From chris... at gmail.com Mon May 1 14:35:23 2017 From: chris... at gmail.com (Chris Campbell) Date: Mon, 1 May 2017 07:35:23 -0700 (PDT) Subject: restrict to initial spins (BS Section) In-Reply-To: <009f0af7-fb1e-49b3-830b-11f92d409185@googlegroups.com> References: <9fa7d569-08c4-4dc5-ae27-fc103cb65477@googlegroups.com> <009f0af7-fb1e-49b3-830b-11f92d409185@googlegroups.com> Message-ID: <61a27d33-000d-4f52-aeb2-f0b1358f4082@googlegroups.com> Hello, Perhaps my optimisation is abit crude, I will try address this. Great thank you for the help, Ill have a look. Cheers, Chri -------------- next part -------------- An HTML attachment was scrubbed... URL: From ashishd... at gmail.com Wed May 3 12:35:44 2017 From: ashishd... at gmail.com (ashish dabral) Date: Wed, 3 May 2017 05:35:44 -0700 (PDT) Subject: Evaluate phase stability of a material. Message-ID: <1e838c2e-17a3-4d66-bbfd-4fa533c3c900@googlegroups.com> Hi, I would like to know how I can find if a particular material phase is stable or not. I have a material, say A, that shows layers of some phase B inside A in the form of lamellae. B can be monolayers or more but mostly A appears in the growth. I would like to know how I can test the stability of the phase B using CP2K? I just want to know if B can really exist on its own or is an intermediate phase between A and some other form of the same material C. The question seems rather general but I am looking for a general procedure to develop a routine for testing such a scenario. Thanks in advance for your inputs. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lbb10... at gmail.com Wed May 3 13:28:29 2017 From: lbb10... at gmail.com (binbin lu) Date: Wed, 3 May 2017 21:28:29 +0800 Subject: Some errors about PIGLET Message-ID: Dear all, Recently, I tried to learn cp2k and combine Generalized Langevin Equation Thermostat(GLET) and path integeral(PI). But I meet some questions.If I don't use GELT or LET, then the input file can run. There are some errors if I add the GLET and LET. The error is below: Forrtl: severe (66): output statement overflows record, unit -5, file Internal List-Directed Write The part of input file is below: &MOTION &PINT P 8 #beads PROC_PER_REPLICA 8 NUM_STEPS 2 TEMP 1500.0 DT 0.2 NRESPA 8 TRANSFORMATION NORMAL PROPAGATOR RPMD # HARM_INT EXACT &PIGLET SMATRIX_INIT DIAGONAL MATRICES_FILE_NAME PIGLET_P8_2000K &END PIGLET &END PINT &PRINT &VELOCITIES &END VELOCITIES &END PRINT &END MOTION Could you please help me? Thank you in advance. Binbin -------------- next part -------------- An HTML attachment was scrubbed... URL: From xuse... at gmail.com Fri May 5 07:56:37 2017 From: xuse... at gmail.com (Sen Xu) Date: Fri, 5 May 2017 00:56:37 -0700 (PDT) Subject: AVBMC Message-ID: <5ba3e2d1-49f9-4a1a-b605-412f3fab82e8@googlegroups.com> I study the method of AVBMC,but i just find the AVBMC1.I want to know whether the cp2k can use the method of AVBMC2 and AVBMC3 or not ?and how ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From heig... at gmail.com Fri May 5 10:10:19 2017 From: heig... at gmail.com (Heigo Ers) Date: Fri, 5 May 2017 03:10:19 -0700 (PDT) Subject: Segmentation fault after activating LDOS feature Message-ID: Dear all, I have received following error after turning on LDOS feature in my input. If You have any idea how to overcome this error I would be very grateful. I have also enclosed my input for this calculation. Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x7F46ADF9AE08 #1 0x7F46ADF99F90 #2 0x7F46AD6CC4AF #3 0x192F017 in __atomic_kind_types_MOD_get_atomic_kind at atomic_kind_types.F:166 (discriminator 1) #4 0xDEE135 in __qs_pdos_MOD_calculate_projected_dos at qs_pdos.F:591 #5 0x7EF165 in __qs_scf_post_gpw_MOD_write_mo_dependent_results at qs_scf_post_gpw.F:2095 #6 0x802102 in __qs_scf_post_gpw_MOD_write_available_results at qs_scf_post_gpw.F:1937 #7 0x12F9D32 in __qs_scf_post_scf_MOD_qs_scf_compute_properties at qs_scf_post_scf.F:68 #8 0xC8C127 in __qs_scf_MOD_scf at qs_scf.F:217 (discriminator 1) #9 0x9A7EFC in __qs_energy_MOD_qs_energies at qs_energy.F:85 #10 0x770005 in calcs_on_isolated_molecules at mscfg_methods.F:265 #11 0x428500 in __cp2k_runs_MOD_cp2k_run at cp2k_runs.F:317 #12 0x42B3DB in __cp2k_runs_MOD_run_input at cp2k_runs.F:1099 #13 0x426458 in MAIN__ at cp2k.F:281 Segmentation fault (core dumped) Yours sincerely, Heigo Ers -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NaCl.in Type: application/octet-stream Size: 2840 bytes Desc: not available URL: From stefan... at gmail.com Fri May 5 10:14:35 2017 From: stefan... at gmail.com (Stefan Becuwe) Date: Fri, 5 May 2017 03:14:35 -0700 (PDT) Subject: Many errors with Intel 2017 compilers in test suite (popt, 3.0 and 4.1) Message-ID: <6a1871e4-2cb4-41e4-8772-c184a0bd56e2@googlegroups.com> Hello, Has anyone experience with the Intel 2017 compilers (update 3)? For the sopt version (just bare, no libxc, libint, ...), 3.0 and 4.1 produce 0 failed and 0 wrong tests. Great! However, running the same tests for the popt version (just bare, no libxc, libint, ...), we get 125 failed and 840 wrong tests for 3.0, and 134 failed and 902 wrong tests for 4.1. Has someone already investigated this issue? Any suggestions? Regards, Stefan -------------- next part -------------- An HTML attachment was scrubbed... URL: From andreas... at gmail.com Sat May 6 07:42:20 2017 From: andreas... at gmail.com (=?UTF-8?Q?Andreas_Gl=C3=B6ss?=) Date: Sat, 6 May 2017 00:42:20 -0700 (PDT) Subject: Many errors with Intel 2017 compilers in test suite (popt, 3.0 and 4.1) In-Reply-To: <6a1871e4-2cb4-41e4-8772-c184a0bd56e2@googlegroups.com> References: <6a1871e4-2cb4-41e4-8772-c184a0bd56e2@googlegroups.com> Message-ID: <443b4c69-dbc1-4bbd-b7f2-43e8bf4dd40f@googlegroups.com> Dear Stefan, Intel 2017 parallel compiler suite seems to have a bug in their FFT interface - already reported to Intel. What works quite well for CP2K-trunk, is using the compiler suite for Scalapack/Blacs, MKL, MPI/OMP and leave FFTs to a self-compiled version of FFTW3. The bug can easily be reproduced - just run test/QS/benchmark/H2O-64.inp with more than one MPI rank. The SCF-energy should diverge rapidly when using Intels FFT. Best regards, and hope this helps, Andreas -------------- next part -------------- An HTML attachment was scrubbed... URL: From taosun... at gmail.com Sun May 7 02:01:04 2017 From: taosun... at gmail.com (Sun Tao) Date: Sat, 6 May 2017 19:01:04 -0700 (PDT) Subject: TZV2P basis set causes "Cholesky decompose failed", while DZVP could run Message-ID: <0c83f28f-c356-40a2-ac46-886606b3982e@googlegroups.com> Dear experts: I am running a system in ab inito MD with CP2K. When I was using TZV2P basis set the simulation crashed with the following error: Cholesky decompose failed: the matrix is not positive definite or ill-conditioned. fm/cp_fm_cholesky.F:94 When I changed into DZVP basis set, the simulation could go through and no error was reported. I am wondering does the size of basis set causing the ill-conditioned hamiltonian matrix? The input and output files are attached. Thanks ~ Tao -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TZV2P.tar.gz Type: application/octet-stream Size: 397373 bytes Desc: not available URL: From tku... at gmail.com Sun May 7 07:21:23 2017 From: tku... at gmail.com (=?utf-8?Q?Thomas_K=C3=BChne?=) Date: Sun, 7 May 2017 09:21:23 +0200 Subject: FYI: [CP2K:8990] TZV2P basis set causes "Cholesky decompose failed", while DZVP could run In-Reply-To: <0c83f28f-c356-40a2-ac46-886606b3982e@googlegroups.com> References: <0c83f28f-c356-40a2-ac46-886606b3982e@googlegroups.com> Message-ID: <42D40416-B6C2-4CEA-85D2-CD9DE40DFA8F@gmail.com> Dear Sudhir, please register to the CP2K users list in case you haven?t already. Best, Thomas > Am 07.05.2017 um 04:01 schrieb Sun Tao : > > Dear experts: > > I am running a system in ab inito MD with CP2K. When I was using TZV2P basis set the simulation crashed with the following error: > > Cholesky decompose failed: the matrix is not positive definite or > ill-conditioned. > > fm/cp_fm_cholesky.F:94 > > When I changed into DZVP basis set, the simulation could go through and no error was reported. > > I am wondering does the size of basis set causing the ill-conditioned hamiltonian matrix? > > The input and output files are attached. > > Thanks ~ > > Tao > > -- > 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 stefan... at gmail.com Mon May 8 08:22:16 2017 From: stefan... at gmail.com (Stefan Becuwe) Date: Mon, 8 May 2017 01:22:16 -0700 (PDT) Subject: Issues with different Intel compilers? Message-ID: Hello, Apart from the FFT issues with Intel 2017 compilers [ https://groups.google.com/d/msg/cp2k/A2Rf79443D4/wjYK6lBbAQAJ], we guess there might be issues with other compilers versions too... This post is a follow up of [https://groups.google.com/d/msg/cp2k/EFggHvw_Rdw/SSKJUWteEAAJ] Using other input files (attached), we were able to reproduce the behavior. We compiled CP2K 2.6, 3.0 and 4.1 with following Intel compilers: 15.0.1.133 Build 20141023 16.0.1.150 Build 20151021 16.0.3.210 Build 20160415 17.0.3.191 Build 20170404 Using the first two compilers, CP2K 2.6 and 3.0 