000000000 -0.0000000000 Total charge density on r-space grids: 0.0000001809 Total charge density g-space grids: 0.0000001809 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -1339.283048088288524 MD_ENERGIES| Initialization proceeding ******************************** GO CP2K GO! ********************************** INITIAL POTENTIAL ENERGY[hartree] = -0.133928304809E+04 INITIAL KINETIC ENERGY[hartree] = 0.315198655887E+00 INITIAL TEMPERATURE[K] = 299.344 INITIAL VOLUME[bohr^3] = 0.636456570504E+05 INITIAL CELL LNTHS[bohr] = 0.2545915E+02 0.2939771E+02 0.8503768E+02 INITIAL CELL ANGLS[deg] = 0.9000000E+02 0.9000000E+02 0.9000000E+02 ******************************** GO CP2K GO! 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Name: v2.5.1.inp Type: chemical/x-gamess-input Size: 38786 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: v3.0.inp Type: chemical/x-gamess-input Size: 38786 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: dftd3.dat Type: application/octet-stream Size: 1959318 bytes Desc: not available URL: From hut... at chem.uzh.ch Mon Feb 20 09:51:27 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Mon, 20 Feb 2017 10:51:27 +0100 Subject: [CP2K:8716] Re: Isolated system Geometry Optimizations In-Reply-To: <1c927d4b-0f91-49b5-a976-80b9316e1ccd@googlegroups.com> References: <1c927d4b-0f91-49b5-a976-80b9316e1ccd@googlegroups.com>, <1a744090-32fc-4286-a8ff-a32fbcb27c07@googlegroups.com> Message-ID: Hi yes, the changes (jumps) in energy when changing the cell size is a well known phenomenon in plane wave calculations. You can avoid it by using a constant plane wave instead as constant cutoff calculation. In CP2K you get this by defining a reference cell (REF_CELL). regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Babgen Manookian Sent by: cp... at googlegroups.com Date: 02/17/2017 10:18PM Subject: [CP2K:8716] Re: Isolated system Geometry Optimizations Hey Juerg, Thank you so much for the reply. I re-converged my cutoff values for the larger cell size and found that 400Ry and 80Ry produce energies which have much less deviation. What I do notice is that there is still the oscillation of the energy as the cell size changes. Is there a reason for this oscillation occurring? My thoughts on this are that the planewaves are being cut at the cell wall at different values as the cell size changes which in turn causes the energy to oscillate. I would imagine if I could force the calculation to set the density equal to zero at the cell wall then there would be no oscillation. I am not sure if this reasoning is correct. Bobby? On Tuesday, February 14, 2017 at 1:21:43 PM UTC-5, Babgen Manookian wrote:Hey Everyone, I am a new cp2k user and have been working on a test system in order to get a feel for how the program works. My test system is a cyclohexane molecule and I am interested in determining the energy difference between boat and chair conformations. I am using a wavelet poisson solver with periodicity turned off and the molecule centered in the cell. I attached the template input file which I used to create the different inputs with varying cells size. What I have noticed is that as I increase my cell size the energy does not converge on a single value, instead it seems to oscillate. The graphs below show the energies of each conformation and their differences as functions of cell size. I am very curious as to what is causing these oscillations. If I have a single cyclohexane molecule centered in my cell, as I increase my cell size, I would think that the extra vacuum space around the molecule will not affect the energy.? If there is anyone out there who could provide any sort of input on this it would be much appreciated. Thanks,Bobby -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. From olive... at gmail.com Mon Feb 20 18:26:14 2017 From: olive... at gmail.com (Luiz Fernando Lopes Oliveira) Date: Mon, 20 Feb 2017 10:26:14 -0800 (PST) Subject: [CP2K:6407] Re: CP2K Hangs In-Reply-To: <3e7a15d1-e3e6-4279-9bab-5b2fa3c6788f@googlegroups.com> References: <6d3b67a8-c8d2-4a5f-8f1d-d453697527af@googlegroups.com> <1e5d81c4-a61e-4131-927d-ace2437cc46b@googlegroups.com> <70a052bb-29c1-4a85-b347-6183b801c022@googlegroups.com> <08476ecd-6418-4357-8e97-d78861d4c102@googlegroups.com> <3e7a15d1-e3e6-4279-9bab-5b2fa3c6788f@googlegroups.com> Message-ID: <079aac0f-6d4e-4cd9-bd9c-90a5e163e7b0@googlegroups.com> Hi Manav. We are having similar problems and were wondering if you had a solution for that. Do you think the problem was finally with the intel compilers? Thanks! On Saturday, April 25, 2015 at 2:26:16 AM UTC-7, Manav Kumar wrote: > > Hi James, > > No, I haven't tried that yet. I will pass on the information to the system > administrators at our HPC and see what they say. Did that fix the issue > with you? > > Best, > Manav Kumar > > > On Saturday, April 25, 2015 at 5:05:16 AM UTC-4, JamesChen wrote: >> >> Hi Manav, >> I have a similar issue with mvapich2 and some buggy version of Intel >> compilers. It seems that you are using rather standard software stack. Have >> you ever downgraded your openmpi to 1.6.5 (prior stable version)? >> James >> >> On Sat, Apr 25, 2015 at 6:08 AM, Manav Kumar wrote: >> >>> Hi James, >>> >>> I'm assuming when you say the software environment, you mean the >>> dependencies for CP2K. Here are the dependencies that are added to my >>> environment when I use the CP2K module: >>> >>> 'gcc/4.9.1' >>> >>> 'openmpi/gcc_4.9.1/1.8.3' >>> >>> 'mpiblacs/gcc_4.9.1/openmpi_1.8.3/2.0.2' >>> >>> 'lapack/gcc_4.9.1/3.5.0' >>> >>> 'scalapack/gcc_4.9.1/openmpi_1.8.3/2.0.2' >>> >>> 'fftw3/gcc_4.9.1/3.3.4' >>> >>> >>> Let me know if there is any other information that might help! >>> >>> >>> Best, >>> >>> MK >>> >>> On Friday, April 24, 2015 at 5:56:32 PM UTC-4, JamesChen wrote: >>>> >>>> Hi, >>>> Could you provide us your software environment? Are you using mvapich2 >>>> as MPI? I will suggest you follow the CP2K manual and choose Gfortran/Gnu >>>> compiler, Netlib Math library and Openmpi as the reference software stack. >>>> http://www.cp2k.org/howto:compile >>>> >>>> Cheers, >>>> James >>>> >>>> On Sat, Apr 25, 2015 at 5:08 AM, Manav Kumar wrote: >>>> >>>>> Hi Matt, >>>>> >>>>> Thank you for your response! >>>>> >>>>> I'm sorry I mis-spoke earlier, I meant to say that NVT not NVE that's >>>>> my mistake. When I ran NVT with CP2K module it worked fine. >>>>> >>>>> I ran a cell optimization using the CP2K module, and it went through >>>>> fine. >>>>> >>>>> I have talked to some of the other members in my group, and they >>>>> mentioned that it is possible that when I am running the simulation on >>>>> multiple nodes that one of them is faulty and therefore causing the >>>>> calculations to hang. However, it seems like the probability of me hitting >>>>> the same faulty node every time I submit a job seems highly unlikely. Also, >>>>> if this was the case then wouldn't the jobs that I submit using my own >>>>> compiled version of CP2K also hang? >>>>> >>>>> When you said that the it was a problem with the cell size, what did >>>>> you mean exactly? >>>>> >>>>> Best, >>>>> Manav Kumar >>>>> >>>>> >>>>> On Friday, April 24, 2015 at 11:51:29 AM UTC-4, Matt W wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> nothing is obviously wrong with your input that I can see. Maybe (i) >>>>>> problem with the executable (ii) problem with cell size. >>>>>> >>>>>> >>>>>> To start debugging - >>>>>> You say you can run NVE - can you run NVT as you've got it set up? >>>>>> Can you run a cell optimization, maybe just a few steps, to check >>>>>> that the stress tensor/cell volume change is working OK. >>>>>> >>>>>> Matt >>>>>> >>>>>> On Friday, April 24, 2015 at 12:52:48 PM UTC+1, Manav Kumar wrote: >>>>>>> >>>>>>> Hi users and developers, >>>>>>> >>>>>>> This is my first project using CP2K, so I'm sorry in advance if some >>>>>>> of the things I say might be wrong. >>>>>>> >>>>>>> I am currently trying to generate a trajectory for a simulation of >>>>>>> diacetone diperoxide (DADP) using a NPT ensemble. I am attaching the input >>>>>>> file, and the submit script below. >>>>>>> >>>>>>> The HPC that I am using has a CP2K module. I performed a >>>>>>> wave-function optimization, geometry optimization, cell optimization, and a >>>>>>> NVE ensemble calculation all using the module. However, now that I am >>>>>>> running the NPT calculation using the module it seems to hang. It reads in >>>>>>> all the parameters from a previous restart file, it starts to initiate the >>>>>>> process but gets stuck in the SCF optimization routine. It doesn't print an >>>>>>> error message, it just stays at that position until the wall time comes >>>>>>> along and kills the process. Sometimes it completes a lot of SCF >>>>>>> optimization steps, sometimes it gets through none. >>>>>>> >>>>>>> What I've done so far to try to remedy the problem is that I've >>>>>>> tried compiling CP2K myself and running the calculation using that >>>>>>> executable instead of the module. I've had a bit more success with my own >>>>>>> compiled executable, but even with that it sometimes hangs. The system >>>>>>> administrators responsible for the HPC checked the binaries and said that >>>>>>> everything was fine. >>>>>>> >>>>>>> Has anyone else had an issue similar to this? >>>>>>> >>>>>>> Best, >>>>>>> Manav Kumar >>>>>>> >>>>>>> I will attach my input file, output file, and submit script below so >>>>>>> that you can see what I have been doing. >>>>>>> >>>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "cp2k" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to cp2k+... at googlegroups.com. >>>>> To post to this group, send email to cp... at googlegroups.com. >>>>> Visit this group at http://groups.google.com/group/cp2k. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> -- >>> You received this message because you are subscribed to the Google >>> Groups "cp2k" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to cp2k+... at googlegroups.com. >>> To post to this group, send email to cp... at googlegroups.com. >>> Visit this group at http://groups.google.com/group/cp2k. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From mk3... at nyu.edu Mon Feb 20 20:36:14 2017 From: mk3... at nyu.edu (Manav Kumar) Date: Mon, 20 Feb 2017 12:36:14 -0800 (PST) Subject: [CP2K:6407] Re: CP2K Hangs In-Reply-To: <079aac0f-6d4e-4cd9-bd9c-90a5e163e7b0@googlegroups.com> References: <6d3b67a8-c8d2-4a5f-8f1d-d453697527af@googlegroups.com> <1e5d81c4-a61e-4131-927d-ace2437cc46b@googlegroups.com> <70a052bb-29c1-4a85-b347-6183b801c022@googlegroups.com> <08476ecd-6418-4357-8e97-d78861d4c102@googlegroups.com> <3e7a15d1-e3e6-4279-9bab-5b2fa3c6788f@googlegroups.com> <079aac0f-6d4e-4cd9-bd9c-90a5e163e7b0@googlegroups.com> Message-ID: <3625a917-9dad-4aa7-8d3b-1406ce5939e7@googlegroups.com> Hi Luiz, James's recommendation of using a downgraded version of openmpi worked. If there is a CP2K module that you are using, you might want to ask your HPC system administrators to re-compile it for you. There are some tests that come with CP2K that weren't run and they revealed the problem with our version of CP2K. Best, Manav On Monday, February 20, 2017 at 1:26:14 PM UTC-5, Luiz Fernando Lopes Oliveira wrote: > > Hi Manav. > > We are having similar problems and were wondering if you had a solution > for that. > > Do you think the problem was finally with the intel compilers? > > Thanks! > > On Saturday, April 25, 2015 at 2:26:16 AM UTC-7, Manav Kumar wrote: >> >> Hi James, >> >> No, I haven't tried that yet. I will pass on the information to the >> system administrators at our HPC and see what they say. Did that fix the >> issue with you? >> >> Best, >> Manav Kumar >> >> >> On Saturday, April 25, 2015 at 5:05:16 AM UTC-4, JamesChen wrote: >>> >>> Hi Manav, >>> I have a similar issue with mvapich2 and some buggy version of Intel >>> compilers. It seems that you are using rather standard software stack. Have >>> you ever downgraded your openmpi to 1.6.5 (prior stable version)? >>> James >>> >>> On Sat, Apr 25, 2015 at 6:08 AM, Manav Kumar wrote: >>> >>>> Hi James, >>>> >>>> I'm assuming when you say the software environment, you mean the >>>> dependencies for CP2K. Here are the dependencies that are added to my >>>> environment when I use the CP2K module: >>>> >>>> 'gcc/4.9.1' >>>> >>>> 'openmpi/gcc_4.9.1/1.8.3' >>>> >>>> 'mpiblacs/gcc_4.9.1/openmpi_1.8.3/2.0.2' >>>> >>>> 'lapack/gcc_4.9.1/3.5.0' >>>> >>>> 'scalapack/gcc_4.9.1/openmpi_1.8.3/2.0.2' >>>> >>>> 'fftw3/gcc_4.9.1/3.3.4' >>>> >>>> >>>> Let me know if there is any other information that might help! >>>> >>>> >>>> Best, >>>> >>>> MK >>>> >>>> On Friday, April 24, 2015 at 5:56:32 PM UTC-4, JamesChen wrote: >>>>> >>>>> Hi, >>>>> Could you provide us your software environment? Are you using mvapich2 >>>>> as MPI? I will suggest you follow the CP2K manual and choose Gfortran/Gnu >>>>> compiler, Netlib Math library and Openmpi as the reference software stack. >>>>> http://www.cp2k.org/howto:compile >>>>> >>>>> Cheers, >>>>> James >>>>> >>>>> On Sat, Apr 25, 2015 at 5:08 AM, Manav Kumar wrote: >>>>> >>>>>> Hi Matt, >>>>>> >>>>>> Thank you for your response! >>>>>> >>>>>> I'm sorry I mis-spoke earlier, I meant to say that NVT not NVE that's >>>>>> my mistake. When I ran NVT with CP2K module it worked fine. >>>>>> >>>>>> I ran a cell optimization using the CP2K module, and it went through >>>>>> fine. >>>>>> >>>>>> I have talked to some of the other members in my group, and they >>>>>> mentioned that it is possible that when I am running the simulation on >>>>>> multiple nodes that one of them is faulty and therefore causing the >>>>>> calculations to hang. However, it seems like the probability of me hitting >>>>>> the same faulty node every time I submit a job seems highly unlikely. Also, >>>>>> if this was the case then wouldn't the jobs that I submit using my own >>>>>> compiled version of CP2K also hang? >>>>>> >>>>>> When you said that the it was a problem with the cell size, what did >>>>>> you mean exactly? >>>>>> >>>>>> Best, >>>>>> Manav Kumar >>>>>> >>>>>> >>>>>> On Friday, April 24, 2015 at 11:51:29 AM UTC-4, Matt W wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> nothing is obviously wrong with your input that I can see. Maybe (i) >>>>>>> problem with the executable (ii) problem with cell size. >>>>>>> >>>>>>> >>>>>>> To start debugging - >>>>>>> You say you can run NVE - can you run NVT as you've got it set up? >>>>>>> Can you run a cell optimization, maybe just a few steps, to check >>>>>>> that the stress tensor/cell volume change is working OK. >>>>>>> >>>>>>> Matt >>>>>>> >>>>>>> On Friday, April 24, 2015 at 12:52:48 PM UTC+1, Manav Kumar wrote: >>>>>>>> >>>>>>>> Hi users and developers, >>>>>>>> >>>>>>>> This is my first project using CP2K, so I'm sorry in advance if >>>>>>>> some of the things I say might be wrong. >>>>>>>> >>>>>>>> I am currently trying to generate a trajectory for a simulation of >>>>>>>> diacetone diperoxide (DADP) using a NPT ensemble. I am attaching the input >>>>>>>> file, and the submit script below. >>>>>>>> >>>>>>>> The HPC that I am using has a CP2K module. I performed a >>>>>>>> wave-function optimization, geometry optimization, cell optimization, and a >>>>>>>> NVE ensemble calculation all using the module. However, now that I am >>>>>>>> running the NPT calculation using the module it seems to hang. It reads in >>>>>>>> all the parameters from a previous restart file, it starts to initiate the >>>>>>>> process but gets stuck in the SCF optimization routine. It doesn't print an >>>>>>>> error message, it just stays at that position until the wall time comes >>>>>>>> along and kills the process. Sometimes it completes a lot of SCF >>>>>>>> optimization steps, sometimes it gets through none. >>>>>>>> >>>>>>>> What I've done so far to try to remedy the problem is that I've >>>>>>>> tried compiling CP2K myself and running the calculation using that >>>>>>>> executable instead of the module. I've had a bit more success with my own >>>>>>>> compiled executable, but even with that it sometimes hangs. The system >>>>>>>> administrators responsible for the HPC checked the binaries and said that >>>>>>>> everything was fine. >>>>>>>> >>>>>>>> Has anyone else had an issue similar to this? >>>>>>>> >>>>>>>> Best, >>>>>>>> Manav Kumar >>>>>>>> >>>>>>>> I will attach my input file, output file, and submit script below >>>>>>>> so that you can see what I have been doing. >>>>>>>> >>>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "cp2k" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to cp2k+... at googlegroups.com. >>>>>> To post to this group, send email to cp... at googlegroups.com. >>>>>> Visit this group at http://groups.google.com/group/cp2k. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> >>>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "cp2k" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to cp2k+... at googlegroups.com. >>>> To post to this group, send email to cp... at googlegroups.com. >>>> Visit this group at http://groups.google.com/group/cp2k. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Tue Feb 21 08:38:45 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Tue, 21 Feb 2017 09:38:45 +0100 Subject: [CP2K:8724] Dispersion energy in different versions of CP2K In-Reply-To: <5c699144-a795-4001-aab8-4afae79188b4@googlegroups.com> References: <5c699144-a795-4001-aab8-4afae79188b4@googlegroups.com> Message-ID: Hi version 2.6 had a major bug fix for C9 terms in periodic systems. Besides that only refactoring of the code for SMP parallelism has been done. Switching off the C9 term should give you a hint on the source of the error. regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Barak Hirshberg Sent by: cp... at googlegroups.com Date: 02/20/2017 11:31AM Subject: [CP2K:8724] Dispersion energy in different versions of CP2K Hello, I want to compare calculations done with different (admittedly old) versions of CP2K.I used an identical input file (attached) for CP2K versions 3.0 and 2.5.1.The simulations are MD runs using the PBE functional with the D3 dispersion correction, the TZV2P basis set and GTH pseudo-potentials.The initial SCF (before taking even one MD step) converges fine and all energy components (Core, Hartree and XC) are very similar between the different versions.The only difference which is significant is dispersion energy term. which is?-0.20577238097721 Hartree in the 2.5.1 version and?-0.20735192667451 in the 3.0 version.This is despite the fact that I used the exact same parameter file (dftd3.dat attached) for both calculations.I have also attached the relevant parts of the output files. I would really appreciate your help in understanding the origin of the difference.Thanks, Barak -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. [attachment "v3.0.log" removed by J?rg Hutter/at/UZH] [attachment "v2.5.1.log" removed by J?rg Hutter/at/UZH] [attachment "v2.5.1.inp" removed by J?rg Hutter/at/UZH] [attachment "v3.0.inp" removed by J?rg Hutter/at/UZH] [attachment "dftd3.dat" removed by J?rg Hutter/at/UZH] From olive... at gmail.com Tue Feb 21 19:34:54 2017 From: olive... at gmail.com (Luiz Fernando Lopes Oliveira) Date: Tue, 21 Feb 2017 11:34:54 -0800 (PST) Subject: [CP2K:6407] Re: CP2K Hangs In-Reply-To: <3625a917-9dad-4aa7-8d3b-1406ce5939e7@googlegroups.com> References: <6d3b67a8-c8d2-4a5f-8f1d-d453697527af@googlegroups.com> <1e5d81c4-a61e-4131-927d-ace2437cc46b@googlegroups.com> <70a052bb-29c1-4a85-b347-6183b801c022@googlegroups.com> <08476ecd-6418-4357-8e97-d78861d4c102@googlegroups.com> <3e7a15d1-e3e6-4279-9bab-5b2fa3c6788f@googlegroups.com> <079aac0f-6d4e-4cd9-bd9c-90a5e163e7b0@googlegroups.com> <3625a917-9dad-4aa7-8d3b-1406ce5939e7@googlegroups.com> Message-ID: <80cd180a-7773-4d8c-9cab-1720c8c7cbe2@googlegroups.com> Thanks a lot, Manav. I'm compiling it myself. Could you please point me to tests files that you mentioned revealed the problem? Thanks On Monday, February 20, 2017 at 12:36:14 PM UTC-8, Manav Kumar wrote: > > Hi Luiz, > > James's recommendation of using a downgraded version of openmpi worked. If > there is a CP2K module that you are using, you might want to ask your HPC > system administrators to re-compile it for you. There are some tests that > come with CP2K that weren't run and they revealed the problem with our > version of CP2K. > > Best, > Manav > > > On Monday, February 20, 2017 at 1:26:14 PM UTC-5, Luiz Fernando Lopes > Oliveira wrote: >> >> Hi Manav. >> >> We are having similar problems and were wondering if you had a solution >> for that. >> >> Do you think the problem was finally with the intel compilers? >> >> Thanks! >> >> On Saturday, April 25, 2015 at 2:26:16 AM UTC-7, Manav Kumar wrote: >>> >>> Hi James, >>> >>> No, I haven't tried that yet. I will pass on the information to the >>> system administrators at our HPC and see what they say. Did that fix the >>> issue with you? >>> >>> Best, >>> Manav Kumar >>> >>> >>> On Saturday, April 25, 2015 at 5:05:16 AM UTC-4, JamesChen wrote: >>>> >>>> Hi Manav, >>>> I have a similar issue with mvapich2 and some buggy version of Intel >>>> compilers. It seems that you are using rather standard software stack. Have >>>> you ever downgraded your openmpi to 1.6.5 (prior stable version)? >>>> James >>>> >>>> On Sat, Apr 25, 2015 at 6:08 AM, Manav Kumar wrote: >>>> >>>>> Hi James, >>>>> >>>>> I'm assuming when you say the software environment, you mean the >>>>> dependencies for CP2K. Here are the dependencies that are added to my >>>>> environment when I use the CP2K module: >>>>> >>>>> 'gcc/4.9.1' >>>>> >>>>> 'openmpi/gcc_4.9.1/1.8.3' >>>>> >>>>> 'mpiblacs/gcc_4.9.1/openmpi_1.8.3/2.0.2' >>>>> >>>>> 'lapack/gcc_4.9.1/3.5.0' >>>>> >>>>> 'scalapack/gcc_4.9.1/openmpi_1.8.3/2.0.2' >>>>> >>>>> 'fftw3/gcc_4.9.1/3.3.4' >>>>> >>>>> >>>>> Let me know if there is any other information that might help! >>>>> >>>>> >>>>> Best, >>>>> >>>>> MK >>>>> >>>>> On Friday, April 24, 2015 at 5:56:32 PM UTC-4, JamesChen wrote: >>>>>> >>>>>> Hi, >>>>>> Could you provide us your software environment? Are you using >>>>>> mvapich2 as MPI? I will suggest you follow the CP2K manual and choose >>>>>> Gfortran/Gnu compiler, Netlib Math library and Openmpi as the reference >>>>>> software stack. >>>>>> http://www.cp2k.org/howto:compile >>>>>> >>>>>> Cheers, >>>>>> James >>>>>> >>>>>> On Sat, Apr 25, 2015 at 5:08 AM, Manav Kumar wrote: >>>>>> >>>>>>> Hi Matt, >>>>>>> >>>>>>> Thank you for your response! >>>>>>> >>>>>>> I'm sorry I mis-spoke earlier, I meant to say that NVT not NVE >>>>>>> that's my mistake. When I ran NVT with CP2K module it worked fine. >>>>>>> >>>>>>> I ran a cell optimization using the CP2K module, and it went through >>>>>>> fine. >>>>>>> >>>>>>> I have talked to some of the other members in my group, and they >>>>>>> mentioned that it is possible that when I am running the simulation on >>>>>>> multiple nodes that one of them is faulty and therefore causing the >>>>>>> calculations to hang. However, it seems like the probability of me hitting >>>>>>> the same faulty node every time I submit a job seems highly unlikely. Also, >>>>>>> if this was the case then wouldn't the jobs that I submit using my own >>>>>>> compiled version of CP2K also hang? >>>>>>> >>>>>>> When you said that the it was a problem with the cell size, what did >>>>>>> you mean exactly? >>>>>>> >>>>>>> Best, >>>>>>> Manav Kumar >>>>>>> >>>>>>> >>>>>>> On Friday, April 24, 2015 at 11:51:29 AM UTC-4, Matt W wrote: >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> nothing is obviously wrong with your input that I can see. Maybe >>>>>>>> (i) problem with the executable (ii) problem with cell size. >>>>>>>> >>>>>>>> >>>>>>>> To start debugging - >>>>>>>> You say you can run NVE - can you run NVT as you've got it set up? >>>>>>>> Can you run a cell optimization, maybe just a few steps, to check >>>>>>>> that the stress tensor/cell volume change is working OK. >>>>>>>> >>>>>>>> Matt >>>>>>>> >>>>>>>> On Friday, April 24, 2015 at 12:52:48 PM UTC+1, Manav Kumar wrote: >>>>>>>>> >>>>>>>>> Hi users and developers, >>>>>>>>> >>>>>>>>> This is my first project using CP2K, so I'm sorry in advance if >>>>>>>>> some of the things I say might be wrong. >>>>>>>>> >>>>>>>>> I am currently trying to generate a trajectory for a simulation of >>>>>>>>> diacetone