finish for the given input. (We only tried 2.6 and 3.0 for these compilers.) Using the last two compilers, CP2K 2.6, 3.0 and 4.1 seem to "hang", i.e., it does no longer produce any output (see output file in attachment) and the job crashes when the walltime has been reached. Do you have any advice which Intel compilers are known to work with CP2K or which issues are known? Thanks! Regards, Stefan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: input.tgz Type: application/x-gtar Size: 413619 bytes Desc: not available URL: From stefan... at gmail.com Mon May 8 08:26:38 2017 From: stefan... at gmail.com (Stefan Becuwe) Date: Mon, 8 May 2017 01:26:38 -0700 (PDT) Subject: Many errors with Intel 2017 compilers in test suite (popt, 3.0 and 4.1) In-Reply-To: <443b4c69-dbc1-4bbd-b7f2-43e8bf4dd40f@googlegroups.com> References: <6a1871e4-2cb4-41e4-8772-c184a0bd56e2@googlegroups.com> <443b4c69-dbc1-4bbd-b7f2-43e8bf4dd40f@googlegroups.com> Message-ID: Dear Andreas, Thanks for the info! We will try to install a version of CP2K with FFTW3. I'll post the results. We already noticed that reducing 2 MPI ranks (default) to 1 MPI rank the number of errors dropped: from 134 FAILED, 902 WRONG to 0 FAILED en 2 WRONG. We also noticed some other issues with different Intel compilers... I started a new thread for that one [ https://groups.google.com/d/msg/cp2k/WlUieY2TEsI/R8O0waf6AQAJ] Regards, Stefan -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan... at gmail.com Mon May 8 10:00:40 2017 From: stefan... at gmail.com (Stefan Becuwe) Date: Mon, 8 May 2017 03:00:40 -0700 (PDT) Subject: Many errors with Intel 2017 compilers in test suite (popt, 3.0 and 4.1) In-Reply-To: <443b4c69-dbc1-4bbd-b7f2-43e8bf4dd40f@googlegroups.com> References: <6a1871e4-2cb4-41e4-8772-c184a0bd56e2@googlegroups.com> <443b4c69-dbc1-4bbd-b7f2-43e8bf4dd40f@googlegroups.com> Message-ID: <1bbbb15e-e48d-4313-bd6c-b9a02d889ab9@googlegroups.com> Dear Andreas, Intel 2017 parallel compiler suite seems to have a bug in their FFT > interface - already reported to Intel. What works quite well for > CP2K-trunk, is using the compiler suite for Scalapack/Blacs, MKL, MPI/OMP > and leave FFTs to a self-compiled version of FFTW3. > Are there any guidelines how to use MKL on the one hand and use an "external" FFTW3 on the other hand? I found in src/pw/fft/fftw3_lib.F following line, which gives me the impression it's maybe not that simple to decouple MKL and MKL's FFT. #if defined (__INTEL_COMPILER) && defined (__MKL) && defined (__FFTW3) Thanks! Regards, Stefan -------------- next part -------------- An HTML attachment was scrubbed... URL: From andreas... at gmail.com Mon May 8 11:08:14 2017 From: andreas... at gmail.com (=?UTF-8?Q?Andreas_Gl=C3=B6ss?=) Date: Mon, 8 May 2017 04:08:14 -0700 (PDT) Subject: Many errors with Intel 2017 compilers in test suite (popt, 3.0 and 4.1) In-Reply-To: <1bbbb15e-e48d-4313-bd6c-b9a02d889ab9@googlegroups.com> References: <6a1871e4-2cb4-41e4-8772-c184a0bd56e2@googlegroups.com> <443b4c69-dbc1-4bbd-b7f2-43e8bf4dd40f@googlegroups.com> <1bbbb15e-e48d-4313-bd6c-b9a02d889ab9@googlegroups.com> Message-ID: <134f78a1-f038-4e51-aab5-fe90eed186e7@googlegroups.com> Hi Stefan, This line: #if defined (__INTEL_COMPILER) && defined (__MKL) && defined (__FFTW3) and the following just ensure that we are using a thread-safe MKL. Since MKL 2011.02, this should be fine. Therefore, the following (schematic) lib, inc, preproc and compiler flag lines should do the trick (for psmp version). LIBS = -Wl,--start-group \ ${FFTW_LIB}/libfftw3.a \ ${FFTW_LIB}/libfftw3_omp.a \ -Wl,--end-group LIBS += ${MKLROOT}/lib/intel64/libmkl_scalapack_lp64.a \ -Wl,--start-group \ ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a \ ${MKLROOT}/lib/intel64/libmkl_sequential.a \ ${MKLROOT}/lib/intel64/libmkl_core.a \ ${MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_lp64.a \ -Wl,--end-group \ -lpthread -lm -ldl INCS = -I${FFTW_INCLUDE} INCS += -I${MKLROOT}/include DFLAGS = -D__parallel -D__SCALAPACK -D__MPI_VERSION=3 \ -D__FFTW3 \ -D__HAS_ISO_C_BINDING CFLAGS += $(INCS) FCFLAGS += $(INCS) LDFLAGS += $(INCS) ... plus all the rest of your original ARCH file ... Best regards, Andreas -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan... at gmail.com Mon May 8 14:26:32 2017 From: stefan... at gmail.com (Stefan Becuwe) Date: Mon, 8 May 2017 07:26:32 -0700 (PDT) Subject: Many errors with Intel 2017 compilers in test suite (popt, 3.0 and 4.1) In-Reply-To: <134f78a1-f038-4e51-aab5-fe90eed186e7@googlegroups.com> References: <6a1871e4-2cb4-41e4-8772-c184a0bd56e2@googlegroups.com> <443b4c69-dbc1-4bbd-b7f2-43e8bf4dd40f@googlegroups.com> <1bbbb15e-e48d-4313-bd6c-b9a02d889ab9@googlegroups.com> <134f78a1-f038-4e51-aab5-fe90eed186e7@googlegroups.com> Message-ID: <8466b7e6-1521-4667-b701-6fb87daabb52@googlegroups.com> Dear Andreas, Thanks for information. Number of errors in the test suite has been reduced to 0! Kind regards, Stefan -------------- next part -------------- An HTML attachment was scrubbed... URL: From natalie.... at colorado.edu Mon May 8 18:45:02 2017 From: natalie.... at colorado.edu (Natalie Schieber) Date: Mon, 8 May 2017 11:45:02 -0700 (PDT) Subject: incorrect number of frequencies in vibrational analysis Message-ID: Dear all, I am trying to obtain the vibrational frequencies of a periodic system of four benzene molecules. When I run the vibrational analysis with no restriction, I obtain the correct number of frequencies (141), but some of them are negative. However, when I restrict the range of the search, I obtain positive wavenumbers, but more frequencies than should be physically present (152). When I try to run the vibrational analysis with tighter convergence but no range, I get an error. The relevant part of the input is below. Any help on obtaining 141 positive numbers is appreciated! &VIBRATIONAL_ANALYSIS &MODE_SELECTIVE EPS_MAX_VAL 0.0000000005 EPS_NORM 0.00000002 &END MODE_SELECTIVE &END VIBRATIONAL_ANALYSIS Returns an error: no frequency, range or involved atoms specified &VIBRATIONAL_ANALYSIS &END VIBRATIONAL_ANALYSIS returns 141 wavenumbers with negatives &VIBRATIONAL_ANALYSIS &MODE_SELECTIVE EPS_MAX_VAL 0.0000000005 EPS_NORM 0.00000002 RANGE 0 50000 &END MODE_SELECTIVE &END VIBRATIONAL_ANALYSIS returns 152 positive numbers Best, Natalie Schieber -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Tue May 9 07:35:18 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Tue, 9 May 2017 09:35:18 +0200 Subject: [CP2K:8997] incorrect number of frequencies in vibrational analysis In-Reply-To: References: Message-ID: Hi the MODE_SELECTIVE method should not be used to calculate the complete vibrational spectrum. The method is best and most efficient for the calculation of a small number of local (space or frequency) modes. In your case you probably got some modes multiple times. There are no negative modes because you excluded them explicitly. To get rid (or reduce) possible negative frequencies in the complete spectrum you have to increase the numerical accuracy. This might need changing default parameters in all parts of the calculation. - Integral accuracy -> EPS_DEFAULT - PW cutoff -> CUTOFF and REL_CUTOFF - Geometry optimization -> MAX_FORCE, RMS_FORCE - SCF convergence -> EPS_SCF - Step length in finit difference -> DX 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: Natalie Schieber Sent by: cp... at googlegroups.com Date: 05/08/2017 08:45PM Subject: [CP2K:8997] incorrect number of frequencies in vibrational analysis Dear all, I am trying to obtain the vibrational frequencies of a periodic system of four benzene molecules. When I run the vibrational analysis with no restriction, I obtain the correct number of frequencies (141), but some of them are negative. However, when I restrict the range of the search, I obtain positive wavenumbers, but more frequencies than should be physically present (152). When I try to run the vibrational analysis with tighter convergence but no range, I get an error.? The relevant part of the input is below. Any help on obtaining 141 positive numbers is appreciated! &VIBRATIONAL_ANALYSIS &MODE_SELECTIVE EPS_MAX_VAL 0.0000000005 EPS_NORM 0.00000002 &END MODE_SELECTIVE &END VIBRATIONAL_ANALYSIS Returns an error:? no frequency, range or involved atoms specified? &VIBRATIONAL_ANALYSIS &END VIBRATIONAL_ANALYSIS returns 141 wavenumbers with negatives &VIBRATIONAL_ANALYSIS &MODE_SELECTIVE EPS_MAX_VAL 0.0000000005 EPS_NORM 0.00000002 RANGE 0 50000 &END MODE_SELECTIVE &END VIBRATIONAL_ANALYSIS returns 152 positive numbers Best, Natalie Schieber -- 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 rybk... at gmail.com Wed May 10 08:07:57 2017 From: rybk... at gmail.com (Vladimir Rybkin) Date: Wed, 10 May 2017 01:07:57 -0700 (PDT) Subject: How can I estimate the uncertainty on a calculated energy value? In-Reply-To: References: Message-ID: <1e984df2-afb2-4799-a6b9-c1c9d9b093eb@googlegroups.com> Dear Cristiana, the question has no correct answer. To give a few points: 1) the energy here is in Hartree (that's the only thing for sure here) 2) the energy itself is meaningless, what is reported is the energy difference. In kJ/mol people report them with one digit, which, however does not mean that the uncertainty is 0.05. It's just a convention. 