diperoxide (DADP) using a NPT ensemble. I am attaching the input >>>>>>>>> file, and the submit script below. >>>>>>>>> >>>>>>>>> The HPC that I am using has a CP2K module. I performed a >>>>>>>>> wave-function optimization, geometry optimization, cell optimization, and a >>>>>>>>> NVE ensemble calculation all using the module. However, now that I am >>>>>>>>> running the NPT calculation using the module it seems to hang. It reads in >>>>>>>>> all the parameters from a previous restart file, it starts to initiate the >>>>>>>>> process but gets stuck in the SCF optimization routine. It doesn't print an >>>>>>>>> error message, it just stays at that position until the wall time comes >>>>>>>>> along and kills the process. Sometimes it completes a lot of SCF >>>>>>>>> optimization steps, sometimes it gets through none. >>>>>>>>> >>>>>>>>> What I've done so far to try to remedy the problem is that I've >>>>>>>>> tried compiling CP2K myself and running the calculation using that >>>>>>>>> executable instead of the module. I've had a bit more success with my own >>>>>>>>> compiled executable, but even with that it sometimes hangs. The system >>>>>>>>> administrators responsible for the HPC checked the binaries and said that >>>>>>>>> everything was fine. >>>>>>>>> >>>>>>>>> Has anyone else had an issue similar to this? >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> Manav Kumar >>>>>>>>> >>>>>>>>> I will attach my input file, output file, and submit script below >>>>>>>>> so that you can see what I have been doing. >>>>>>>>> >>>>>>>> -- >>>>>>> You received this message because you are subscribed to the Google >>>>>>> Groups "cp2k" group. >>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>> send an email to cp2k+... at googlegroups.com. >>>>>>> To post to this group, send email to cp... at googlegroups.com. >>>>>>> Visit this group at http://groups.google.com/group/cp2k. >>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>> >>>>>> >>>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "cp2k" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to cp2k+... at googlegroups.com. >>>>> To post to this group, send email to cp... at googlegroups.com. >>>>> Visit this group at http://groups.google.com/group/cp2k. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From olive... at gmail.com Tue Feb 21 19:41:01 2017 From: olive... at gmail.com (Luiz Fernando Lopes Oliveira) Date: Tue, 21 Feb 2017 11:41:01 -0800 (PST) Subject: PLUMED output files update In-Reply-To: References: <6bb70af6-2f02-4b6b-ae3a-5349fe4d3490@googlegroups.com> Message-ID: <719e3b82-8ea6-46cc-ab72-26f1eb9bc1b4@googlegroups.com> Thanks, Conrad. That solved my problem. However, I don't think that it is a feature of Plumed. In Gromacs and AMBER the output is written every step without the FLUSH keyword. On Thursday, February 9, 2017 at 11:35:29 PM UTC-8, Conrad wrote: > > Hi Luiz, > > This is a feature of Plumed. > > Try adding FLUSH STRIDE=1 to the end of your Plumed input. > This will force the output to be written every step to HILLS and COLVAR. > Normally > writing is buffered, so this forces the buffer to be flushed regularly. > > Best wishes, > Conrad > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mk3... at nyu.edu Tue Feb 21 19:46:36 2017 From: mk3... at nyu.edu (Manav Kumar) Date: Tue, 21 Feb 2017 11:46:36 -0800 (PST) Subject: [CP2K:6407] Re: CP2K Hangs In-Reply-To: <80cd180a-7773-4d8c-9cab-1720c8c7cbe2@googlegroups.com> References: <6d3b67a8-c8d2-4a5f-8f1d-d453697527af@googlegroups.com> <1e5d81c4-a61e-4131-927d-ace2437cc46b@googlegroups.com> <70a052bb-29c1-4a85-b347-6183b801c022@googlegroups.com> <08476ecd-6418-4357-8e97-d78861d4c102@googlegroups.com> <3e7a15d1-e3e6-4279-9bab-5b2fa3c6788f@googlegroups.com> <079aac0f-6d4e-4cd9-bd9c-90a5e163e7b0@googlegroups.com> <3625a917-9dad-4aa7-8d3b-1406ce5939e7@googlegroups.com> <80cd180a-7773-4d8c-9cab-1720c8c7cbe2@googlegroups.com> Message-ID: <26802bed-ffa8-4c75-bbda-ebb6ed587f48@googlegroups.com> Hey Luiz, There should be some test files that come with the source code. Best, Manav On Tuesday, February 21, 2017 at 2:34:55 PM UTC-5, Luiz Fernando Lopes Oliveira wrote: > > Thanks a lot, Manav. I'm compiling it myself. Could you please point me > to tests files that you mentioned revealed the problem? > > Thanks > > On Monday, February 20, 2017 at 12:36:14 PM UTC-8, Manav Kumar wrote: >> >> Hi Luiz, >> >> James's recommendation of using a downgraded version of openmpi worked. >> If there is a CP2K module that you are using, you might want to ask your >> HPC system administrators to re-compile it for you. There are some tests >> that come with CP2K that weren't run and they revealed the problem with our >> version of CP2K. >> >> Best, >> Manav >> >> >> On Monday, February 20, 2017 at 1:26:14 PM UTC-5, Luiz Fernando Lopes >> Oliveira wrote: >>> >>> Hi Manav. >>> >>> We are having similar problems and were wondering if you had a solution >>> for that. >>> >>> Do you think the problem was finally with the intel compilers? >>> >>> Thanks! >>> >>> On Saturday, April 25, 2015 at 2:26:16 AM UTC-7, Manav Kumar wrote: >>>> >>>> Hi James, >>>> >>>> No, I haven't tried that yet. I will pass on the information to the >>>> system administrators at our HPC and see what they say. Did that fix the >>>> issue with you? >>>> >>>> Best, >>>> Manav Kumar >>>> >>>> >>>> On Saturday, April 25, 2015 at 5:05:16 AM UTC-4, JamesChen wrote: >>>>> >>>>> Hi Manav, >>>>> I have a similar issue with mvapich2 and some buggy version of Intel >>>>> compilers. It seems that you are using rather standard software stack. Have >>>>> you ever downgraded your openmpi to 1.6.5 (prior stable version)? >>>>> James >>>>> >>>>> On Sat, Apr 25, 2015 at 6:08 AM, Manav Kumar wrote: >>>>> >>>>>> Hi James, >>>>>> >>>>>> I'm assuming when you say the software environment, you mean the >>>>>> dependencies for CP2K. Here are the dependencies that are added to my >>>>>> environment when I use the CP2K module: >>>>>> >>>>>> 'gcc/4.9.1' >>>>>> >>>>>> 'openmpi/gcc_4.9.1/1.8.3' >>>>>> >>>>>> 'mpiblacs/gcc_4.9.1/openmpi_1.8.3/2.0.2' >>>>>> >>>>>> 'lapack/gcc_4.9.1/3.5.0' >>>>>> >>>>>> 'scalapack/gcc_4.9.1/openmpi_1.8.3/2.0.2' >>>>>> >>>>>> 'fftw3/gcc_4.9.1/3.3.4' >>>>>> >>>>>> >>>>>> Let me know if there is any other information that might help! >>>>>> >>>>>> >>>>>> Best, >>>>>> >>>>>> MK >>>>>> >>>>>> On Friday, April 24, 2015 at 5:56:32 PM UTC-4, JamesChen wrote: >>>>>>> >>>>>>> Hi, >>>>>>> Could you provide us your software environment? Are you using >>>>>>> mvapich2 as MPI? I will suggest you follow the CP2K manual and choose >>>>>>> Gfortran/Gnu compiler, Netlib Math library and Openmpi as the reference >>>>>>> software stack. >>>>>>> http://www.cp2k.org/howto:compile >>>>>>> >>>>>>> Cheers, >>>>>>> James >>>>>>> >>>>>>> On Sat, Apr 25, 2015 at 5:08 AM, Manav Kumar wrote: >>>>>>> >>>>>>>> Hi Matt, >>>>>>>> >>>>>>>> Thank you for your response! >>>>>>>> >>>>>>>> I'm sorry I mis-spoke earlier, I meant to say that NVT not NVE >>>>>>>> that's my mistake. When I ran NVT with CP2K module it worked fine. >>>>>>>> >>>>>>>> I ran a cell optimization using the CP2K module, and it went >>>>>>>> through fine. >>>>>>>> >>>>>>>> I have talked to some of the other members in my group, and they >>>>>>>> mentioned that it is possible that when I am running the simulation on >>>>>>>> multiple nodes that one of them is faulty and therefore causing the >>>>>>>> calculations to hang. However, it seems like the probability of me hitting >>>>>>>> the same faulty node every time I submit a job seems highly unlikely. Also, >>>>>>>> if this was the case then wouldn't the jobs that I submit using my own >>>>>>>> compiled version of CP2K also hang? >>>>>>>> >>>>>>>> When you said that the it was a problem with the cell size, what >>>>>>>> did you mean exactly? >>>>>>>> >>>>>>>> Best, >>>>>>>> Manav Kumar >>>>>>>> >>>>>>>> >>>>>>>> On Friday, April 24, 2015 at 11:51:29 AM UTC-4, Matt W wrote: >>>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> nothing is obviously wrong with your input that I can see. Maybe >>>>>>>>> (i) problem with the executable (ii) problem with cell size. >>>>>>>>> >>>>>>>>> >>>>>>>>> To start debugging - >>>>>>>>> You say you can run NVE - can you run NVT as you've got it set up? >>>>>>>>> Can you run a cell optimization, maybe just a few steps, to check >>>>>>>>> that the stress tensor/cell volume change is working OK. >>>>>>>>> >>>>>>>>> Matt >>>>>>>>> >>>>>>>>> On Friday, April 24, 2015 at 12:52:48 PM UTC+1, Manav Kumar wrote: >>>>>>>>>> >>>>>>>>>> Hi users and developers, >>>>>>>>>> >>>>>>>>>> This is my first project using CP2K, so I'm sorry in advance if >>>>>>>>>> some of the things I say might be wrong. >>>>>>>>>> >>>>>>>>>> I am currently trying to generate a trajectory for a simulation >>>>>>>>>> of diacetone diperoxide (DADP) using a NPT ensemble. I am attaching the >>>>>>>>>> input file, and the submit script below. >>>>>>>>>> >>>>>>>>>> The HPC that I am using has a CP2K module. I performed a >>>>>>>>>> wave-function optimization, geometry optimization, cell optimization, and a >>>>>>>>>> NVE ensemble calculation all using the module. However, now that I am >>>>>>>>>> running the NPT calculation using the module it seems to hang. It reads in >>>>>>>>>> all the parameters from a previous restart file, it starts to initiate the >>>>>>>>>> process but gets stuck in the SCF optimization routine. It doesn't print an >>>>>>>>>> error message, it just stays at that position until the wall time comes >>>>>>>>>> along and kills the process. Sometimes it completes a lot of SCF >>>>>>>>>> optimization steps, sometimes it gets through none. >>>>>>>>>> >>>>>>>>>> What I've done so far to try to remedy the problem is that I've >>>>>>>>>> tried compiling CP2K myself and running the calculation using that >>>>>>>>>> executable instead of the module. I've had a bit more success with my own >>>>>>>>>> compiled executable, but even with that it sometimes hangs. The system >>>>>>>>>> administrators responsible for the HPC checked the binaries and said that >>>>>>>>>> everything was fine. >>>>>>>>>> >>>>>>>>>> Has anyone else had an issue similar to this? >>>>>>>>>> >>>>>>>>>> Best, >>>>>>>>>> Manav Kumar >>>>>>>>>> >>>>>>>>>> I will attach my input file, output file, and submit script below >>>>>>>>>> so that you can see what I have been doing. >>>>>>>>>> >>>>>>>>> -- >>>>>>>> You received this message because you are subscribed to the Google >>>>>>>> Groups "cp2k" group. >>>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>>> send an email to cp2k+... at googlegroups.com. >>>>>>>> To post to this group, send email to cp... at googlegroups.com. >>>>>>>> Visit this group at http://groups.google.com/group/cp2k. >>>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>>> >>>>>>> >>>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "cp2k" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to cp2k+... at googlegroups.com. >>>>>> To post to this group, send email to cp... at googlegroups.com. >>>>>> Visit this group at http://groups.google.com/group/cp2k. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> >>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From olive... at gmail.com Tue Feb 21 19:58:11 2017 From: olive... at gmail.com (Luiz Fernando Lopes Oliveira) Date: Tue, 21 Feb 2017 11:58:11 -0800 (PST) Subject: [CP2K:6407] Re: CP2K Hangs In-Reply-To: <26802bed-ffa8-4c75-bbda-ebb6ed587f48@googlegroups.com> References: <6d3b67a8-c8d2-4a5f-8f1d-d453697527af@googlegroups.com> <1e5d81c4-a61e-4131-927d-ace2437cc46b@googlegroups.com> <70a052bb-29c1-4a85-b347-6183b801c022@googlegroups.com> <08476ecd-6418-4357-8e97-d78861d4c102@googlegroups.com> <3e7a15d1-e3e6-4279-9bab-5b2fa3c6788f@googlegroups.com> <079aac0f-6d4e-4cd9-bd9c-90a5e163e7b0@googlegroups.com> <3625a917-9dad-4aa7-8d3b-1406ce5939e7@googlegroups.com> <80cd180a-7773-4d8c-9cab-1720c8c7cbe2@googlegroups.com> <26802bed-ffa8-4c75-bbda-ebb6ed587f48@googlegroups.com> Message-ID: Sure. But, are there some particular tests for these types of problems. I asked because there so many and there are really specific. On Tuesday, February 21, 2017 at 11:46:36 AM UTC-8, Manav Kumar wrote: > > Hey Luiz, > > There should be some test files that come with the source code. > > Best, > Manav > > On Tuesday, February 21, 2017 at 2:34:55 PM UTC-5, Luiz Fernando Lopes > Oliveira wrote: >> >> Thanks a lot, Manav. I'm compiling it myself. Could you please point me >> to tests files that you mentioned revealed the problem? >> >> Thanks >> >> On Monday, February 20, 2017 at 12:36:14 PM UTC-8, Manav Kumar wrote: >>> >>> Hi Luiz, >>> >>> James's recommendation of using a downgraded version of openmpi worked. >>> If there is a CP2K module that you are using, you might want to ask your >>> HPC system administrators to re-compile it for you. There are some tests >>> that come with CP2K that weren't run and they revealed the problem with our >>> version of CP2K. >>> >>> Best, >>> Manav >>> >>> >>> On Monday, February 20, 2017 at 1:26:14 PM UTC-5, Luiz Fernando Lopes >>> Oliveira wrote: >>>> >>>> Hi Manav. >>>> >>>> We are having similar problems and were wondering if you had a solution >>>> for that. >>>> >>>> Do you think the problem was finally with the intel compilers? >>>> >>>> Thanks! >>>> >>>> On Saturday, April 25, 2015 at 2:26:16 AM UTC-7, Manav Kumar wrote: >>>>> >>>>> Hi James, >>>>> >>>>> No, I haven't tried that yet. I will pass on the information to the >>>>> system administrators at our HPC and see what they say. Did that fix the >>>>> issue with you? >>>>> >>>>> Best, >>>>> Manav Kumar >>>>> >>>>> >>>>> On Saturday, April 25, 2015 at 5:05:16 AM UTC-4, JamesChen wrote: >>>>>> >>>>>> Hi Manav, >>>>>> I have a similar issue with mvapich2 and some buggy version of Intel >>>>>> compilers. It seems that you are using rather standard software stack. Have >>>>>> you ever downgraded your openmpi to 1.6.5 (prior stable version)? >>>>>> James >>>>>> >>>>>> On Sat, Apr 25, 2015 at 6:08 AM, Manav Kumar wrote: >>>>>> >>>>>>> Hi James, >>>>>>> >>>>>>> I'm assuming when you say the software environment, you mean the >>>>>>> dependencies for CP2K. Here are the dependencies that are added to my >>>>>>> environment when I use the CP2K module: >>>>>>> >>>>>>> 'gcc/4.9.1' >>>>>>> >>>>>>> 'openmpi/gcc_4.9.1/1.8.3' >>>>>>> >>>>>>> 'mpiblacs/gcc_4.9.1/openmpi_1.8.3/2.0.2' >>>>>>> >>>>>>> 'lapack/gcc_4.9.1/3.5.0' >>>>>>> >>>>>>> 'scalapack/gcc_4.9.1/openmpi_1.8.3/2.0.2' >>>>>>> >>>>>>> 'fftw3/gcc_4.9.1/3.3.4' >>>>>>> >>>>>>> >>>>>>> Let me know if there is any other information that might help! >>>>>>> >>>>>>> >>>>>>> Best, >>>>>>> >>>>>>> MK >>>>>>> >>>>>>> On Friday, April 24, 2015 at 5:56:32 PM UTC-4, JamesChen wrote: >>>>>>>> >>>>>>>> Hi, >>>>>>>> Could you provide us your software environment? Are you using >>>>>>>> mvapich2 as MPI? I will suggest you follow the CP2K manual and choose >>>>>>>> Gfortran/Gnu compiler, Netlib Math library and Openmpi as the reference >>>>>>>> software stack. >>>>>>>> http://www.cp2k.org/howto:compile >>>>>>>> >>>>>>>> Cheers, >>>>>>>> James >>>>>>>> >>>>>>>> On Sat, Apr 25, 2015 at 5:08 AM, Manav Kumar >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi Matt, >>>>>>>>> >>>>>>>>> Thank you for your response! >>>>>>>>> >>>>>>>>> I'm sorry I mis-spoke earlier, I meant to say that NVT not NVE >>>>>>>>> that's my mistake. When I ran NVT with CP2K module it worked fine. >>>>>>>>> >>>>>>>>> I ran a cell optimization using the CP2K module, and it went >>>>>>>>> through fine. >>>>>>>>> >>>>>>>>> I have talked to some of the other members in my group, and they >>>>>>>>> mentioned that it is possible that when I am running the simulation on >>>>>>>>> multiple nodes that one of them is faulty and therefore causing the >>>>>>>>> calculations to hang. However, it seems like the probability of me hitting >>>>>>>>> the same faulty node every time I submit a job seems highly unlikely. Also, >>>>>>>>> if this was the case then wouldn't the jobs that I submit using my own >>>>>>>>> compiled version of CP2K also hang? >>>>>>>>> >>>>>>>>> When you said that the it was a problem with the cell size, what >>>>>>>>> did you mean exactly? >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> Manav Kumar >>>>>>>>> >>>>>>>>> >>>>>>>>> On Friday, April 24, 2015 at 11:51:29 AM UTC-4, Matt W wrote: >>>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> nothing is obviously wrong with your input that I can see. Maybe >>>>>>>>>> (i) problem with the executable (ii) problem with cell size. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> To start debugging - >>>>>>>>>> You say you can run NVE - can you run NVT as you've got it set up? >>>>>>>>>> Can you run a cell optimization, maybe just a few steps, to check >>>>>>>>>> that the stress tensor/cell volume change is working OK. >>>>>>>>>> >>>>>>>>>> Matt >>>>>>>>>> >>>>>>>>>> On Friday, April 24, 2015 at 12:52:48 PM UTC+1, Manav Kumar wrote: >>>>>>>>>>> >>>>>>>>>>> Hi users and developers, >>>>>>>>>>> >>>>>>>>>>> This is my first project using CP2K, so I'm sorry in advance if >>>>>>>>>>> some of the things I say might be wrong. >>>>>>>>>>> >>>>>>>>>>> I am currently trying to generate a trajectory for a simulation >>>>>>>>>>> of diacetone diperoxide (DADP) using a NPT ensemble. I am attaching the >>>>>>>>>>> input file, and the submit script below. >>>>>>>>>>> >>>>>>>>>>> The HPC that I am using has a CP2K module. I performed a >>>>>>>>>>> wave-function optimization, geometry optimization, cell optimization, and a >>>>>>>>>>> NVE ensemble calculation all using the module. However, now that I am >>>>>>>>>>> running the NPT calculation using the module it seems to hang. It reads in >>>>>>>>>>> all the parameters from a previous restart file, it starts to initiate the >>>>>>>>>>> process but gets stuck in the SCF optimization routine. It doesn't print an >>>>>>>>>>> error message, it just stays at that position until the wall time comes >>>>>>>>>>> along and kills the process. Sometimes it completes a lot of SCF >>>>>>>>>>> optimization steps, sometimes it gets through none. >>>>>>>>>>> >>>>>>>>>>> What I've done so far to try to remedy the problem is that I've >>>>>>>>>>> tried compiling CP2K myself and running the calculation using that >>>>>>>>>>> executable instead of the module. I've had a bit more success with my own >>>>>>>>>>> compiled executable, but even with that it sometimes hangs. The system >>>>>>>>>>> administrators responsible for the HPC checked the binaries and said that >>>>>>>>>>> everything was fine. >>>>>>>>>>> >>>>>>>>>>> Has anyone else had an issue similar to this? >>>>>>>>>>> >>>>>>>>>>> Best, >>>>>>>>>>> Manav Kumar >>>>>>>>>>> >>>>>>>>>>> I will attach my input file, output file, and submit script >>>>>>>>>>> below so that you can see what I have been doing. >>>>>>>>>>> >>>>>>>>>> -- >>>>>>>>> You received this message because you are subscribed to the Google >>>>>>>>> Groups "cp2k" group. >>>>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>>>> send an email to cp2k+... at googlegroups.com. >>>>>>>>> To post to this group, send email to cp... at googlegroups.com. >>>>>>>>> Visit this group at http://groups.google.com/group/cp2k. >>>>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>> You received this message because you are subscribed to the Google >>>>>>> Groups "cp2k" group. >>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>> send an email to cp2k+... at googlegroups.com. >>>>>>> To post to this group, send email to cp... at googlegroups.com. >>>>>>> Visit this group at http://groups.google.com/group/cp2k. >>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>> >>>>>> >>>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From marci... at gmail.com Wed Feb 22 09:12:34 2017 From: marci... at gmail.com (marcella Iannuzzi) Date: Wed, 22 Feb 2017 10:12:34 +0100 Subject: [CP2K:8686] negative homo - lumo gap In-Reply-To: <334d6355-4ff5-46ea-9c3f-dfa3be07ed2e@googlegroups.com> References: <334d6355-4ff5-46ea-9c3f-dfa3be07ed2e@googlegroups.com> Message-ID: <0ECB38E5-C662-4EAE-AF6C-C2CE3670A0A0@gmail.com> Hi Ian, without more information about the calculation you are performing it is hard to guess what is going on. By default, the unoccupied states are calculated only a posteriori. Here the problem seems to be that the ground state is not properly optimised. Either the system has no gap, i.e., it is metallic, or there is some problem with the DFT settings. If the system is metallic, one should use a different scheme for the optimisation that is able to apply the partial occupation of the KS states, by assigning the occupation number as a function of the KS energy and of the Fermi energy. This is not possible using OT. From your message it is not clear what did Claudio actually try to correct the problem. Best Marcella > On 13 Feb 2017, at 17:58, Ian Hamilton wrote: > > Hi Marcella, > > One of my students has encountered this problem. He tried changing the OT and increasing the number of MOs (we don't know what you mean by "smearing the occupation numbers around the Fermi energy") but it didn't correct the problem. I?m posting this on his behalf because he was unable to- he got a message that he had ?limited access to public groups in his domain.? > > Do you (or anyone else) have another suggestion? In his pdos files all the levels look fine except for the HOMO and LUMO. > > From his output: > Fermi Energy [eV] : -5.966796 > Lowest Eigenvalues of the unoccupied subspace spin 1 > ----------------------------------------------------- > Reached convergence in 149 iterations > -0.23489989 -0.21167052 -0.18538586 -0.17943768 > -0.13796253 -0.13007839 > HOMO - LUMO gap [eV] : -0.425155 > ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -1076.972424168399129 > > Best regards, > Ian Haminton > > On Sunday, November 22, 2009 at 6:13:06 AM UTC-5, Claudio wrote: > Dear all, > > sometimes after I converge a calculation to an accuracy of say 1.0E-5 > I get things like > > HOMO - LUMO gap [eV] : -0.980594 > > This is because the Homo Energy is 0.22417642 and the Lumo Energy is > 0.18814027 in AU. > > I have requested the same accuracy for homo and lumo and have added > enough iterations to the lumo calculation loop to make sure the > program claims it is converged. I am using the OT method. How do I > prevent this from happening? I mean how do I ensure that the > calculation yields Lumo energies that are higher than the homo energy? > > > Sorry to bother you and thanks for your help! > > Claudio > > > -- > You received this message because you are subscribed to the Google Groups "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com . > To post to this group, send email to cp... at googlegroups.com . > Visit this group at https://groups.google.com/group/cp2k . > For more options, visit https://groups.google.com/d/optout . -------------- next part -------------- An HTML attachment was scrubbed... URL: From igla... at gmail.com Thu Feb 23 08:15:42 2017 From: igla... at gmail.com (Ivan Gladich) Date: Thu, 23 Feb 2017 00:15:42 -0800 (PST) Subject: Box movement in Adaptive Buffered Force QM/MM (AdBF-QM/MM) Message-ID: <7db980d7-7da8-42f8-9f04-02761b78422a@googlegroups.com> Dear all, I am trying to model some surfactants on a liquid water slab using AdBF-QMMM. The system was pre-euilibrated using classical MD and I remove the CoM movement using COMVEL_TOL 1.0E-10 By the way, even after removing the CoM, the system experience some CoM movement. The trajectory looks like "shaking". I placed the trajectory and the X,Y,Z-position of my QM atom (file Br_pos.dat) together with my input at https://drive.google.com/open?id=0B9kQhpI16-FudWhuUUxNT1AwQlE Is this something excepted in QMMM due to the way in which forces are computed? I remember, but I not sure, that the code should try place the QM dynamical region in order to avoid crossing with the PBC box. But again, not sure of that... Thank you for any possible help Ivan -------------- next part -------------- An HTML attachment was scrubbed... URL: From ywta... at gmail.com Thu Feb 23 21:48:01 2017 From: ywta... at gmail.com (William Tao) Date: Thu, 23 Feb 2017 13:48:01 -0800 (PST) Subject: Multi-threading not actually working on another machine Message-ID: <1ad94a20-1472-4d7e-9dc5-44b3b6eeaf54@googlegroups.com> Dear friends, I compiled the cp2k version 4.1 on a 8-core CPU machine. When I run the binary cp2k.ssmp on another machine with 40-core CPU, the output prints that the number of threads is 40. However, when I check with "top" command, the process could use up to 800% CPU. Does anybody know what is going on? William -------------- next part -------------- An HTML attachment was scrubbed... URL: From rtsy... at gmail.com Thu Feb 23 22:09:51 2017 From: rtsy... at gmail.com (Roman Tsyshevskiy) Date: Thu, 23 Feb 2017 14:09:51 -0800 (PST) Subject: Problems running XAS calculations Message-ID: <8c083664-854e-47c1-8229-a048d2694443@googlegroups.com> Dear developers and CP2K community, I tried to calculate XAS spectrum for water molecule using CP2K 3.0. My calculations finished with the following error forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source cp2k.popt 0000000005A33965 Unknown Unknown Unknown cp2k.popt 0000000005A31587 Unknown Unknown Unknown cp2k.popt 00000000059D4BE4 Unknown Unknown Unknown cp2k.popt 00000000059D49F6 Unknown Unknown Unknown cp2k.popt 0000000005978096 Unknown Unknown Unknown cp2k.popt 000000000597F1A0 Unknown Unknown Unknown cp2k.popt 0000000002B492C0 Unknown Unknown Unknown cp2k.popt 00000000013F188F Unknown Unknown Unknown cp2k.popt 00000000013EC4F9 Unknown Unknown Unknown cp2k.popt 0000000000AB2065 Unknown Unknown Unknown cp2k.popt 0000000000F5444C Unknown Unknown Unknown cp2k.popt 00000000011F7EBE Unknown Unknown Unknown cp2k.popt 00000000011F6691 Unknown Unknown Unknown cp2k.popt 000000000102170E Unknown Unknown Unknown cp2k.popt 000000000042B2FD Unknown Unknown Unknown cp2k.popt 000000000041391E Unknown Unknown Unknown cp2k.popt 000000000041257E Unknown Unknown Unknown cp2k.popt 0000000005A4FC70 Unknown Unknown Unknown cp2k.popt 0000000000412467 Unknown Unknown Unknown I tried to repeat the same calculations using cp2k/2.5.1 version installed on different computer and got similar error. Below is my input file I used for my calculations. &GLOBAL PROJECT H2O RUN_TYPE ENERGY_FORCE PRINT_LEVEL LOW &END GLOBAL &FORCE_EVAL METHOD QS &SUBSYS &CELL ABC 12.4138 12.4138 12.4138 &END CELL &COORD O 12.235322 1.376642 10.869880 H 12.415139 2.233125 11.257611 H 11.922476 1.573799 9.986994 &END COORD &KIND H BASIS_SET 6-31G* POTENTIAL All &END KIND &KIND O BASIS_SET 6-31G* POTENTIAL All &END KIND &END SUBSYS &DFT UKS .True. BASIS_SET_FILE_NAME ./BASIS_SET # POTENTIAL_FILE_NAME ./GTH_POTENTIALS &QS EPS_DEFAULT 1.0E-7 METHOD GAPW &END QS &MGRID CUTOFF 200 NGRIDS 4 REL_CUTOFF 30 &END MGRID &SCF SCF_GUESS ATOMIC EPS_SCF 1.0E-05 MAX_SCF 200 &DIAGONALIZATION T ALGORITHM STANDARD &END DIAGONALIZATION &PRINT &RESTART OFF &END RESTART &END PRINT &END SCF &XC &XC_FUNCTIONAL BLYP &END XC_FUNCTIONAL &END XC &XAS ATOMS_LIST 1 METHOD DSCF STATE_SEARCH = 1 STATE_TYPE 1S &PRINT &XAS_SPECTRUM ADD_LAST NO &END XAS_SPECTRUM &END PRINT &END XAS &END DFT &END FORCE_EVAL Best Regards, Roman -------------- next part -------------- An HTML attachment was scrubbed... URL: From ywta... at gmail.com Thu Feb 23 22:34:04 2017 From: ywta... at gmail.com (William Tao) Date: Thu, 23 Feb 2017 14:34:04 -0800 (PST) Subject: B3LYP In-Reply-To: <3a8b7bf6-2b0a-460c-816b-8cfd6343018f@j2g2000yqb.googlegroups.com> References: <3a8b7bf6-2b0a-460c-816b-8cfd6343018f@j2g2000yqb.googlegroups.com> Message-ID: <61e48c07-bc54-4de3-9773-e4c217f32b8f@googlegroups.com> Very helpful. Thank you! ? 2011?5?24???? UTC-5??5:26:15?jacopos??? > > Dear all > i would like to run calculations using B3LYP, are there example input > files for this functional? > > Thanks > > Jacopo -------------- next part -------------- An HTML attachment was scrubbed... URL: From liufe... at gmail.com Fri Feb 24 05:51:15 2017 From: liufe... at gmail.com (feihu liu) Date: Thu, 23 Feb 2017 21:51:15 -0800 (PST) Subject: convergence problem of EPR calculation In-Reply-To: References: <81a0c0f1-b4b0-4304-bd4c-a0a5469df124@googlegroups.com> Message-ID: Thank you very much! I will try your suggestions. Best regards, Feihu ? 2017?1?20???? UTC+8??5:15:17?Marcella Iannuzzi??? > > > Dear feihu liu , > > the convergence problem is due to numerical errors in the conjugate > gradient algorithm. > You can try to play with the parameters related to the minimisation > procedure, > for example the preconditioner. > > The EMSL basis sets can be used with GAPW, provided that you slightly > modify > the format to make it properly readable by cp2k. > > Is the ground state calculation also giving different results by changing > XC_DERIV and > XC_SMOOTH_RHO? If yes, first you need to converge at best the GS, before > starting any linear response. > With a bad GS starting point the LS can give very wrong results. > > Kind regards, > Marcella > > On Monday, January 9, 2017 at 6:11:39 AM UTC+1, feihu liu wrote: >> >> Dear Marcella >> >> Thanks for your patience and kindly explanations. >> >> I have ecountered other problems, which I can not fix it all by myself: >> >> 1. The convergence problem sometimes can be fixed, sometimes not.I have >> no idea what has happened. >> Can you tell me the reasons in some detail? Like what the error >> massage "tr()<0" means? That would be very helpful! >> >> 2. The Guassian basis sets used in my calculation were taken from the >> EMSL basis set exchange library. >> Are they compatible with CP2K? >> >> #################################################### >> EMSL:(in Gaussian94 format) >> **** >> Na 0 >> S 7 1.00 >> 0.219036D+05 0.796012D-03 >> 0.328624D+04 0.614434D-02 >> 0.748016D+03 0.313507D-01 >> 0.211598D+03 0.119245D+00 >> 0.684819D+02 0.324337D+00 >> 0.242414D+02 0.500000D+00 >> 0.890835D+01 0.277280D+00 >> S 3 1.00 >> 0.209903D+02 -0.780809D-01 >> 0.200831D+01 0.527383D+00 >> 0.637279D+00 0.500000D+00 >> S 1 1.00 >> 0.587726D-01 1.0000000 >> S 1 1.00 >> 0.233057D-01 1.0000000 >> P 5 1.00 >> 0.882297D+03 0.432459D-03 >> 0.135738D+03 0.804650D-02 >> 0.316045D+02 0.615841D-01 >> 0.968275D+01 0.234223D+00 >> 0.336969D+01 0.500000D+00 >> P 1 1.00 >> 0.117061D+01 1.0000000 >> P 1 1.00 >> 0.376739D+00 1.0000000 >> P 1 1.00 >> 0.750000D-01 1.0000000 >> **** >> Cl 0 >> S 7 1.00 >> 0.560994D+05 0.739546D-03 >> 0.841587D+04 0.571202D-02 >> 0.191547D+04 0.292323D-01 >> 0.541853D+03 0.112459D+00 >> 0.175685D+03 0.314046D+00 >> 0.627047D+02 0.500000D+00 >> 0.234082D+02 0.301981D+00 >> S 3 1.00 >> 0.522083D+02 -0.898067D-01 >> 0.565919D+01 0.573660D+00 >> 0.224102D+01 0.500000D+00 >> S 1 1.00 >> 0.456248D+00 1.0000000 >> S 1 1.00 >> 0.159554D+00 1.0000000 >> P 5 1.00 >> 0.282726D+04 0.330198D-03 >> 0.434964D+03 0.633287D-02 >> 0.102165D+03 0.510518D-01 >> 0.321545D+02 0.210174D+00 >> 0.116187D+02 0.500000D+00 >> P 1 1.00 >> 0.441005D+01 1.0000000 >> P 1 1.00 >> 0.168514D+01 1.0000000 >> P 1 1.00 >> 0.537066D+00 1.0000000 >> P 1 1.00 >> 0.154770D+00 1.0000000 >> D 1 1.00 >> 0.600000D+00 1.0000000 >> **** >> >> #################################################### >> CP2K: >> **** >> Na pcSseg-1 >> 8 >> 1 0 0 7 1 >> 0.219036D+05 0.796012D-03 >> 0.328624D+04 0.614434D-02 >> 0.748016D+03 0.313507D-01 >> 0.211598D+03 0.119245D+00 >> 0.684819D+02 0.324337D+00 >> 0.242414D+02 0.500000D+00 >> 0.890835D+01 0.277280D+00 >> 1 0 0 3 1 >> 0.209903D+02 -0.780809D-01 >> 0.200831D+01 0.527383D+00 >> 0.637279D+00 0.500000D+00 >> 1 0 0 1 1 >> 0.587726D-01 1.0000000 >> 1 0 0 1 1 >> 0.233057D-01 1.0000000 >> 1 1 1 5 1 >> 0.882297D+03 0.432459D-03 >> 0.135738D+03 0.804650D-02 >> 0.316045D+02 0.615841D-01 >> 0.968275D+01 0.234223D+00 >> 0.336969D+01 0.500000D+00 >> 1 1 1 1 1 >> 0.117061D+01 1.0000000 >> 1 1 1 1 1 >> 0.376739D+00 1.0000000 >> 1 1 1 1 1 >> 0.750000D-01 1.0000000 >> **** >> Cl pcSseg-1 >> 10 >> 1 0 0 7 1 >> 0.560994D+05 0.739546D-03 >> 0.841587D+04 0.571202D-02 >> 0.191547D+04 0.292323D-01 >> 0.541853D+03 0.112459D+00 >> 0.175685D+03 0.314046D+00 >> 0.627047D+02 0.500000D+00 >> 0.234082D+02 0.301981D+00 >> 1 0 0 3 1 >> 0.522083D+02 -0.898067D-01 >> 0.565919D+01 0.573660D+00 >> 0.224102D+01 0.500000D+00 >> 1 0 0 1 1 >> 0.456248D+00 1.0000000 >> 1 0 0 1 1 >> 0.159554D+00 1.0000000 >> 1 1 1 5 1 >> 0.282726D+04 0.330198D-03 >> 0.434964D+03 0.633287D-02 >> 0.102165D+03 0.510518D-01 >> 0.321545D+02 0.210174D+00 >> 0.116187D+02 0.500000D+00 >> 1 1 1 1 1 >> 0.441005D+01 1.0000000 >> 1 1 1 1 1 >> 0.168514D+01 1.0000000 >> 1 1 1 1 1 >> 0.537066D+00 1.0000000 >> 1 1 1 1 1 >> 0.154770D+00 1.0000000 >> 1 2 2 1 1 >> 0.600000D+00 1.0000000 >> >> #################################################### >> #################################################### >> >> 3. When I changed the Keyword "XC_DERIV" from "PW" to "SPLINE3_SMOOTH" >> and set the Keyword "XC_SMOOTH_RHO" to be "SPLINE3", >> the "gmatrix_so" and "gmatrix_soo" numerial results became very >> different: >> >> The result of the code with keyword "XC_DERIV PW" : >> >> #################################################### >> G tensor >> >> gmatrix_zke >> XX= -0.0006462559 XY= 0.0000000000 XZ= 0.0000000000 >> YX= 0.0000000000 YY= -0.0006462559 YZ= 0.0000000000 >> ZX= 0.0000000000 ZY= 0.0000000000 ZZ= -0.0006462559 >> gmatrix_so >> XX= 0.0167865861 XY= 0.0013125477 XZ= -0.0002725164 >> YX= 0.0013335361 YY= 0.0954078621 YZ= -0.0004370711 >> ZX= -0.0000138193 ZY= -0.0004878867 ZZ= -0.5337450957 >> gmatrix_soo >> XX= -0.0019441017 XY= 0.0000042103 XZ= -0.0000001610 >> YX= 0.0000189745 YY= -0.0005102328 YZ= -0.0000072659 >> ZX= -0.0000004234 ZY= -0.0000017359 ZZ= -0.0082253502 >> gmatrix_total >> XX= 2.0165155328 XY= 0.0013167581 XZ= -0.0002726774 >> YX= 0.0013525106 YY= 2.0965706778 YZ= -0.0004443370 >> ZX= -0.0000142426 ZY= -0.0004896226 ZZ= 1.4597026025 >> gtensor_total >> XX= 2.0165155328 XY= 0.0013346344 XZ= -0.0001434600 >> YX= 0.0013346344 YY= 2.0965706778 YZ= -0.0004669798 >> ZX= -0.0001434600 ZY= -0.0004669798 ZZ= 1.4597026025 >> delta_g principal values in ppm >> -542617.081 X= 0.0002558885 Y= 0.0007327073 Z= 0.9999996988 >> 14174.017 X= 0.9998610842 Y= -0.0166659190 Z= -0.0002436417 >> 94273.963 X= 0.0166657355 Y= 0.9998608455 Z= -0.0007368701 >> >> #################################################### >> >> The result of the code with keyword "XC_DERIV SPLINE3_SMOOTH" and >> "XC_SMOOTH_RHO" to "SPLINE3": >> >> #################################################### >> G tensor >> >> gmatrix_zke >> XX= -0.0006449787 XY= 0.0000000000 XZ= 0.0000000000 >> YX= 0.0000000000 YY= -0.0006449787 YZ= 0.0000000000 >> ZX= 0.0000000000 ZY= 0.0000000000 ZZ= -0.0006449787 >> gmatrix_so >> XX= -0.0038638400 XY= -0.0056517380 XZ= -0.0110404769 >> YX= 0.0008011139 YY= 0.0830525555 YZ= -0.0210224862 >> ZX= -0.0008832411 ZY= -0.0332392956 ZZ= -42.4640419140 >> gmatrix_soo >> XX= -0.0021564411 XY= 0.0000141640 XZ= 0.0000044636 >> YX= 0.0000222413 YY= -0.0005084349 YZ= -0.0005802508 >> ZX= -0.0000115884 ZY= -0.0001023809 ZZ= -0.4934013012 >> gmatrix_total >> XX= 1.9956540447 XY= -0.0056375740 XZ= -0.0110360132 >> YX= 0.0008233552 YY= 2.0842184463 YZ= -0.0216027369 >> ZX= -0.0008948295 ZY= -0.0333416765 ZZ= -40.9557688894 >> gtensor_total >> XX= 1.9956540447 XY= -0.0024071094 XZ= -0.0059654214 >> YX= -0.0024071094 YY= 2.0842184463 YZ= -0.0274722067 >> ZX= -0.0059654214 ZY= -0.0274722067 ZZ= -40.9557688894 >> delta_g principal values in ppm >> -42958106.558 X= 0.0001389233 Y= 0.0006383023 Z= 0.9999997866 >> -6729.587 X= 0.9996326859 Y= 0.0271010869 Z= -0.0001561710 >> 81981.834 X= -0.0271011808 Y= 0.9996324943 Z= -0.0006343029 >> #################################################### >> >> Kind regards >> Feihu >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alfio.... at gmail.com Fri Feb 24 07:47:37 2017 From: alfio.... at gmail.com (Alfio Lazzaro) Date: Thu, 23 Feb 2017 23:47:37 -0800 (PST) Subject: Multi-threading not actually working on another machine In-Reply-To: <1ad94a20-1472-4d7e-9dc5-44b3b6eeaf54@googlegroups.com> References: <1ad94a20-1472-4d7e-9dc5-44b3b6eeaf54@googlegroups.com> Message-ID: <184c7bb4-753c-4442-b2bd-440620d89a6f@googlegroups.com> Dear William, CP2K uses OpenMP for the threading. The number of threads is set by using the environment variable OMP_NUM_THREADS and it goes at runtime, therefore there is no relation with the compilation (you can specify the number of threads at runtime). By default, if you don't set the variable, OpenMP assumes the maximum number of available threads on the system (8 and 40 in your case). That's why you see 40 threads. However, you should consider that it is very hard to get good scalability for such large number of threads (actually it depends on your workload), that's why in "average" (what you see from top command) you are using 8 corresponding fully loaded threads. I can suggest to experiment with setting a different number of threads. Just use: export OMP_NUM_THREADS= before running CP2K. Another better solution would be to use MPI and OpenMP (psmp version), by using 4 MPI ranks and 10 threads (for example). Likely it would give you better performance... Alfio Il giorno gioved? 