3) try to find benchmarks on your systems and use the recommended methods with estimated accuracy. Yours, Vladimir ???????????, 24 ?????? 2017 ?., 10:55:29 UTC+2 ???????????? Cristiana Passiu ???????: > > Dear all, > assuming that a model is correct and that the functional chosen is > suitable for the system, is there a standard uncertainty that can be > attributed to the final energy values? In other words, how many > significative digits can I report in the results? > > What is the default unit of measurement for the energy in the output? For > example, if I have this in the output: > > Total energy: > -158.42425955059213 > ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): > -158.424259550592126 > > are the values in Rydberg or in Hartree? In order to convert them to eV, > do I have to multiply them by 27.2113838668? > > Many thanks, > Cristiana > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fsai... at gmail.com Wed May 10 10:03:06 2017 From: fsai... at gmail.com (Fernan Saiz) Date: Wed, 10 May 2017 03:03:06 -0700 (PDT) Subject: overlap matrix failure Message-ID: Hello CP2k developers, I am trying to minimise the geometry of 2x2x2 molecules of triethoxyvinylsilane. Unfortunately, once the wavefunction is first minimised, cp2k/5.0.17657 crashes showing an error message on the building of the overlap matrix. I have tried different functionals and basis, and removing the OT subsection, but I still get the same error. I was wondering if I could get any suggestions to solve this problem. This problem only goes away if I run it with one molecule using a cubic simulation cell with a side length of 0.7616 nm. ******************************************************************************* * ___ * * / \ * * [ABORT] * * \___/ CPASSERT failed * * | * * O/| * * /| | * * / \ qs_overlap.F:360 * ******************************************************************************* ===== Routine Calling Stack ===== 8 build_overlap_matrix 7 build_core_hamiltonian_matrix_forces 6 qs_forces 5 cp_eval_at 4 cp_cg_main 3 geoopt_cg 2 cp_geo_opt 1 CP2K Best regards, Fernan Saiz, PhD Department of Chemistry Imperial College London -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: log.out Type: application/octet-stream Size: 28392 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: data_cp2k_tri_222_pbe_cp2k_0.coord Type: application/octet-stream Size: 10784 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: triethoxyvinylsilane.inp Type: chemical/x-gamess-input Size: 2021 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: BASIS_SET Type: application/octet-stream Size: 193659 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: POTENTIAL Type: application/octet-stream Size: 73903 bytes Desc: not available URL: From uido... at libero.it Wed May 10 11:42:44 2017 From: uido... at libero.it (Cristiana Passiu) Date: Wed, 10 May 2017 04:42:44 -0700 (PDT) Subject: How can I estimate the uncertainty on a calculated energy value? In-Reply-To: <1e984df2-afb2-4799-a6b9-c1c9d9b093eb@googlegroups.com> References: <1e984df2-afb2-4799-a6b9-c1c9d9b093eb@googlegroups.com> Message-ID: Dear Vladimir, thank you for your answer. It will be helpful for knowing how to express the results of the calculations. Best regards, Cristiana Il giorno mercoled? 10 maggio 2017 10:07:57 UTC+2, Vladimir Rybkin ha scritto: > > Dear Cristiana, > > the question has no correct answer. To give a few points: > 1) the energy here is in Hartree (that's the only thing for sure here) > 2) the energy itself is meaningless, what is reported is the energy > difference. In kJ/mol people report them with one digit, which, however > does not mean that the uncertainty is 0.05. It's just a convention. > 3) try to find benchmarks on your systems and use the recommended methods > with estimated accuracy. > > Yours, > > Vladimir > > ???????????, 24 ?????? 2017 ?., 10:55:29 UTC+2 ???????????? Cristiana > Passiu ???????: >> >> Dear all, >> assuming that a model is correct and that the functional chosen is >> suitable for the system, is there a standard uncertainty that can be >> attributed to the final energy values? In other words, how many >> significative digits can I report in the results? >> >> What is the default unit of measurement for the energy in the output? For >> example, if I have this in the output: >> >> Total energy: >> -158.42425955059213 >> ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): >> -158.424259550592126 >> >> are the values in Rydberg or in Hartree? In order to convert them to eV, >> do I have to multiply them by 27.2113838668? >> >> Many thanks, >> Cristiana >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Wed May 10 11:43:43 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Wed, 10 May 2017 13:43:43 +0200 Subject: [CP2K:9001] overlap matrix failure In-Reply-To: References: Message-ID: Hi this problem is due to an inconsistency in sparsity patterns detected by the code. The inconsistency is introduced by your special choice of integral accuracy and matrix filtering values. The easy way out is not to set EPS_FILTER_MATRIX, which defaults to zero. BTW you can speed up your calculation by using: MINIMIZER DIIS PRECONDITIONER FULL_SINGLE_INVERSE and set MAX_SCF 10 (in SCF and OUTER_SCF) I also assume you are using the SZV-GTH-PADE basis just for some initial testing. DZVP basis sets a the absolute minimum requirement to get useful results. 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: Fernan Saiz Sent by: cp... at googlegroups.com Date: 05/10/2017 12:03PM Subject: [CP2K:9001] overlap matrix failure Hello CP2k developers, I am trying to minimise the geometry of 2x2x2 molecules of triethoxyvinylsilane. Unfortunately, once the wavefunction is first minimised, cp2k/5.0.17657 crashes showing an error message on the building of the overlap matrix. I have tried different functionals and basis, and removing the OT subsection, but I still get the same error. I was wondering if I could get any suggestions to solve this problem. This problem only goes away if I run it with one molecule using a cubic simulation cell with a side length of 0.7616 nm. ?******************************************************************************* ?*?? ___?????????????????????????????????????????????????????????????????????? * ?*? /?? \????????????????????????????????????????????????????????????????????? * ?* [ABORT]???????????????????????????????????????????????????????????????????? * ?*? \___/???????????????????????????? CPASSERT failed????????????????????????? * ?*??? |??????????????????????????????????????????????????????????????????????? * ?*? O/|??????????????????????????????????????????????????????????????????????? * ?* /| |??????????????????????????????????????????????????????????????????????? * ?* / \??????????????????????????????????????????????????????? qs_overlap.F:360 * ?******************************************************************************* ?===== Routine Calling Stack ===== ??????????? 8 build_overlap_matrix ??????????? 7 build_core_hamiltonian_matrix_forces ??????????? 6 qs_forces ??????????? 5 cp_eval_at ??????????? 4 cp_cg_main ??????????? 3 geoopt_cg ??????????? 2 cp_geo_opt ??????????? 1 CP2K Best regards, ? Fernan Saiz, PhD ? Department of Chemistry ? Imperial College London -- 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 "log.out" removed by J?rg Hutter/at/UZH] [attachment "data_cp2k_tri_222_pbe_cp2k_0.coord" removed by J?rg Hutter/at/UZH] [attachment "triethoxyvinylsilane.inp" removed by J?rg Hutter/at/UZH] [attachment "BASIS_SET" removed by J?rg Hutter/at/UZH] [attachment "POTENTIAL" removed by J?rg Hutter/at/UZH] From fsai... at gmail.com Wed May 10 13:47:21 2017 From: fsai... at gmail.com (Fernan Saiz) Date: Wed, 10 May 2017 06:47:21 -0700 (PDT) Subject: [CP2K:9001] overlap matrix failure In-Reply-To: References: Message-ID: Hello, Yes, removing the EPS_FILTER_MATRIX statement makes the simulation work. The basis set SZV-GTH-PADE was indeed used for testing purposes. Many thanks, Fernan On Wednesday, May 10, 2017 at 12:43:48 PM UTC+1, jgh wrote: > > Hi > > this problem is due to an inconsistency in sparsity patterns > detected by the code. The inconsistency is introduced by your > special choice of integral accuracy and matrix filtering values. > > The easy way out is not to set EPS_FILTER_MATRIX, which defaults to zero. > > BTW you can speed up your calculation by using: > > MINIMIZER DIIS > PRECONDITIONER FULL_SINGLE_INVERSE > > and set > MAX_SCF 10 (in SCF and OUTER_SCF) > > I also assume you are using the SZV-GTH-PADE basis just for some > initial testing. DZVP basis sets a the absolute minimum requirement > to get useful results. > > 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: Fernan Saiz > Sent by: cp... at googlegroups.com > Date: 05/10/2017 12:03PM > Subject: [CP2K:9001] overlap matrix failure > > Hello CP2k developers, > I am trying to minimise the geometry of 2x2x2 molecules of > triethoxyvinylsilane. Unfortunately, once the