23 febbraio 2017 22:48:01 UTC+1, William Tao ha scritto: > > Dear friends, > > I compiled the cp2k version 4.1 on a 8-core CPU machine. > When I run the binary cp2k.ssmp on another machine with 40-core CPU, the > output prints that the number of threads is 40. > However, when I check with "top" command, the process could use up to 800% > CPU. > > Does anybody know what is going on? > > > William > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ywta... at gmail.com Fri Feb 24 16:06:49 2017 From: ywta... at gmail.com (William Tao) Date: Fri, 24 Feb 2017 08:06:49 -0800 (PST) Subject: Multi-threading not actually working on another machine In-Reply-To: <184c7bb4-753c-4442-b2bd-440620d89a6f@googlegroups.com> References: <1ad94a20-1472-4d7e-9dc5-44b3b6eeaf54@googlegroups.com> <184c7bb4-753c-4442-b2bd-440620d89a6f@googlegroups.com> Message-ID: <83abfa0e-2143-418b-a5ce-93554eddc2e5@googlegroups.com> Dear Alfio, I did set up the OMP_NUM_THREADS as 40 for my calculation. And here is part of my output in the very beginning. GLOBAL| Force Environment number 1 GLOBAL| Basis set file name HFX_BASIS GLOBAL| Potential file name GTH_POTENTIALS GLOBAL| MM Potential file name MM_POTENTIAL GLOBAL| Coordinate file name atm309.xyz GLOBAL| Method name CP2K GLOBAL| Project name ATOM-309 GLOBAL| Preferred FFT library FFTW3 GLOBAL| Preferred diagonalization lib. SL GLOBAL| Run type MD GLOBAL| All-to-all communication in single precision F GLOBAL| FFTs using library dependent lengths F GLOBAL| Global print level LOW GLOBAL| Total number of message passing processes 1 * GLOBAL| Number of threads for this process 40* GLOBAL| This output is from process 0 GLOBAL| CPU model name : Intel(R) Xeon(R) CPU E7-8891 v3 @ 2.80GHz However, when running, it could only use up to 8 threads. Thank you. William ? 2017?2?24???? UTC-6??1:47:37?Alfio Lazzaro??? > > Dear William, > CP2K uses OpenMP for the threading. The number of threads is set by using > the environment variable OMP_NUM_THREADS and it goes at runtime, therefore > there is no relation with the compilation (you can specify the number of > threads at runtime). By default, if you don't set the variable, OpenMP > assumes the maximum number of available threads on the system (8 and 40 in > your case). That's why you see 40 threads. However, you should consider > that it is very hard to get good scalability for such large number of > threads (actually it depends on your workload), that's why in "average" > (what you see from top command) you are using 8 corresponding fully loaded > threads. > > I can suggest to experiment with setting a different number of threads. > Just use: > > export OMP_NUM_THREADS= > > before running CP2K. > > Another better solution would be to use MPI and OpenMP (psmp version), by > using 4 MPI ranks and 10 threads (for example). Likely it would give you > better performance... > > Alfio > > > > Il giorno gioved? 23 febbraio 2017 22:48:01 UTC+1, William Tao ha scritto: >> >> Dear friends, >> >> I compiled the cp2k version 4.1 on a 8-core CPU machine. >> When I run the binary cp2k.ssmp on another machine with 40-core CPU, the >> output prints that the number of threads is 40. >> However, when I check with "top" command, the process could use up to >> 800% CPU. >> >> Does anybody know what is going on? >> >> >> William >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From ianpha... at gmail.com Fri Feb 24 20:07:19 2017 From: ianpha... at gmail.com (Ian Hamilton) Date: Fri, 24 Feb 2017 12:07:19 -0800 (PST) Subject: [CP2K:8686] negative homo - lumo gap In-Reply-To: <0ECB38E5-C662-4EAE-AF6C-C2CE3670A0A0@gmail.com> References: <334d6355-4ff5-46ea-9c3f-dfa3be07ed2e@googlegroups.com> <0ECB38E5-C662-4EAE-AF6C-C2CE3670A0A0@gmail.com> Message-ID: Hi Marcella, Thank you for your reply. Let me tell you a little bit about the system and why, although a negative HOMO-LUMO gap doesn't make sense, I'm no longer worried about the situation. The student is doing calculations on graphene quantum dots which (unlike graphene) are well-known to gave a gap. He is looking at the effect on the gap of replacing hydrogens with either electron donating or electron withdrawing groups. He is also looking at the effect on the gap of replacing hydrogens with bulkier groups at either armchair or zigzag positions since it has been suggested that a gap can form in graphene if it is strained and that the effect is different for strain in the armchair versus zigzag directions. The calculation for which he got the negative HOMO-LUMO gap, was one in which, due to too much strain or congestion, the "optimized" geometry was completely nonphysical. Best, Ian On Wednesday, February 22, 2017 at 4:12:39 AM UTC-5, Marcella Iannuzzi wrote: > > Hi Ian, > > without more information about the calculation you are performing it is > hard to guess what is going on. > By default, the unoccupied states are calculated only a posteriori. Here > the problem seems to be that the ground state is not properly optimised. > Either the system has no gap, i.e., it is metallic, or there is some > problem with the DFT settings. > If the system is metallic, one should use a different scheme for the > optimisation that is able to apply the partial occupation of the KS states, > by assigning the occupation number as a function of the KS energy and of > the Fermi energy. > This is not possible using OT. From your message it is not clear what did > Claudio actually try to correct the problem. > Best > Marcella > > > On 13 Feb 2017, at 17:58, Ian Hamilton > > wrote: > > Hi Marcella, > > One of my students has encountered this problem. He tried changing the OT > and increasing the number of MOs (we don't know what you mean by "smearing > the occupation numbers around the Fermi energy") but it didn't correct the > problem. I?m posting this on his behalf because he was unable to- he got a > message that he had ?limited access to public groups in his domain.? > > Do you (or anyone else) have another suggestion? In his pdos files all the > levels look fine except for the HOMO and LUMO. > > From his output: > Fermi Energy [eV] : -5.966796 > Lowest Eigenvalues of the unoccupied subspace spin 1 > ----------------------------------------------------- > Reached convergence in 149 iterations > -0.23489989 -0.21167052 -0.18538586 -0.17943768 > -0.13796253 -0.13007839 > HOMO - LUMO gap [eV] : -0.425155 > ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): > -1076.972424168399129 > > Best regards, > Ian Haminton > > On Sunday, November 22, 2009 at 6:13:06 AM UTC-5, Claudio wrote: >> >> Dear all, >> >> sometimes after I converge a calculation to an accuracy of say 1.0E-5 >> I get things like >> >> HOMO - LUMO gap [eV] : -0.980594 >> >> This is because the Homo Energy is 0.22417642 and the Lumo Energy is >> 0.18814027 in AU. >> >> I have requested the same accuracy for homo and lumo and have added >> enough iterations to the lumo calculation loop to make sure the >> program claims it is converged. I am using the OT method. How do I >> prevent this from happening? I mean how do I ensure that the >> calculation yields Lumo energies that are higher than the homo energy? >> >> >> Sorry to bother you and thanks for your help! >> >> Claudio >> >> > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+... at googlegroups.com . > To post to this group, send email to cp... at googlegroups.com . > Visit this group at https://groups.google.com/group/cp2k. > For more options, visit https://groups.google.com/d/optout. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alfio.... at gmail.com Sat Feb 25 06:26:40 2017 From: alfio.... at gmail.com (Alfio Lazzaro) Date: Fri, 24 Feb 2017 22:26:40 -0800 (PST) Subject: Multi-threading not actually working on another machine In-Reply-To: <83abfa0e-2143-418b-a5ce-93554eddc2e5@googlegroups.com> References: <1ad94a20-1472-4d7e-9dc5-44b3b6eeaf54@googlegroups.com> <184c7bb4-753c-4442-b2bd-440620d89a6f@googlegroups.com> <83abfa0e-2143-418b-a5ce-93554eddc2e5@googlegroups.com> Message-ID: <42ea21cf-56e3-4c1a-8dbb-23b2dbc3a581@googlegroups.com> The CP2K output is fine. Now, if you rely on top command to see how many threads you are running, that is somehow underestimated (it will show you the average CPU utilization). You can use the options in the second answer of this post http://stackoverflow.com/questions/15933801/openmp-creates-many-threads-but-seems-to-use-only-one-core to disaggregate all the running threads. Another test is to set less number of threads (for example OMP_NUM_THREADS=4) and see how it goes. In any case, as I mentioned in my previous email, for such large number of cores you should consider to run the PSMP version, i.e. MPI+OpenMP (your 40 cores are using different NUMA domains, so you should set at least one MPI rank per NUMA domain). Alfio Il giorno venerd? 24 febbraio 2017 17:06:49 UTC+1, William Tao ha scritto: > > Dear Alfio, > > I did set up the OMP_NUM_THREADS as 40 for my calculation. And here is > part of my output in the very beginning. > > GLOBAL| Force Environment number > 1 > GLOBAL| Basis set file name > HFX_BASIS > GLOBAL| Potential file name > GTH_POTENTIALS > GLOBAL| MM Potential file name > MM_POTENTIAL > GLOBAL| Coordinate file name > atm309.xyz > GLOBAL| Method name > CP2K > GLOBAL| Project name ATOM-309 > GLOBAL| Preferred FFT library > FFTW3 > GLOBAL| Preferred diagonalization lib. > SL > GLOBAL| Run type > MD > GLOBAL| All-to-all communication in single precision > F > GLOBAL| FFTs using library dependent lengths > F > GLOBAL| Global print level > LOW > GLOBAL| Total number of message passing processes > 1 > * GLOBAL| Number of threads for this process > 40* > GLOBAL| This output is from process > 0 > GLOBAL| CPU model name : Intel(R) Xeon(R) CPU E7-8891 v3 @ 2.80GHz > > > However, when running, it could only use up to 8 threads. > > Thank you. > > William > > > > ? 2017?2?24???? UTC-6??1:47:37?Alfio Lazzaro??? >> >> Dear William, >> CP2K uses OpenMP for the threading. The number of threads is set by using >> the environment variable OMP_NUM_THREADS and it goes at runtime, therefore >> there is no relation with the compilation (you can specify the number of >> threads at runtime). By default, if you don't set the variable, OpenMP >> assumes the maximum number of available threads on the system (8 and 40 in >> your case). That's why you see 40 threads. However, you should consider >> that it is very hard to get good scalability for such large number of >> threads (actually it depends on your workload), that's why in "average" >> (what you see from top command) you are using 8 corresponding fully loaded >> threads. >> >> I can suggest to experiment with setting a different number of threads. >> Just use: >> >> export OMP_NUM_THREADS= >> >> before running CP2K. >> >> Another better solution would be to use MPI and OpenMP (psmp version), by >> using 4 MPI ranks and 10 threads (for example). Likely it would give you >> better performance... >> >> Alfio >> >> >> >> Il giorno gioved? 