wavefunction is first > minimised, cp2k/5.0.17657 crashes showing an error message on the building > of the overlap matrix. I have tried different functionals and basis, and > removing the OT subsection, but I still get the same error. I was wondering > if I could get any suggestions to solve this problem. This problem only > goes away if I run it with one molecule using a cubic simulation cell with > a side length of 0.7616 nm. > > ******************************************************************************* > > * > ___ * > * / > \ * > * > [ABORT] > * > * \___/ CPASSERT > failed * > * > | * > * > O/| > * > * /| > | * > * / \ > qs_overlap.F:360 * > ******************************************************************************* > > > > ===== Routine Calling Stack ===== > > 8 build_overlap_matrix > 7 build_core_hamiltonian_matrix_forces > 6 qs_forces > 5 cp_eval_at > 4 cp_cg_main > 3 geoopt_cg > 2 cp_geo_opt > 1 CP2K > > Best regards, > Fernan Saiz, PhD > Department of Chemistry > Imperial College London > > > > > -- > > 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 "log.out" removed by J?rg Hutter/at/UZH] > [attachment "data_cp2k_tri_222_pbe_cp2k_0.coord" removed by J?rg > Hutter/at/UZH] > [attachment "triethoxyvinylsilane.inp" removed by J?rg Hutter/at/UZH] > [attachment "BASIS_SET" removed by J?rg Hutter/at/UZH] > [attachment "POTENTIAL" removed by J?rg Hutter/at/UZH] > -------------- next part -------------- An HTML attachment was scrubbed... URL: From filipe.t... at gmail.com Thu May 11 09:59:30 2017 From: filipe.t... at gmail.com (Filipe Teixeira) Date: Thu, 11 May 2017 02:59:30 -0700 (PDT) Subject: How can I estimate the uncertainty on a calculated energy value? In-Reply-To: References: <1e984df2-afb2-4799-a6b9-c1c9d9b093eb@googlegroups.com> Message-ID: Hello In the early 2000's Irikura introduced the concept of "virtual meassurement" (J. Phys. Chem. A, 2005, 109, 8430). In this article one of the sources of error he explored is the error associated with the SCF of optimied geometries (which may depend, for example on the initial geometry being optimized and the propagation of numerical errors in the SCF procedures). It is an interesting reading if you are interested on that matter, but (spoiller allert) those errors (even in 2005 when 32-bit machines were common) are minor compared to the errors of the methodologies themselves. Nowadays, with 64-bit machines being the norm, I doubt machine round-up will be a big source of error for most applications... I hope this helps. Best regards, Filipe Teixeira On Wednesday, May 10, 2017 at 12:42:45 PM UTC+1, Cristiana Passiu wrote: > > Dear Vladimir, > thank you for your answer. It will be helpful for knowing how to express > the results of the calculations. > > Best regards, > Cristiana > > > > > Il giorno mercoled? 10 maggio 2017 10:07:57 UTC+2, Vladimir Rybkin ha > scritto: >> >> Dear Cristiana, >> >> the question has no correct answer. To give a few points: >> 1) the energy here is in Hartree (that's the only thing for sure here) >> 2) the energy itself is meaningless, what is reported is the energy >> difference. In kJ/mol people report them with one digit, which, however >> does not mean that the uncertainty is 0.05. It's just a convention. >> 3) try to find benchmarks on your systems and use the recommended methods >> with estimated accuracy. >> >> Yours, >> >> Vladimir >> >> ???????????, 24 ?????? 2017 ?., 10:55:29 UTC+2 ???????????? Cristiana >> Passiu ???????: >>> >>> Dear all, >>> assuming that a model is correct and that the functional chosen is >>> suitable for the system, is there a standard uncertainty that can be >>> attributed to the final energy values? In other words, how many >>> significative digits can I report in the results? >>> >>> What is the default unit of measurement for the energy in the output? >>> For example, if I have this in the output: >>> >>> Total energy: >>> -158.42425955059213 >>> ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): >>> -158.424259550592126 >>> >>> are the values in Rydberg or in Hartree? In order to convert them to eV, >>> do I have to multiply them by 27.2113838668? >>> >>> Many thanks, >>> Cristiana >>> >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From uido... at libero.it Thu May 11 14:41:26 2017 From: uido... at libero.it (Cristiana Passiu) Date: Thu, 11 May 2017 07:41:26 -0700 (PDT) Subject: How can I estimate the uncertainty on a calculated energy value? In-Reply-To: References: <1e984df2-afb2-4799-a6b9-c1c9d9b093eb@googlegroups.com> Message-ID: Dear Filipe, thank you for your reply and for the interesting paper suggested. Kind regards, Cristiana Il giorno gioved? 11 maggio 2017 11:59:30 UTC+2, Filipe Teixeira ha scritto: > > Hello > > In the early 2000's Irikura introduced the concept of "virtual > meassurement" (J. Phys. Chem. A, 2005, 109, 8430). In this article one of > the sources of error he explored is the error associated with the SCF of > optimied geometries (which may depend, for example on the initial geometry > being optimized and the propagation of numerical errors in the SCF > procedures). It is an interesting reading if you are interested on that > matter, but (spoiller allert) those errors (even in 2005 when 32-bit > machines were common) are minor compared to the errors of the methodologies > themselves. Nowadays, with 64-bit machines being the norm, I doubt machine > round-up will be a big source of error for most applications... > > I hope this helps. > > Best regards, > Filipe Teixeira > > On Wednesday, May 10, 2017 at 12:42:45 PM UTC+1, Cristiana Passiu wrote: >> >> Dear Vladimir, >> thank you for your answer. It will be helpful for knowing how to express >> the results of the calculations. >> >> Best regards, >> Cristiana >> >> >> >> >> Il giorno mercoled? 10 maggio 2017 10:07:57 UTC+2, Vladimir Rybkin ha >> scritto: >>> >>> Dear Cristiana, >>> >>> the question has no correct answer. To give a few points: >>> 1) the energy here is in Hartree (that's the only thing for sure here) >>> 2) the energy itself is meaningless, what is reported is the energy >>> difference. In kJ/mol people report them with one digit, which, however >>> does not mean that the uncertainty is 0.05. It's just a convention. >>> 3) try to find benchmarks on your systems and use the recommended >>> methods with estimated accuracy. >>> >>> Yours, >>> >>> Vladimir >>> >>> ???????????, 24 ?????? 2017 ?., 10:55:29 UTC+2 ???????????? Cristiana >>> Passiu ???????: >>>> >>>> Dear all, >>>> assuming that a model is correct and that the functional chosen is >>>> suitable for the system, is there a standard uncertainty that can be >>>> attributed to the final energy values? In other words, how many >>>> significative digits can I report in the results? >>>> >>>> What is the default unit of measurement for the energy in the output? >>>> For example, if I have this in the output: >>>> >>>> Total energy: >>>> -158.42425955059213 >>>> ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): >>>> -158.424259550592126 >>>> >>>> are the values in Rydberg or in Hartree? In order to convert them to >>>> eV, do I have to multiply them by 27.2113838668? >>>> >>>> Many thanks, >>>> Cristiana >>>> >>>> >>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhj... at gmail.com Fri May 12 04:38:38 2017 From: zhj... at gmail.com (zhj... at gmail.com) Date: Thu, 11 May 2017 21:38:38 -0700 (PDT) Subject: cp2k revision 17894 compile fatal error Message-ID: <43993c55-6e33-4e65-80c9-879bd969d56a@googlegroups.com> Dear CP2K Developers and Users, When I compile cp2k revision 17894 by using *parallel_studio_xe_2015_update2* and *parallel_studio_xe_2016_update4*, there was a fatal error: *catastrophic error: **Internal compiler error: segmentation violation signal raised** Please report this error along with the circumstances in which it occurred in a Software Problem Report. Note: File and line given may not be explicit cause of this error.* *compilation aborted for dbcsr_tensor_test.F90 (code 1)make[3]: *** [dbcsr_tensor_test.o] Error 1make[3]: *** Waiting for unfinished jobs....make[2]: *** [all] Error 2make[1]: *** [popt] Error 2make: *** [all] Error 2* But when I use *parallel_studio_xe_2017_update3* instead, this error was gone, but the MKL lib have some errors. Using cp2k compiled by *parallel_studio_xe_2017_update3*, the energy can not converge. The compiled version is *Linux-x86-64-intel-host.popt*. I will upload some files about compiled. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Linux-x86-64-intel-mic.psmp Type: application/octet-stream Size: 11139 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: compile error_file Type: application/octet-stream Size: 673597 bytes Desc: not available URL: From iinf... at gmail.com Sat May 13 22:40:47 2017 From: iinf... at gmail.com (Ivan Infante) Date: Sat, 13 May 2017 15:40:47 -0700 (PDT) Subject: Problems with Maximum Overlap Model (MOM) Message-ID: <5eab1b0e-af55-41d8-b5c1-a67479063054@googlegroups.com> Hi, I am trying to use MOM and I have some problems. I start from a ground state closed-shell converged wavefunction, and I use the restart file for the MOM calculation. I just de-occupy the beta HOMO to occupy the LUMO beta. The HOMO-LUMO gap of this system is around 2.0 eV, so there shouldnt be any problem to converge the excited state. However, after a few iterations, when the DIIS kicks in, it immediately swaps to the ground state energy (E = -5725.1289....) . Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ 1 P_Mix/Diag. 0.40E+00 13.8 0.32547826 -5724.9981579203 -5.72E+03 2 P_Mix/Diag. 0.40E+00 16.1 0.18145011 -5725.0429211687 -4.48E-02 3 P_Mix/Diag. 0.40E+00 16.0 0.11353690 -5725.0753406595 -3.24E-02 4 P_Mix/Diag. 0.40E+00 16.1 0.06733805 -5725.0961299910 -2.08E-02 5 DIIS/Diag. 0.20E-02 16.1 0.04123847 -5725.1090261343 -1.29E-02 6 DIIS/Diag. 0.11E-02 16.1 0.00192988 -5725.1289018949 -1.99E-02 7 DIIS/Diag. 0.31E-03 16.1 0.00128342 -5725.1289258147 -2.39E-05 8 DIIS/Diag. 0.28E-03 16.1 0.00032442 -5725.1289261285 -3.14E-07 9 DIIS/Diag. 0.96E-04 16.1 0.00018951 -5725.1289310034 -4.87E-06 10 DIIS/Diag. 0.45E-04 16.1 0.00004841 -5725.1289312796 -2.76E-07 11 DIIS/Diag. 0.17E-04 16.1 0.00003119 -5725.1289314498 -1.70E-07 12 DIIS/Diag. 0.11E-04 16.1 0.00001487 -5725.1289314674 -1.76E-08 13 DIIS/Diag. 0.28E-05 16.1 0.00000367 -5725.1289314718 -4.34E-09 *** SCF run converged in 13 steps *** I tried to play with the alpha mixing parameter, with a EPS_DIIS tight (to avoid that the DIIS interfere) but no success: 1 P_Mix/Diag. 0.10E-03 13.8 0.32547826 -5724.9981579203 -5.72E+03 2 P_Mix/Diag. 0.10E-03 16.1 0.32544318 -5724.9981819920 -2.41E-05 3 P_Mix/Diag. 0.10E-03 16.1 0.32540810 -5724.9982060548 -2.41E-05 4 P_Mix/Diag. 0.10E-03 16.1 0.32537302 -5724.9982301087 -2.41E-05 5 P_Mix/Diag. 0.10E-03 16.1 0.32533795 -5724.9982541538 -2.40E-05 6 P_Mix/Diag. 0.10E-03 16.1 0.32530289 -5724.9982781901 -2.40E-05 7 P_Mix/Diag. 0.10E-03 16.1 0.32526782 -5724.9983022175 -2.40E-05 8 P_Mix/Diag. 0.10E-03 16.1 0.32523276 -5724.9983262361 -2.40E-05 9 P_Mix/Diag. 0.10E-03 16.1 0.32519771 -5724.9983502459 -2.40E-05 10 P_Mix/Diag. 0.10E-03 16.1 0.32516265 -5724.9983742469 -2.40E-05 11 P_Mix/Diag. 0.10E-03 16.1 0.32512760 -5724.9983982391 -2.40E-05 12 P_Mix/Diag. 0.10E-03 16.1 0.32509256 -5724.9984222225 -2.40E-05 13 P_Mix/Diag. 0.10E-03 16.1 0.32505752 -5724.9984461970 -2.40E-05 14 P_Mix/Diag. 0.10E-03 16.1 0.32502248 -5724.9984701628 -2.40E-05 15 P_Mix/Diag. 0.10E-03 16.1 0.32498745 -5724.9984941198 -2.40E-05 16 P_Mix/Diag. 0.10E-03 16.1 0.32495242 -5724.9985180680 -2.39E-05 Here it seems that is converging, but the EPS_SCF remains very high. When I use intermediete values of ALPHA, like 0.1 or 0.05, the calculation goes slow, but tends still to converge to the ground state. Is there something that I can use to converge my calculation to the excited state ? Thanks, Ivan -------------- next part -------------- An HTML attachment was scrubbed... URL: From mattwa... at gmail.com Mon May 15 08:49:34 2017 From: mattwa... at gmail.com (Matt W) Date: Mon, 15 May 2017 01:49:34 -0700 (PDT) Subject: Problems with Maximum Overlap Model (MOM) In-Reply-To: References: <5eab1b0e-af55-41d8-b5c1-a67479063054@googlegroups.com> Message-ID: <8ec342ed-4450-4843-9a4c-ba3c4818265a@googlegroups.com> Yes, unfortunately that has been our experience too. Possibly the algorithm depends quite strongly on the convergence accelerator used and something better than linear mixing, but less aggressive than DIIS is needed. Nothing that is directly available in CP2K seems optimal anyway. Matt On Monday, May 15, 2017 at 9:36:54 AM UTC+1, Vladimir Rybkin wrote: > > Dear Ivan, > > according to my own experience MOM is not the most reliable approach. For > non-trivial systems, I was never able to achieve convergence and always > collapsed to the ground states, independently of my settings. I would not > high hopes if I were you. > > Yours, > > Vladimir > > ???????????, 14 ??? 2017 ?., 0:40:47 UTC+2 ???????????? Ivan Infante > ???????: >> >> Hi, >> >> I am trying to use MOM and I have some problems. >> I start from a ground state closed-shell converged wavefunction, and I >> use the restart file for the MOM calculation. I just de-occupy the beta >> HOMO to occupy the LUMO beta. >> The HOMO-LUMO gap of this system is around 2.0 eV, so there shouldnt be >> any problem to converge the excited state. >> However, after a few iterations, when the DIIS kicks in, it immediately >> swaps to the ground state energy (E = -5725.1289....) . >> >> Step Update method Time Convergence Total energy >> Change >> >> >> ------------------------------------------------------------------------------ >> >> 1 P_Mix/Diag. 0.40E+00 13.8 0.32547826 -5724.9981579203 >> -5.72E+03 >> >> 2 P_Mix/Diag. 0.40E+00 16.1 0.18145011 -5725.0429211687 >> -4.48E-02 >> >> 3 P_Mix/Diag. 0.40E+00 16.0 0.11353690 -5725.0753406595 >> -3.24E-02 >> >> 4 P_Mix/Diag. 0.40E+00 16.1 0.06733805 -5725.0961299910 >> -2.08E-02 >> >> 5 DIIS/Diag. 0.20E-02 16.1 0.04123847 -5725.1090261343 >> -1.29E-02 >> >> 6 DIIS/Diag. 0.11E-02 16.1 0.00192988 -5725.1289018949 >> -1.99E-02 >> >> 7 DIIS/Diag. 0.31E-03 16.1 0.00128342 -5725.1289258147 >> -2.39E-05 >> >> 8 DIIS/Diag. 0.28E-03 16.1 0.00032442 -5725.1289261285 >> -3.14E-07 >> >> 9 DIIS/Diag. 0.96E-04 16.1 0.00018951 -5725.1289310034 >> -4.87E-06 >> >> 10 DIIS/Diag. 0.45E-04 16.1 0.00004841 -5725.1289312796 >> -2.76E-07 >> >> 11 DIIS/Diag. 0.17E-04 16.1 0.00003119 -5725.1289314498 >> -1.70E-07 >> >> 12 DIIS/Diag. 0.11E-04 16.1 0.00001487 -5725.1289314674 >> -1.76E-08 >> >> 13 DIIS/Diag. 0.28E-05 16.1 0.00000367 -5725.1289314718 >> -4.34E-09 >> >> >> *** SCF run converged in 13 steps *** >> >> I tried to play with the alpha mixing parameter, with a EPS_DIIS tight >> (to avoid that the DIIS interfere) but no success: >> >> 1 P_Mix/Diag. 0.10E-03 13.8 0.32547826 -5724.9981579203 >> -5.72E+03 >> >> 2 P_Mix/Diag. 0.10E-03 16.1 0.32544318 -5724.9981819920 >> -2.41E-05 >> >> 3 P_Mix/Diag. 0.10E-03 16.1 0.32540810 -5724.9982060548 >> -2.41E-05 >> >> 4 P_Mix/Diag. 0.10E-03 16.1 0.32537302 -5724.9982301087 >> -2.41E-05 >> >> 5 P_Mix/Diag. 0.10E-03 16.1 0.32533795 -5724.9982541538 >> -2.40E-05 >> >> 6 P_Mix/Diag. 0.10E-03 16.1 0.32530289 -5724.9982781901 >> -2.40E-05 >> >> 7 P_Mix/Diag. 0.10E-03 16.1 0.32526782 -5724.9983022175 >> -2.40E-05 >> >> 8 P_Mix/Diag. 0.10E-03 16.1 0.32523276 -5724.9983262361 >> -2.40E-05 >> >> 9 P_Mix/Diag. 0.10E-03 16.1 0.32519771 -5724.9983502459 >> -2.40E-05 >> >> 10 P_Mix/Diag. 0.10E-03 16.1 0.32516265 -5724.9983742469 >> -2.40E-05 >> >> 11 P_Mix/Diag. 0.10E-03 16.1 0.32512760 -5724.9983982391 >> -2.40E-05 >> >> 12 P_Mix/Diag. 0.10E-03 16.1 0.32509256 -5724.9984222225 >> -2.40E-05 >> >> 13 P_Mix/Diag. 0.10E-03 16.1 0.32505752 -5724.9984461970 >> -2.40E-05 >> >> 14 P_Mix/Diag. 0.10E-03 16.1 0.32502248 -5724.9984701628 >> -2.40E-05 >> >> 15 P_Mix/Diag. 0.10E-03 16.1 0.32498745 -5724.9984941198 >> -2.40E-05 >> >> 16 P_Mix/Diag. 0.10E-03 16.1 0.32495242 -5724.9985180680 >> -2.39E-05 >> >> Here it seems that is converging, but the EPS_SCF remains very high. >> When I use intermediete values of ALPHA, like 0.1 or 0.05, the >> calculation goes slow, but tends still to converge to the ground state. >> >> Is there something that I can use to converge my calculation to the >> excited state ? >> >> Thanks, >> Ivan >> >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From rybk... at gmail.com Mon May 15 08:55:50 2017 From: rybk... at gmail.com (Vladimir Rybkin) Date: Mon, 15 May 2017 01:55:50 -0700 (PDT) Subject: Problems with Maximum Overlap Model (MOM) In-Reply-To: <5eab1b0e-af55-41d8-b5c1-a67479063054@googlegroups.com> References: <5eab1b0e-af55-41d8-b5c1-a67479063054@googlegroups.com> Message-ID: Dear Ivan, according to my own experience MOM is not the most reliable approach. For non-trivial systems, I was never able to achieve convergence and always collapsed to the ground states, independently of my settings. I would not have high hopes if I were you. Yours, Vladimir ???????????, 14 ??? 2017 ?., 0:40:47 UTC+2 ???????????? Ivan Infante ???????: > > Hi, > > I am trying to use MOM and I have some problems. > I start from a ground state closed-shell converged wavefunction, and I use > the restart file for the MOM calculation. I just de-occupy the beta HOMO to > occupy the LUMO beta. > The HOMO-LUMO gap of this system is around 2.0 eV, so there shouldnt be > any problem to converge the excited state. > However, after a few iterations, when the DIIS kicks in, it immediately > swaps to the ground state energy (E = -5725.1289....) . > > Step Update method Time Convergence Total energy > Change > > > ------------------------------------------------------------------------------ > > 1 P_Mix/Diag. 0.40E+00 13.8 0.32547826 -5724.9981579203 > -5.72E+03 > > 2 P_Mix/Diag. 0.40E+00 16.1 0.18145011 -5725.0429211687 > -4.48E-02 > > 3 P_Mix/Diag. 0.40E+00 16.0 0.11353690 -5725.0753406595 > -3.24E-02 > > 4 P_Mix/Diag. 0.40E+00 16.1 0.06733805 -5725.0961299910 > -2.08E-02 > > 5 DIIS/Diag. 0.20E-02 16.1 0.04123847 -5725.1090261343 > -1.29E-02 > > 6 DIIS/Diag. 0.11E-02 16.1 0.00192988 -5725.1289018949 > -1.99E-02 > > 7 DIIS/Diag. 0.31E-03 16.1 0.00128342 -5725.1289258147 > -2.39E-05 > > 8 DIIS/Diag. 0.28E-03 16.1 0.00032442 -5725.1289261285 > -3.14E-07 > > 9 DIIS/Diag. 0.96E-04 16.1 0.00018951 -5725.1289310034 > -4.87E-06 > > 10 DIIS/Diag. 0.45E-04 16.1 0.00004841 -5725.1289312796 > -2.76E-07 > > 11 DIIS/Diag. 0.17E-04 16.1 0.00003119 -5725.1289314498 > -1.70E-07 > > 12 DIIS/Diag. 0.11E-04 16.1 0.00001487 -5725.1289314674 > -1.76E-08 > > 13 DIIS/Diag. 0.28E-05 16.1 0.00000367 -5725.1289314718 > -4.34E-09 > > > *** SCF run converged in 13 steps *** > > I tried to play with the alpha mixing parameter, with a EPS_DIIS tight (to > avoid that the DIIS interfere) but no success: > > 1 P_Mix/Diag. 0.10E-03 13.8 0.32547826 -5724.9981579203 > -5.72E+03 > > 2 P_Mix/Diag. 0.10E-03 16.1 0.32544318 -5724.9981819920 > -2.41E-05 > > 3 P_Mix/Diag. 0.10E-03 16.1 0.32540810 -5724.9982060548 > -2.41E-05 > > 4 P_Mix/Diag. 0.10E-03 16.1 0.32537302 -5724.9982301087 > -2.41E-05 > > 5 P_Mix/Diag. 0.10E-03 16.1 0.32533795 -5724.9982541538 > -2.40E-05 > > 6 P_Mix/Diag. 0.10E-03 16.1 0.32530289 -5724.9982781901 > -2.40E-05 > > 7 P_Mix/Diag. 0.10E-03 16.1 0.32526782 -5724.9983022175 > -2.40E-05 > > 8 P_Mix/Diag. 0.10E-03 16.1 0.32523276 -5724.9983262361 > -2.40E-05 > > 9 P_Mix/Diag. 0.10E-03 16.1 0.32519771 -5724.9983502459 > -2.40E-05 > > 10 P_Mix/Diag. 0.10E-03 16.1 0.32516265 -5724.9983742469 > -2.40E-05 > > 11 P_Mix/Diag. 0.10E-03 16.1 0.32512760 -5724.9983982391 > -2.40E-05 > > 12 P_Mix/Diag. 0.10E-03 16.1 0.32509256 -5724.9984222225 > -2.40E-05 > > 13 P_Mix/Diag. 0.10E-03 16.1 0.32505752 -5724.9984461970 > -2.40E-05 > > 14 P_Mix/Diag. 0.10E-03 16.1 0.32502248 -5724.9984701628 > -2.40E-05 > > 15 P_Mix/Diag. 0.10E-03 16.1 0.32498745 -5724.9984941198 > -2.40E-05 > > 16 P_Mix/Diag. 0.10E-03 16.1 0.32495242 -5724.9985180680 > -2.39E-05 > > Here it seems that is converging, but the EPS_SCF remains very high. > When I use intermediete values of ALPHA, like 0.1 or 0.05, the calculation > goes slow, but tends still to converge to the ground state. > > Is there something that I can use to converge my calculation to the > excited state ? > > Thanks, > Ivan > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdsimula... at gmail.com Tue May 16 14:58:53 2017 From: mdsimula... at gmail.com (mdsimula... at gmail.com) Date: Tue, 16 May 2017 07:58:53 -0700 (PDT) Subject: Semiempirical method PM7 Message-ID: <836903f8-a41a-4a7f-80aa-956428f95590@googlegroups.com> Hi all, Does anyone know if the semiempirical method PM7 will be added to CP2K in the near future? PM7 paper: http://link.springer.com/article/10.1007/s00894-012-1667-x/fulltext.html What would it take to add the method? Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From andreas... at gmail.com Wed May 17 08:01:58 2017 From: andreas... at gmail.com (=?UTF-8?Q?Andreas_Gl=C3=B6ss?=) Date: Wed, 17 May 2017 01:01:58 -0700 (PDT) Subject: Announcement: CP2K User Tutorial 2017 - "Advanced ab-inito MD methods" Message-ID: <05af1278-22a8-4c7e-819f-6d9cb559550e@googlegroups.com> Dear CP2K Users, We are pleased to announce that the registration for the upcoming *"CP2K User Tutorial on Advanced ab-initio MD methods"* is now open. The goal of this CP2K tutorial is to provide to experienced researchers and students in the field of molecular simulations a survey of the most relevant computational MD tools implemented within the CP2K program package. For further information, see: https://www.cp2k.org/events:2017_user_tutorial:about For researchers interested in CP2K development: There will be a "CP2K Developer Meeting" on July 11th, 2017 - just one day before the tutorial starts. Please add a note to your registration in case you want to attend. Best regards, Andreas Gloess -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Wed May 17 08:46:36 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Wed, 17 May 2017 10:46:36 +0200 Subject: [CP2K:9010] Semiempirical method PM7 In-Reply-To: <836903f8-a41a-4a7f-80aa-956428f95590@googlegroups.com> References: <836903f8-a41a-4a7f-80aa-956428f95590@googlegroups.com> Message-ID: Hi as far as I know there is nobody planning to implement PM7. It wouldn't be too hard, most of the work would be "typing" the parameters and testing. The code changes for the adjusted functional forms should be rather easy. 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: mdsimula... at gmail.com Sent by: cp... at googlegroups.com Date: 05/16/2017 04:59PM Subject: [CP2K:9010] Semiempirical method PM7 Hi all, Does anyone know if the semiempirical method PM7 will be added to CP2K in the near future? PM7 paper: http://link.springer.com/article/10.1007/s00894-012-1667-x/fulltext.html What would it take to add the method? 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. From heig... at gmail.com Wed May 17 13:16:31 2017 From: heig... at gmail.com (Heigo Ers) Date: Wed, 17 May 2017 06:16:31 -0700 (PDT) Subject: ALMO Analysis not printing Message-ID: <08f8ed55-021b-449e-80f1-3e7b61847304@googlegroups.com> Dear CP2K Users, I am running ALMO calculations and want to print out detailed ALMO decomposition analysis results with using ANALYSIS subsection in ALMO_SCF. The calculation executes normally but it doesn't print out the files from subsections ALMO CTA or ALMO EDA CT. I would like to know that if fault is in my input or is this a bug in Trunk version. I have enclosed my input to this post. Yours Sincerely, Heigo Ers -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: almo_analysis.in Type: application/octet-stream Size: 4545 bytes Desc: not available URL: From syf.ta... at gmail.com Wed May 17 20:54:40 2017 From: syf.ta... at gmail.com (Yifei Shi) Date: Wed, 17 May 2017 13:54:40 -0700 (PDT) Subject: BLYP functional and smoothing Message-ID: Dear cp2k users, I'm trying to run a MD simulation with NPT_I ensemble of liquid water with BLYP XC functional and dispersion. Without XC functional smoothing there's a small energy drift, but the density is very close to well established values(~1.04). But when I added smoothing, although the conserved quantity is constant, the density then changed to a substantially value(~1.2). The only difference between the 2 runs is the second one has the smoothing section: &XC_GRID XC_SMOOTH_RHO NN10 XC_DERIV SPLINE2_SMOOTH &END XC_GRID I'm wondering if the smoothing I used was inappropriate. I also attached the input file with smoothing. Thanks very much for any suggestions! Best, Yifei -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: BLYP_smoothing.inp Type: chemical/x-gamess-input Size: 33709 bytes Desc: not available URL: From zhj... at gmail.com Fri May 19 05:13:10 2017 From: zhj... at gmail.com (zhj... at gmail.com) Date: Thu, 18 May 2017 22:13:10 -0700 (PDT) Subject: Run cp2k test error for ADMM (QS/regtest-hfx-wfn-fitting/CH4-HSE06.inp) Message-ID: Dear all, I am trying to run the test of QS/regtest-hfx-wfn-fitting/CH4-HSE06.inp, but an Error message appeared immediately after starting this calculation: *forrtl: severe (174): SIGSEGV, segmentation fault occurred* *Image PC Routine Line Source* *cp2k.popt 00000000076355A1 Unknown Unknown Unknown* *cp2k.popt 0000000007633CF7 Unknown Unknown Unknown* *cp2k.popt 00000000075EF624 Unknown Unknown Unknown* *cp2k.popt 00000000075EF436 Unknown Unknown Unknown* *cp2k.popt 000000000759E2FF Unknown Unknown Unknown* *cp2k.popt 00000000075A561D Unknown Unknown Unknown* *libpthread.so.0 00007F7F9B26E100 Unknown Unknown Unknown* *cp2k.popt 000000000132A4BE Unknown Unknown Unknown* *cp2k.popt 000000000084877E Unknown Unknown Unknown* *cp2k.popt 0000000000843CA5 Unknown Unknown Unknown* *cp2k.popt 0000000000A33524 Unknown Unknown Unknown* *cp2k.popt 0000000000A31563 Unknown Unknown Unknown* *cp2k.popt 00000000009A9289 Unknown Unknown Unknown* *cp2k.popt 00000000016F6EB8 Unknown Unknown Unknown* *cp2k.popt 00000000016F5619 Unknown Unknown Unknown* *cp2k.popt 0000000000E16383 Unknown Unknown Unknown* *cp2k.popt 000000000041326D Unknown Unknown Unknown* *cp2k.popt 00000000004085B2 Unknown Unknown Unknown* *cp2k.popt 0000000000407B1E Unknown Unknown Unknown* *libc.so.6 00007F7F99A94B15 Unknown Unknown Unknown* *cp2k.popt 0000000000407A29 Unknown Unknown Unknown* If the section of *ADMM* and* AUX_FIT_BASIS_SET* is removed, then the test will run without error occurred. Can anyone tell me how to solve this proplem ? Thanks ! -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- DBCSR| Multiplication driver XSMM DBCSR| Multrec recursion limit 512 DBCSR| Multiplication stack size 1000 DBCSR| Maximum elements for images UNLIMITED DBCSR| Multiplicative factor virtual images 1 DBCSR| Multiplication size stacks 3 DBCSR| Number of 3D layers SINGLE DBCSR| Use MPI memory allocation T DBCSR| Use RMA algorithm F DBCSR| Use Communication thread T DBCSR| Communication thread load 87 **** **** ****** ** PROGRAM STARTED AT 2017-05-18 23:45:12.160 ***** ** *** *** ** PROGRAM STARTED ON node02 ** **** ****** PROGRAM STARTED BY cp2k ***** ** ** ** ** PROGRAM PROCESS ID 32714 **** ** ******* ** PROGRAM STARTED IN /home/cp2k/tests/QS/regtest-hfx-wfn-f itting CP2K| version string: CP2K version 5.0 (Development Version) CP2K| source code revision number: CP2K| cp2kflags: libint fftw3 libxc parallel mpi3 scalapack