23 febbraio 2017 22:48:01 UTC+1, William Tao ha scritto: >>> >>> Dear friends, >>> >>> I compiled the cp2k version 4.1 on a 8-core CPU machine. >>> When I run the binary cp2k.ssmp on another machine with 40-core CPU, the >>> output prints that the number of threads is 40. >>> However, when I check with "top" command, the process could use up to >>> 800% CPU. >>> >>> Does anybody know what is going on? >>> >>> >>> William >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From manoo... at gmail.com Sat Feb 25 20:39:03 2017 From: manoo... at gmail.com (Babgen Manookian) Date: Sat, 25 Feb 2017 12:39:03 -0800 (PST) Subject: Isolated system Geometry Optimizations In-Reply-To: <1a744090-32fc-4286-a8ff-a32fbcb27c07@googlegroups.com> References: <1a744090-32fc-4286-a8ff-a32fbcb27c07@googlegroups.com> Message-ID: <620c8b5f-944e-42f1-ac5d-aff668578ec4@googlegroups.com> Hey Juerg, So I looked in the input manual and could not find the REF_CELL keyword. Also, it is still a little unclear what is actually being changed in terms of the calculation. Could you elaborate on that for me please? Does this have anything to do with setting density to be zero at the cell wall? Thank you in advance, Bobby On Tuesday, February 14, 2017 at 1:21:43 PM UTC-5, Babgen Manookian wrote: > > Hey Everyone, > > I am a new cp2k user and have been working on a test system in order to > get a feel for how the program works. My test system is a cyclohexane > molecule and I am interested in determining the energy difference between > boat and chair conformations. I am using a wavelet poisson solver with > periodicity turned off and the molecule centered in the cell. I attached > the template input file which I used to create the different inputs with > varying cells size. > > What I have noticed is that as I increase my cell size the energy does not > converge on a single value, instead it seems to oscillate. The graphs below > show the energies of each conformation and their differences as functions > of cell size. I am very curious as to what is causing these oscillations. > If I have a single cyclohexane molecule centered in my cell, as I increase > my cell size, I would think that the extra vacuum space around the molecule > will not affect the energy. > > If there is anyone out there who could provide any sort of input on this > it would be much appreciated. > > Thanks, > Bobby > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From yanfa... at gmail.com Mon Feb 27 00:48:49 2017 From: yanfa... at gmail.com (Fangyong Yan) Date: Sun, 26 Feb 2017 16:48:49 -0800 (PST) Subject: a question about constrained MD, shake algorithm and the free energy calculation using Lagrange multiplier In-Reply-To: <1c9465c2-8cde-4a69-bbee-b900a62b83b6@googlegroups.com> References: <1c9465c2-8cde-4a69-bbee-b900a62b83b6@googlegroups.com> Message-ID: <6cbd29a8-c548-40a7-8227-4301aa6bee3b@googlegroups.com> personally thinking, the constrained md is kind of biasing to the reaction coordinates, so I personally prefer running a 1000 ps unconstrained MD, to running the same length of constrained md. For some reactions with high free energy barrier, unconstrained MD cannot simulate the reaction. In this case, maybe I can try other methods. On Wednesday, July 6, 2016 at 12:05:25 PM UTC-4, Fangyong Yan wrote: > > Hi, > > I have a question about the free energy calculation using the constrained > MD. For the simplest case, such as constraining a inter-molecular distance > between two atoms, i and j, In the constrain MD in the NVT ensemble, CP2K > uses shake algorithm to update the position and velocity, where the > constrain follows the holonomic constrain, > > sigma = (ri - rj) ** 2 - dij ** 2, where dij is the constrain distance, > and the total force is equal to F_i + G_i, G_i is the constrained force > and is equal to, lamda * the first derivative of simga versus r_i, thus, > G_i = -2 * lamda * r_i, (where these eq. borrows from the original shake > paper, JEAN-PAUL RYCKAERT, GIOVANNI CICCOTTI, AND HERMAN J. C. BERENDSEN, > JOURNAL OF COMPUTATIONAL. PHYSICS 23, 321-341 (1977)). > > In the free energy calculation, I think CP2K uses the eq. derived by > Michiel Sprik and GIOVANNI CICCOTTI, Free energy from constrained molecular > dynamics, J. Chem. Phys., Vol. 109, No. 18, 8 November 1998, where in this > paper, the free energy uses a different constrain, > where constrain is equal to |ri - rj| - dij = 0, "| |" represents the > absolute value, and in this case, the constrained force G_i = - lamda, (see > eq. 13 in the paper). The free energy is equal to > > dW / d Zeta' = < Z^(-1/2) * [ -lamda + kTG] > / < Z^(-1/2)> > > W is the free energy, Zeta is the constrained eq., in this case is equal > to |ri - rj| - dij = 0, Zeta' represent different Zeta's; < > is the > ensemble average, Z is a factor arises from the requirement that when Zeta > is equal to zero for all times, the first derivative of Zeta (the velocity > of this constrain) is also equal to zero for all times. (from E.A. CARTER, > Giovanni CICCOTTI, James T. HYNES, Raymond KAPRAL, Chem. Phys. Lett. 156, > 472 ~1989.); G is equal to > G = (1 / Z^2) * (1/m_i * 1/m_j) * the first derivative of Zeta versus r_i > * the second derivative of Zeta versus r_i and r_j * the first derivative > of Zeta versus r_j, > when Zeta = |r_i - r_j| - dij, the first derivative of Zeta versus r_i = > the first derivative of Zeta versus r_j = 1, the second derivative of Zeta > versus r_i and r_j = 0, thus, the free energy is equal to > > dW / d Zeta' = < Z^(-1/2) * [ -lamda + kTG] > / < Z^(-1/2)> = < Z^(-1/2) * > [ -lamda] > / < Z^(-1/2)>, and Z is a constant in this simple case, thus, > dW / d Zeta' = <-lamda> > > Now my question is, since shake uses Zeta = (r_i - r_J) ** 2 - dij**2 = 0, > in this case, G wont disappear, and the constrained force G_i = - 2 * lamda > * r_i. Since CP2K does use SHAKE algorithm, how does CP2K do the free > energy calculation, do CP2K uses Zeta = (r_i - r_j) ** 2 - dij**2 =0, or > Zeta = |r_i - r_j| - dij = 0, since these two cases the lagrange multiplier > is different. > > Thanks for your patience for reading this, and I hope someone who can help > me with this issue! > > Fangyong > > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Mon Feb 27 10:11:49 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Mon, 27 Feb 2017 11:11:49 +0100 Subject: [CP2K:8745] Re: Isolated system Geometry Optimizations In-Reply-To: <620c8b5f-944e-42f1-ac5d-aff668578ec4@googlegroups.com> References: <620c8b5f-944e-42f1-ac5d-aff668578ec4@googlegroups.com>, <1a744090-32fc-4286-a8ff-a32fbcb27c07@googlegroups.com> Message-ID: Hi sorry, the correct keyword is CP2K_INPUT / FORCE_EVAL / SUBSYS / CELL / CELL_REF this allows you to do constant number of grid point calculations instead of constant cutoff. It results in smoother energy vs. volume curves. regards Juerg -------------------------------------------------------------- Juerg Hutter?????????????????????????Phone : ++41 44 635 4491 Institut f?r Chemie C????????????????FAX???: ++41 44 635 6838 Universit?t Z?rich???????????????????E-mail: hut... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----cp... at googlegroups.com wrote: -----To: cp2k From: Babgen Manookian Sent by: cp... at googlegroups.com Date: 02/25/2017 09:39PM Subject: [CP2K:8745] Re: Isolated system Geometry Optimizations Hey Juerg, So I looked in the input manual and could not find the REF_CELL keyword. Also, it is still a little unclear what is actually being changed in terms of the calculation. Could you elaborate on that for me please? Does this have anything to do with setting density to be zero at the cell wall? Thank you in advance,Bobby? On Tuesday, February 14, 2017 at 1:21:43 PM UTC-5, Babgen Manookian wrote:Hey Everyone, I am a new cp2k user and have been working on a test system in order to get a feel for how the program works. My test system is a cyclohexane molecule and I am interested in determining the energy difference between boat and chair conformations. I am using a wavelet poisson solver with periodicity turned off and the molecule centered in the cell. I attached the template input file which I used to create the different inputs with varying cells size. What I have noticed is that as I increase my cell size the energy does not converge on a single value, instead it seems to oscillate. The graphs below show the energies of each conformation and their differences as functions of cell size. I am very curious as to what is causing these oscillations. If I have a single cyclohexane molecule centered in my cell, as I increase my cell size, I would think that the extra vacuum space around the molecule will not affect the energy.? If there is anyone out there who could provide any sort of input on this it would be much appreciated. Thanks,Bobby -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns... at googlegroups.com. To post to this group, send email to cp... at googlegroups.com. Visit this group at https://groups.google.com/group/cp2k. For more options, visit https://groups.google.com/d/optout. From jia... at vt.edu Mon Feb 27 14:42:30 2017 From: jia... at vt.edu (jia... at vt.edu) Date: Mon, 27 Feb 2017 06:42:30 -0800 (PST) Subject: vibration frequency intensity Message-ID: Dear All, I recently try to calculate the vibration frequency using the following code: I used the fully optimized geometry with the criterion: &GEO_OPT TYPE MINIMIZATION MAX_DR 3.0E-03 MAX_FORCE 0.00005 RMS_DR 1.5E-03 RMS_FORCE 3.0E-04 MAX_ITER 2000 OPTIMIZER CG &CG &LINE_SEARCH TYPE 2PNT &END LINE_SEARCH &END CG &END GEO_OPT &SCF .... EPS_SCF 1.0E-6 .... &END SCF When do the vibration_analysis I change the &SCF &EPS_SCF to 1.0E-8 &VIBRATIONAL_ANALYSIS INTENSITIES NPROC_REP 16 DX 0.001 &MODE_SELECTIVE &INVOLVED_ATOMS INVOLVED_ATOMS 1 2 3 &END INVOLVED_ATOMS &END MODE_SELECTIVE &PRINT &PROGRAM_RUN_INFO ON &END &END &END Submit the job using 2 nodes(1node has 32 processors). 1. I found that with different NPROC_REP value (16, 32,64) it gives similar frequency but with quite different intensity. How does the NPROC_REP affects the intensity? 2. In the output, .... MS| ITERATION STEP 1 MS| TRACKED MODE 313.813098cm-1 NOT CONVERGED ...... FREQUENCY AND CONVERGENCE LIST FREQUENCY INTENSITY MAXVAL CRITERIA NORM CRITERIA CONVERGENCE VIB| 58.079 582.068111 0.263E-06 0.443E-06 YES VIB| 348.828 591.399560 0.101E-05 0.303E-05 NO VIB| 579.845 1.641373 0.249E-05 0.419E-05 NO If it is not converged, it means the system doesn't have this frequency? -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.sassma... at ucl.ac.uk Mon Feb 27 22:22:57 2017 From: j.sassma... at ucl.ac.uk (=?iso-8859-15?q?J=F6rg_Sa=DFmannshausen?=) Date: Mon, 27 Feb 2017 22:22:57 +0000 Subject: CI-NEB calculation: crashes Message-ID: <201702272223.01583.j.sassmannshausen@ucl.ac.uk> Dear all, I am trying to do a CI-NEB calculation but after the first step the calculation crashed which this error message: NEB| Building initial set of coordinates. END ******************************************************************************* BAND TYPE = CI- NEB BAND TYPE OPTIMIZATION = SD STEP NUMBER = 0 RMSD DISTANCE DEFINITION = T NUMBER OF NEB REPLICA = 5 DISTANCES REP = 9.750661 9.750661 9.750661 9.750661 ENERGIES [au] = -648.476382 -647.620195 -646.701277 -647.623017 -648.424927 BAND TOTAL ENERGY [au] = -3238.84579812863058 ******************************************************************************* Trying to move ./WFN_restart.wfn.bak-1 to ./WFN_restart.wfn.bak-2. rename returned status: -1 Problem moving file ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[44988,1],192] Exit code: 1 The SGE error files contains this: cp2k-4.1-avx2.popt:3555 terminated with signal 6 at PC=2ad95d2c35f7 SP=7ffe9c0dbcf8. (I have omitted the backtrace) I am using 256 cores and this is the relevant part of my input file: @SET BAND_TYPE NEB &MOTION &PRINT &VELOCITIES OFF &END &END &BAND NPROC_REP 32 @IF ( ${BAND_TYPE} == NEB ) BAND_TYPE CI-NEB K_SPRING 0.2 ROTATE_FRAMES T &CI_NEB NSTEPS_IT 5 &END @ENDIF @ENDIF NUMBER_OF_REPLICA 5 &CONVERGENCE_CONTROL MAX_FORCE 0.001 RMS_FORCE 0.0005 &END &OPTIMIZE_BAND OPTIMIZE_END_POINTS F OPT_TYPE DIIS &DIIS MAX_STEPS 200 N_DIIS 7 NO_LS STEPSIZE 0.5 MAX_STEPSIZE 1.0 &END &END &REPLICA COORD_FILE_NAME files/start-A.xyz &END &REPLICA COORD_FILE_NAME files/final-C.xyz &END &PROGRAM_RUN_INFO &END &CONVERGENCE_INFO &END &END BAND &END MOTION Could anybody point me in the right direction here? I am trying to get these calculations done for some time now and I am still stuck. I have checked the cluster with a different input file which I know works and so I got some confidence it is not a cluster problem. Anybody any ideas? Please