libxsmm libderiv_ma CP2K| x_am1=5 libint_max_am=6 CP2K| is freely available from https://www.cp2k.org/ CP2K| Program compiled at Thu May 18 23:13:40 CST 2017 CP2K| Program compiled on node02 CP2K| Program compiled for Linux-x86-64-intel-host CP2K| Data directory path /opt/cp2k_noelpa/data CP2K| Input file name CH4-HSE06.inp GLOBAL| Force Environment number 1 GLOBAL| Basis set file name BASIS_MOLOPT 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 CH4-HSE06 GLOBAL| Preferred FFT library FFTW3 GLOBAL| Preferred diagonalization lib. SL GLOBAL| Run type ENERGY_FORCE 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 1 GLOBAL| Number of threads for this process 1 GLOBAL| This output is from process 0 GLOBAL| CPU model name : Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz MEMORY| system memory details [Kb] MEMORY| rank 0 min max average MEMORY| MemTotal 65875016 65875016 65875016 65875016 MEMORY| MemFree 46239364 46239364 46239364 46239364 MEMORY| Buffers 219720 219720 219720 219720 MEMORY| Cached 11531660 11531660 11531660 11531660 MEMORY| Slab 273776 273776 273776 273776 MEMORY| SReclaimable 188768 188768 188768 188768 MEMORY| MemLikelyFree 58179512 58179512 58179512 58179512 *** 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]: 512.000 CELL_TOP| Vector a [angstrom 8.000 0.000 0.000 |a| = 8.000 CELL_TOP| Vector b [angstrom 0.000 8.000 0.000 |b| = 8.000 CELL_TOP| Vector c [angstrom 0.000 0.000 8.000 |c| = 8.000 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]: 512.000 CELL| Vector a [angstrom]: 8.000 0.000 0.000 |a| = 8.000 CELL| Vector b [angstrom]: 0.000 8.000 0.000 |b| = 8.000 CELL| Vector c [angstrom]: 0.000 0.000 8.000 |c| = 8.000 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]: 512.000 CELL_REF| Vector a [angstrom 8.000 0.000 0.000 |a| = 8.000 CELL_REF| Vector b [angstrom 0.000 8.000 0.000 |b| = 8.000 CELL_REF| Vector c [angstrom 0.000 0.000 8.000 |c| = 8.000 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 - 2016) ** ** ** ******************************************************************************* 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 NONE DFT| XC derivatives PW 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)sx=0.000sc=1.000{spin unpolarized} FUNCTIONAL| XWPBE: FUNCTIONAL| Jochen Heyd and Gustavo E. Scuseria, J. Chem. Phys., 120, 7274 {LDA FUNCTIONAL| version} QS| Method: GPW QS| Density plane wave grid type NON-SPHERICAL FULLSPACE QS| Number of grid levels: 4 QS| Density cutoff [a.u.]: 50.0 QS| Multi grid cutoff [a.u.]: 1) grid level 50.0 QS| 2) grid level 16.7 QS| 3) grid level 5.6 QS| 4) grid level 1.9 QS| Grid level progression factor: 3.0 QS| Relative density cutoff [a.u.]: 15.0 QS| Consistent realspace mapping and integration QS| Interaction thresholds: eps_pgf_orb: 1.0E-12 QS| eps_filter_matrix: 0.0E+00 QS| eps_core_charge: 1.0E-12 QS| eps_rho_gspace: 1.0E-10 QS| eps_rho_rspace: 1.0E-10 QS| eps_gvg_rspace: 1.0E-05 QS| eps_ppl: 1.0E-02 QS| eps_ppnl: 1.0E-07 ATOMIC KIND INFORMATION 1. Atomic kind: C Number of atoms: 1 Orbital Basis Set TZV2P-MOLOPT-GTH Number of orbital shell sets: 1 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 6.132625 -0.263661 2.625196 -0.231112 1.045457 0.042712 0.478316 0.306085 0.178617 0.065483 0.075145 0.000568 0.030287 0.000417 1 2 3s 6.132625 0.131937 2.625196 0.414269 1.045457 -0.593590 0.478316 0.644922 0.178617 0.069203 0.075145 -0.145101 0.030287 0.008247 1 3 4s 6.132625 -1.009391 2.625196 -0.608763 1.045457 -0.320627 0.478316 1.417678 0.178617 -0.917862 0.075145 0.286664 0.030287 -0.031483 1 4 3px 6.132625 0.562677 2.625196 0.633910 1.045457 0.379157 0.478316 0.235193 0.178617 0.052379 0.075145 0.003677 0.030287 0.000105 1 4 3py 6.132625 0.562677 2.625196 0.633910 1.045457 0.379157 0.478316 0.235193 0.178617 0.052379 0.075145 0.003677 0.030287 0.000105 1 4 3pz 6.132625 0.562677 2.625196 0.633910 1.045457 0.379157 0.478316 0.235193 0.178617 0.052379 0.075145 0.003677 0.030287 0.000105 1 5 4px 6.132625 -0.472364 2.625196 -0.221326 1.045457 -0.481781 0.478316 0.135466 0.178617 0.072281 0.075145 0.024920 0.030287 0.002706 1 5 4py 6.132625 -0.472364 2.625196 -0.221326 1.045457 -0.481781 0.478316 0.135466 0.178617 0.072281 0.075145 0.024920 0.030287 0.002706 1 5 4pz 6.132625 -0.472364 2.625196 -0.221326 1.045457 -0.481781 0.478316 0.135466 0.178617 0.072281 0.075145 0.024920 0.030287 0.002706 1 6 5px 6.132625 -0.321125 2.625196 -0.513960 1.045457 -0.659092 0.478316 1.236398 0.178617 -0.279443 0.075145 0.042466 0.030287 -0.008547 1 6 5py 6.132625 -0.321125 2.625196 -0.513960 1.045457 -0.659092 0.478316 1.236398 0.178617 -0.279443 0.075145 0.042466 0.030287 -0.008547 1 6 5pz 6.132625 -0.321125 2.625196 -0.513960 1.045457 -0.659092 0.478316 1.236398 0.178617 -0.279443 0.075145 0.042466 0.030287 -0.008547 1 7 4dx2 6.132625 0.874783 2.625196 0.375772 1.045457 0.653959 0.478316 0.191007 0.178617 0.018656 0.075145 0.003649 0.030287 -0.000011 1 7 4dxy 6.132625 1.515169 2.625196 0.650856 1.045457 1.132690 0.478316 0.330834 0.178617 0.032314 0.075145 0.006321 0.030287 -0.000019 1 7 4dxz 6.132625 1.515169 2.625196 0.650856 1.045457 1.132690 0.478316 0.330834 0.178617 0.032314 0.075145 0.006321 0.030287 -0.000019 1 7 4dy2 6.132625 0.874783 2.625196 0.375772 1.045457 0.653959 0.478316 0.191007 0.178617 0.018656 0.075145 0.003649 0.030287 -0.000011 1 7 4dyz 6.132625 1.515169 2.625196 0.650856 1.045457 1.132690 0.478316 0.330834 0.178617 0.032314 0.075145 0.006321 0.030287 -0.000019 1 7 4dz2 6.132625 0.874783 2.625196 0.375772 1.045457 0.653959 0.478316 0.191007 0.178617 0.018656 0.075145 0.003649 0.030287 -0.000011 1 8 5dx2 6.132625 3.037532 2.625196 0.636556 1.045457 2.577237 0.478316 -0.930692 0.178617 0.140536 0.075145 -0.022558 0.030287 0.000345 1 8 5dxy 6.132625 5.261160 2.625196 1.102547 1.045457 4.463906 0.478316 -1.612005 0.178617 0.243416 0.075145 -0.039072 0.030287 0.000598 1 8 5dxz 6.132625 5.261160 2.625196 1.102547 1.045457 4.463906 0.478316 -1.612005 0.178617 0.243416 0.075145 -0.039072 0.030287 0.000598 1 8 5dy2 6.132625 3.037532 2.625196 0.636556 1.045457 2.577237 0.478316 -0.930692 0.178617 0.140536 0.075145 -0.022558 0.030287 0.000345 1 8 5dyz 6.132625 5.261160 2.625196 1.102547 1.045457 4.463906 0.478316 -1.612005 0.178617 0.243416 0.075145 -0.039072 0.030287 0.000598 1 8 5dz2 6.132625 3.037532 2.625196 0.636556 1.045457 2.577237 0.478316 -0.930692 0.178617 0.140536 0.075145 -0.022558 0.030287 0.000345 Auxiliary Fit Basis Set SZV-MOLOPT-GTH Number of orbital shell sets: 1 Number of orbital shells: 2 Number of primitive Cartesian functions: 7 Number of Cartesian basis functions: 4 Number of spherical basis functions: 4 Norm type: 2 Normalised Cartesian orbitals: Set Shell Orbital Exponent Coefficient 1 1 2s 6.132625 -0.263661 2.625196 -0.231112 1.045457 0.042712 0.478316 0.306085 0.178617 0.065483 0.075145 0.000568 0.030287 0.000417 1 2 3px 6.132625 0.562677 2.625196 0.633910 1.045457 0.379157 0.478316 0.235193 0.178617 0.052379 0.075145 0.003677 0.030287 0.000105 1 2 3py 6.132625 0.562677 2.625196 0.633910 1.045457 0.379157 0.478316 0.235193 0.178617 0.052379 0.075145 0.003677 0.030287 0.000105 1 2 3pz 6.132625 0.562677 2.625196 0.633910 1.045457 0.379157 0.478316 0.235193 0.178617 0.052379 0.075145 0.003677 0.030287 0.000105 Potential information for GTH-PBE-q4 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: 4.364419 Electronic configuration (s p d ...): 2 2 Parameters of the local part of the GTH pseudopotential: rloc C1 C2 C3 C4 0.338471 -8.803674 1.339211 Parameters of the non-local part of the GTH pseudopotential: l r(l) h(i,j,l) 0 0.302576 9.622487 1 0.291507 2. Atomic kind: H Number of atoms: 4 Orbital Basis Set TZV2P-MOLOPT-GTH Number of orbital shell sets: 1 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 2s 11.478000 0.129129 3.700759 0.177012 1.446884 0.141285 0.716815 0.245670 0.247919 0.094768 0.066918 0.004062 0.021708 -0.000053 1 2 3s 11.478000 -0.079256 3.700759 -0.152992 1.446884 0.015066 0.716815 -0.331234 0.247919 0.210690 0.066918 0.058630 0.021708 -0.003429 1 3 4s 11.478000 -0.246880 3.700759 0.023016 1.446884 -1.109374 0.716815 1.524652 0.247919 -0.227968 0.066918 -0.037343 0.021708 0.005696 1 4 3px 11.478000 0.325290 3.700759 0.187466 1.446884 0.443300 0.716815 0.267738 0.247919 0.088285 0.066918 0.019092 0.021708 0.000629 1 4 3py 11.478000 0.325290 3.700759 0.187466 1.446884 0.443300 0.716815 0.267738 0.247919 0.088285 0.066918 0.019092 0.021708 0.000629 1 4 3pz 11.478000 0.325290 3.700759 0.187466 1.446884 0.443300 0.716815 0.267738 0.247919 0.088285 0.066918 0.019092 0.021708 0.000629 1 5 4px 11.478000 -1.727188 3.700759 -0.598393 1.446884 -3.813128 0.716815 1.901151 0.247919 -0.262425 0.066918 0.006339 0.021708 0.007345 1 5 4py 11.478000 -1.727188 3.700759 -0.598393 1.446884 -3.813128 0.716815 1.901151 0.247919 -0.262425 0.066918 0.006339 0.021708 0.007345 1 5 4pz 11.478000 -1.727188 3.700759 -0.598393 1.446884 -3.813128 0.716815 1.901151 0.247919 -0.262425 0.066918 0.006339 0.021708 0.007345 Auxiliary Fit Basis Set SZV-MOLOPT-GTH Number of orbital shell sets: 1 Number of orbital shells: 1 Number of primitive Cartesian functions: 7 Number of Cartesian basis functions: 1 Number of spherical basis functions: 1 Norm type: 2 Normalised Cartesian orbitals: Set Shell Orbital Exponent Coefficient 1 1 2s 11.478000 0.129129 3.700759 0.177012 1.446884 0.141285 0.716815 0.245670 0.247919 0.094768 0.066918 0.004062 0.021708 -0.000053 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: 2 - Atoms: 5 - Shell sets: 5 - Shells: 28 - Primitive Cartesian functions: 35 - Cartesian basis functions: 60 - Spherical basis functions: 58 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 C 6 0.000000 0.000000 0.000000 4.00 12.0107 2 2 H 1 0.629700 0.629700 0.629700 1.00 1.0079 3 2 H 1 -0.629700 -0.629700 0.629700 1.00 1.0079 4 2 H 1 -0.629700 0.629700 -0.629700 1.00 1.0079 5 2 H 1 0.629700 -0.629700 -0.629700 1.00 1.0079 SCF PARAMETERS Density guess: ATOMIC -------------------------------------------------------- max_scf: 10 max_scf_history: 0 max_diis: 4 -------------------------------------------------------- eps_scf: 1.00E-06 eps_scf_history: 0.00E+00 eps_diis: 1.00E-01 eps_eigval: 1.00E-05 -------------------------------------------------------- level_shift [a.u.]: 0.00 -------------------------------------------------------- No outer SCF PW_GRID| Information for grid number 1 PW_GRID| Cutoff [a.u.] 100.0 PW_GRID| spherical cutoff: NO PW_GRID| Bounds 1 -36 35 Points: 72 PW_GRID| Bounds 2 -36 35 Points: 72 PW_GRID| Bounds 3 -36 35 Points: 72 PW_GRID| Volume element (a.u.^3) 0.9257E-02 Volume (a.u.^3) 3455.1473 PW_GRID| Grid span FULLSPACE PW_GRID| Information for grid number 2 PW_GRID| Cutoff [a.u.] 50.0 PW_GRID| spherical cutoff: NO PW_GRID| Bounds 1 -27 26 Points: 54 PW_GRID| Bounds 2 -27 26 Points: 54 PW_GRID| Bounds 3 -27 26 Points: 54 PW_GRID| Volume element (a.u.^3) 0.2194E-01 Volume (a.u.^3) 3455.1473 PW_GRID| Grid span FULLSPACE PW_GRID| Information for grid number 3 PW_GRID| Cutoff [a.u.] 16.7 PW_GRID| spherical cutoff: NO PW_GRID| Bounds 1 -13 13 Points: 27 PW_GRID| Bounds 2 -13 13 Points: 27 PW_GRID| Bounds 3 -13 13 Points: 27 PW_GRID| Volume element (a.u.^3) 0.1755 Volume (a.u.^3) 3455.1473 PW_GRID| Grid span FULLSPACE PW_GRID| Information for grid number 4 PW_GRID| Cutoff [a.u.] 5.6 PW_GRID| spherical cutoff: NO PW_GRID| Bounds 1 -9 8 Points: 18 PW_GRID| Bounds 2 -9 8 Points: 18 PW_GRID| Bounds 3 -9 8 Points: 18 PW_GRID| Volume element (a.u.^3) 0.5924 Volume (a.u.^3) 3455.1473 PW_GRID| Grid span FULLSPACE PW_GRID| Information for grid number 5 PW_GRID| Cutoff [a.u.] 1.9 PW_GRID| spherical cutoff: NO PW_GRID| Bounds 1 -4 4 Points: 9 PW_GRID| Bounds 2 -4 4 Points: 9 PW_GRID| Bounds 3 -4 4 Points: 9 PW_GRID| Volume element (a.u.^3) 4.740 Volume (a.u.^3) 3455.1473 PW_GRID| Grid span FULLSPACE POISSON| Solver Martyna-Tuckerman (MT) POISSON| MT| Alpha 7.000 POISSON| MT| Relative cutoff 2.0 POISSON| Periodicity NONE RS_GRID| Information for grid number 2 RS_GRID| Bounds 1 -27 26 Points: 54 RS_GRID| Bounds 2 -27 26 Points: 54 RS_GRID| Bounds 3 -27 26 Points: 54 RS_GRID| Information for grid number 3 RS_GRID| Bounds 1 -13 13 Points: 27 RS_GRID| Bounds 2 -13 13 Points: 27 RS_GRID| Bounds 3 -13 13 Points: 27 RS_GRID| Information for grid number 4 RS_GRID| Bounds 1 -9 8 Points: 18 RS_GRID| Bounds 2 -9 8 Points: 18 RS_GRID| Bounds 3 -9 8 Points: 18 RS_GRID| Information for grid number 5 RS_GRID| Bounds 1 -4 4 Points: 9 RS_GRID| Bounds 2 -4 4 Points: 9 RS_GRID| Bounds 3 -4 4 Points: 9 DISTRIBUTION OF THE PARTICLES (ROWS) Process row Number of particles Number of matrix rows 0 5 -1 Sum 5 -1 DISTRIBUTION OF THE PARTICLES (COLUMNS) Process col Number of particles Number of matrix columns 0 5 -1 Sum 5 -1 HFX_INFO| Replica ID: 1 HFX_INFO| EPS_SCHWARZ: 1.0E-06 HFX_INFO| EPS_SCHWARZ_FORCES 1.0E-06 HFX_INFO| EPS_STORAGE_SCALING: 1.0E-01 HFX_INFO| NBINS: 64 HFX_INFO| BLOCK_SIZE: 1 HFX_INFO| FRACTION: 0.2500000000 HFX_INFO| Interaction Potential: SHORTRANGE HFX_INFO| Omega: 0.1100000000 HFX_INFO| Cutoff Radius [angstrom]: 14.2786927855 HFX_INFO| Number of periodic shells considered: NONE HFX_INFO| Number of periodic cells considered: NONE DISTRIBUTION OF THE NEIGHBOR LISTS Total number of particle pairs: 15 Total number of matrix elements: 2086 Average number of particle pairs: 15 Maximum number of particle pairs: 15 Average number of matrix element: 2086 Maximum number of matrix elements: 2086 DISTRIBUTION OF THE OVERLAP MATRIX Number of non-zero blocks: 15 Percentage non-zero blocks: 100.00 Average number of blocks per CPU: 15 Maximum number of blocks per CPU: 15 Average number of matrix elements per CPU: 2096 Maximum number of matrix elements per CPU: 2096 OVERLAP MATRIX CONDITION NUMBER 1-Norm Condition Number (Estimate) CN : |A|*|A^-1|: 9.895E+000 * 2.101E+002 = 2.079E+003 Log(1-CN): 3.3178 Number of electrons: 8 Number of occupied orbitals: 4 Number of molecular orbitals: 4 Number of orbital functions: 58 Number of independent orbital functions: 58 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: C Electronic structure Total number of core electrons 2.00 Total number of valence electrons 4.00 Total number of electrons 6.00 Multiplicity not specified S [ 2.00] 2.00 P 2.00 ******************************************************************************* Iteration Convergence Energy [au] ******************************************************************************* 1 0.373724 -5.157569832881 2 0.262091 -5.227211063133 3 0.827333E-02 -5.278846743598 4 0.325513E-03 -5.278907304309 5 0.178197E-05 -5.278907348855 6 0.134869E-07 -5.278907348859 Energy components [Hartree] Total Energy :: -5.278907348859 Band Energy :: -1.297504926697 Kinetic Energy :: 3.437573190721 Potential Energy :: -8.716480539581 Virial (-V/T) :: 2.535649441038 Core Energy :: -8.301868307285 XC Energy :: -1.382083074422 Coulomb Energy :: 4.405044032847 Total Pseudopotential Energy :: -11.773288252614 Local Pseudopotential Energy :: -12.379139826445 Nonlocal Pseudopotential Energy :: 0.605851573831 Confinement :: 0.338467546076 Orbital energies State L Occupation Energy[a.u.] Energy[eV] 1 0 2.000 -0.478379 -13.017346 1 1 2.000 -0.170374 -4.636106 Total Electron Density at R=0: 0.000341 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 0.363633E-02 -0.424359639014 2 0.457201E-03 -0.424374328003 3 0.158035E-04 -0.424374562686 4 0.544881E-08 -0.424374562963 Energy components [Hartree] Total Energy :: -0.424374562963 Band Energy :: -0.197817388557 Kinetic Energy :: 0.463739149097 Potential Energy :: -0.888113712060 Virial (-V/T) :: 1.915114809241 Core Energy :: -0.479953896523 XC Energy :: -0.245504363650 Coulomb Energy :: 0.301083697210 Total Pseudopotential Energy :: -0.962570132454 Local Pseudopotential Energy :: -0.962570132454 Nonlocal Pseudopotential Energy :: 0.000000000000 Confinement :: 0.188770868335 Orbital energies State L Occupation Energy[a.u.] Energy[eV] 1 0 1.000 -0.197817 -5.382885 Total Electron Density at R=0: 0.235042 Re-scaling the density matrix to get the right number of electrons # Electrons Trace(P) Scaling factor 8 8.000 1.000 SCF WAVEFUNCTION OPTIMIZATION ----------------------------------- OT --------------------------------------- Minimizer : CG : conjugate gradient Preconditioner : FULL_KINETIC : inversion of T + eS Precond_solver : DEFAULT Line search : 2PNT : 2 energies, one gradient stepsize : 0.15000000 energy_gap : 0.20000000 eps_taylor : 0.10000E-15 max_taylor : 4 ----------------------------------- OT --------------------------------------- Step Update method Time Convergence Total energy Change ------------------------------------------------------------------------------ Trace(PS): 8.0000000000 Electronic density on regular grids: -7.9999980677 0.0000019323 Core density on regular grids: 7.9999969792 -0.0000030208 Total charge density on r-space grids: -0.0000010885 Total charge density g-space grids: -0.0000010885 forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source cp2k.popt 00000000076355A1 Unknown Unknown Unknown cp2k.popt 0000000007633CF7 Unknown Unknown Unknown cp2k.popt 00000000075EF624 Unknown Unknown Unknown cp2k.popt 00000000075EF436 Unknown Unknown Unknown cp2k.popt 000000000759E2FF Unknown Unknown Unknown cp2k.popt 00000000075A561D Unknown Unknown Unknown libpthread.so.0 00007F7F9B26E100 Unknown Unknown Unknown cp2k.popt 000000000132A4BE Unknown Unknown Unknown cp2k.popt 000000000084877E Unknown Unknown Unknown cp2k.popt 0000000000843CA5 Unknown Unknown Unknown cp2k.popt 0000000000A33524 Unknown Unknown Unknown cp2k.popt 0000000000A31563 Unknown Unknown Unknown cp2k.popt 00000000009A9289 Unknown Unknown Unknown cp2k.popt 00000000016F6EB8 Unknown Unknown Unknown cp2k.popt 00000000016F5619 Unknown Unknown Unknown cp2k.popt 0000000000E16383 Unknown Unknown Unknown cp2k.popt 000000000041326D Unknown Unknown Unknown cp2k.popt 00000000004085B2 Unknown Unknown Unknown cp2k.popt 0000000000407B1E Unknown Unknown Unknown libc.so.6 00007F7F99A94B15 Unknown Unknown Unknown cp2k.popt 0000000000407A29 Unknown Unknown Unknown From alfio.... at gmail.com Fri May 19 08:01:07 2017 From: alfio.... at gmail.com (Alfio Lazzaro) Date: Fri, 19 May 2017 01:01:07 -0700 (PDT) Subject: Run cp2k test error for ADMM (QS/regtest-hfx-wfn-fitting/CH4