let me know if you need more informations. All the best from London J?rg -- ************************************************************* Dr. J?rg Sa?mannshausen, MRSC University College London Department of Chemistry 20 Gordon Street London WC1H 0AJ email: j.sassma... at ucl.ac.uk web: http://sassy.formativ.net Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- Q29udGVudC1UeXBlOiBhcHBsaWNhdGlvbi9wZ3Atc2lnbmF0dXJlOyBuYW1lPSJzaWduYXR1cmUu YXNjIg0KQ29udGVudC1EZXNjcmlwdGlvbjogVGhpcyBpcyBhIGRpZ2l0YWxseSBzaWduZWQgbWVz c2FnZSBwYXJ0Lg0KDQotLS0tLUJFR0lOIFBHUCBTSUdOQVRVUkUtLS0tLQ0KVmVyc2lvbjogR251 UEcgdjEuNC4xMiAoR05VL0xpbnV4KQ0KDQppRjRFQUJFSUFBWUZBbGkwcHNFQUNna1FUQ24vTHk5 Uy93ZWEzUUQrTHZ2N0h0dzc0b3RhOEZST2VBSmV2cEhBDQpBem5zZk5rRHgyc1lVSkJtdWlvQS8x dEcvQmJtYXJ0V1JiMFVPWmJZaDJPTVhFbzFwakpZMVc1S2pvTloxdU9zDQo9bk82cA0KLS0tLS1F TkQgUEdQIFNJR05BVFVSRS0tLS0tDQo= From mattwa... at gmail.com Tue Feb 28 11:17:50 2017 From: mattwa... at gmail.com (Matt W) Date: Tue, 28 Feb 2017 03:17:50 -0800 (PST) Subject: CI-NEB calculation: crashes In-Reply-To: <201702272223.01583.j.sassmannshausen@ucl.ac.uk> References: <201702272223.01583.j.sassmannshausen@ucl.ac.uk> Message-ID: <879e834a-62b2-4e0a-86df-d2644c465558@googlegroups.com> Hi J?rg, to me this error message Trying to move ./WFN_restart.wfn.bak-1 to ./WFN_restart.wfn.bak-2. rename returned status: -1 looks suspicious. I would expect the wavefunction files to have some prefixes indicating which replica etc. Maybe several MPI processes are trying to get a file lock on the same file? Have you changed the names of any restart files / output file names etc in you input file? Matt On Monday, February 27, 2017 at 10:23:09 PM UTC, sassy wrote: > > Dear all, > > I am trying to do a CI-NEB calculation but after the first step the > calculation > crashed which this error message: > > NEB| Building initial set of coordinates. END > > ******************************************************************************* > > BAND TYPE = > CI- > NEB > BAND TYPE OPTIMIZATION = > > SD > STEP NUMBER = > > 0 > RMSD DISTANCE DEFINITION = > > T > NUMBER OF NEB REPLICA = > > 5 > DISTANCES REP = 9.750661 9.750661 9.750661 > 9.750661 > ENERGIES [au] = -648.476382 -647.620195 -646.701277 > -647.623017 > -648.424927 > BAND TOTAL ENERGY [au] = > -3238.84579812863058 > ******************************************************************************* > > Trying to move ./WFN_restart.wfn.bak-1 to ./WFN_restart.wfn.bak-2. > rename returned status: -1 > Problem moving file > ------------------------------------------------------- > Primary job terminated normally, but 1 process returned > a non-zero exit code.. Per user-direction, the job has been aborted. > ------------------------------------------------------- > -------------------------------------------------------------------------- > mpirun detected that one or more processes exited with non-zero status, > thus > causing > the job to be terminated. The first process to do so was: > > Process name: [[44988,1],192] > Exit code: 1 > > > The SGE error files contains this: > > cp2k-4.1-avx2.popt:3555 terminated with signal 6 at PC=2ad95d2c35f7 > SP=7ffe9c0dbcf8. > (I have omitted the backtrace) > > I am using 256 cores and this is the relevant part of my input file: > > @SET BAND_TYPE NEB > &MOTION > &PRINT > &VELOCITIES OFF > &END > &END > &BAND > NPROC_REP 32 > @IF ( ${BAND_TYPE} == NEB ) > BAND_TYPE CI-NEB > K_SPRING 0.2 > ROTATE_FRAMES T > &CI_NEB > NSTEPS_IT 5 > &END > @ENDIF > @ENDIF > NUMBER_OF_REPLICA 5 > &CONVERGENCE_CONTROL > MAX_FORCE 0.001 > RMS_FORCE 0.0005 > &END > &OPTIMIZE_BAND > OPTIMIZE_END_POINTS F > OPT_TYPE DIIS > &DIIS > MAX_STEPS 200 > N_DIIS 7 > NO_LS > STEPSIZE 0.5 > MAX_STEPSIZE 1.0 > &END > &END > &REPLICA > COORD_FILE_NAME files/start-A.xyz > &END > &REPLICA > COORD_FILE_NAME files/final-C.xyz > &END > &PROGRAM_RUN_INFO > &END > &CONVERGENCE_INFO > &END > &END BAND > &END MOTION > > > Could anybody point me in the right direction here? I am trying to get > these > calculations done for some time now and I am still stuck. I have checked > the > cluster with a different input file which I know works and so I got some > confidence it is not a cluster problem. > Anybody any ideas? > > Please let me know if you need more informations. > > All the best from London > > J?rg > > > -- > ************************************************************* > Dr. J?rg Sa?mannshausen, MRSC > University College London > Department of Chemistry > 20 Gordon Street > London > WC1H 0AJ > > email: j.sas... at ucl.ac.uk > web: http://sassy.formativ.net > > Please avoid sending me Word or PowerPoint attachments. > See http://www.gnu.org/philosophy/no-word-attachments.html > -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.sassma... at ucl.ac.uk Tue Feb 28 12:09:17 2017 From: j.sassma... at ucl.ac.uk (=?ISO-8859-1?Q?J=F6rg_Sa=DFmannshausen?=) Date: Tue, 28 Feb 2017 12:09:17 +0000 Subject: [CP2K:8750] Re: CI-NEB calculation: crashes In-Reply-To: <879e834a-62b2-4e0a-86df-d2644c465558@googlegroups.com> References: <201702272223.01583.j.sassmannshausen@ucl.ac.uk> <879e834a-62b2-4e0a-86df-d2644c465558@googlegroups.com> Message-ID: <2524554.T43PS78zYO@chemb105> Hi Matt, thanks for the feedback. I think that error message is a bit of a red herring. I am running normal geometry and hessian calculations for some time now and my wavefunction file is always called WFN_restart.wfn in the input file. Originally I suspected it is a problem with the cluster but given that I could repeat the problem with that calculation and not with a different calculation I think that is not the problem. It is running now. All I done was removing the duplicated line @ENDIF in my input file. I don't really know why I had it twice to be honest and it does not make much sense to me that for a SM type of band calculations that did not cause any problems whereas it does for a CI-NEB calculation. I would have thought if there is a problem with the input file, the program crashes right at the beginning and not after the first step. So for now I think we can close that, problem sorted. Thanks for the feedback though. All the best from a sunny London J?rg On Tuesday 28 Feb 2017 03:17:50 Matt W wrote: > Hi J?rg, > > to me this error message > > Trying to move ./WFN_restart.wfn.bak-1 to ./WFN_restart.wfn.bak-2. > rename returned status: -1 > > looks suspicious. I would expect the wavefunction files to have some > prefixes indicating which replica etc. Maybe several MPI processes are > trying to get a file lock on the same file? > > Have you changed the names of any restart files / output file names etc in > you input file? > > Matt > > On Monday, February 27, 2017 at 10:23:09 PM UTC, sassy wrote: > > Dear all, > > > > I am trying to do a CI-NEB calculation but after the first step the > > calculation > > > > crashed which this error message: > > NEB| Building initial set of coordinates. END > > > > ************************************************************************* > > ****** > > > > BAND TYPE = > > CI- > > > > NEB > > > > BAND TYPE OPTIMIZATION = > > > > SD > > > > STEP NUMBER = > > > > 0 > > > > RMSD DISTANCE DEFINITION = > > > > T > > > > NUMBER OF NEB REPLICA = > > > > 5 > > > > DISTANCES REP = 9.750661 9.750661 9.750661 > > > > 9.750661 > > > > ENERGIES [au] = -648.476382 -647.620195 -646.701277 > > > > -647.623017 > > > > -648.424927 > > > > BAND TOTAL ENERGY [au] = > > > > -3238.84579812863058 > > > > ************************************************************************* > > ****** > > > > Trying to move ./WFN_restart.wfn.bak-1 to ./WFN_restart.wfn.bak-2. > > rename returned status: -1 > > Problem moving file > > > > ------------------------------------------------------- > > Primary job terminated normally, but 1 process returned > > a non-zero exit code.. Per user-direction, the job has been aborted. > > ------------------------------------------------------- > > -------------------------------------------------------------------------- > > mpirun detected that one or more processes exited with non-zero status, > > thus > > causing > > > > the job to be terminated. The first process to do so was: > > Process name: [[44988,1],192] > > Exit code: 1 > > > > The SGE error files contains this: > > > > cp2k-4.1-avx2.popt:3555 terminated with signal 6 at PC=2ad95d2c35f7 > > SP=7ffe9c0dbcf8. > > (I have omitted the backtrace) > > > > I am using 256 cores and this is the relevant part of my input file: > > > > @SET BAND_TYPE NEB > > &MOTION > > > > &PRINT > > > > &VELOCITIES OFF > > &END > > > > &END > > &BAND > > > > NPROC_REP 32 > > > > @IF ( ${BAND_TYPE} == NEB ) > > > > BAND_TYPE CI-NEB > > K_SPRING 0.2 > > ROTATE_FRAMES T > > &CI_NEB > > > > NSTEPS_IT 5 > > > > &END > > > > @ENDIF > > @ENDIF > > > > NUMBER_OF_REPLICA 5 > > &CONVERGENCE_CONTROL > > > > MAX_FORCE 0.001 > > RMS_FORCE 0.0005 > > > > &END > > &OPTIMIZE_BAND > > > > OPTIMIZE_END_POINTS F > > OPT_TYPE DIIS > > &DIIS > > > > MAX_STEPS 200 > > N_DIIS 7 > > NO_LS > > STEPSIZE 0.5 > > MAX_STEPSIZE 1.0 > > > > &END > > > > &END > > &REPLICA > > > > COORD_FILE_NAME files/start-A.xyz > > > > &END > > &REPLICA > > > > COORD_FILE_NAME files/final-C.xyz > > > > &END > > &PROGRAM_RUN_INFO > > &END > > &CONVERGENCE_INFO > > &END > > > > &END BAND > > > > &END MOTION > > > > > > Could anybody point me in the right direction here? I am trying to get > > these > > calculations done for some time now and I am still stuck. I have checked > > the > > cluster with a different input file which I know works and so I got some > > confidence it is not a cluster problem. > > Anybody any ideas? > > > > Please let me know if you need more informations. > > > > All the best from London > > > > J?rg > > > > > > > > email: j.sas... at ucl.ac.uk > > web: http://sassy.formativ.net > > > > Please avoid sending me Word or PowerPoint attachments. > > See http://www.gnu.org/philosophy/no-word-attachments.html -- ************************************************************* Dr. J?rg Sa?mannshausen, MRSC University College London Department of Chemistry 20 Gordon Street London WC1H 0AJ email: j.sassma... at ucl.ac.uk web: http://sassy.formativ.net Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 220 bytes Desc: This is a digitally signed message part. URL: From ywta... at gmail.com Tue Feb 28 15:25:03 2017 From: ywta... at gmail.com (William Tao) Date: Tue, 28 Feb 2017 07:25:03 -0800 (PST) Subject: vibration frequency intensity In-Reply-To: References: Message-ID: The simple way to solve this problem is to use serial version to test if your system is not so large. "cp2k.sopt" or "cp2k.ssmp" ? 2017?2?27???? UTC-6??8:42:30?jia... at vt.edu??? > > Dear All, > > I recently try to calculate the vibration frequency using the following > code: > > I used the fully optimized geometry with the criterion: > > &GEO_OPT > > TYPE MINIMIZATION > > MAX_DR 3.0E-03 > > MAX_FORCE 0.00005 > > RMS_DR 1.5E-03 > > RMS_FORCE 3.0E-04 > > MAX_ITER 2000 > > OPTIMIZER CG > > &CG > > &LINE_SEARCH > > TYPE 2PNT > > &END LINE_SEARCH > > &END CG > > &END GEO_OPT > > &SCF > > .... > > EPS_SCF 1.0E-6 > > .... > > &END SCF > > > When do the vibration_analysis I change the &SCF &EPS_SCF to 1.0E-8 > > &VIBRATIONAL_ANALYSIS > > INTENSITIES > > NPROC_REP 16 > > DX 0.001 > > &MODE_SELECTIVE > > &INVOLVED_ATOMS > > INVOLVED_ATOMS 1 2 3 > > &END INVOLVED_ATOMS > > &END MODE_SELECTIVE > > &PRINT > > &PROGRAM_RUN_INFO ON > > &END > > &END > > &END > > > Submit the job using 2 nodes(1node has 32 processors). > > 1. I found that with different NPROC_REP value (16, 32,64) it gives > similar frequency but with quite different intensity. How does the > NPROC_REP affects the intensity? > > 2. In the output, > > .... > > MS| ITERATION STEP 1 > > MS| TRACKED MODE 313.813098cm-1 NOT CONVERGED > > ...... > > FREQUENCY AND CONVERGENCE LIST > > FREQUENCY INTENSITY MAXVAL CRITERIA NORM CRITERIA > CONVERGENCE > > VIB| 58.079 582.068111 0.263E-06 0.443E-06 > YES > > VIB| 348.828 591.399560 0.101E-05 0.303E-05 > NO > > VIB| 579.845 1.641373 0.249E-05 0.419E-05 > NO > > > If it is not converged, it means the system doesn't have this frequency? > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: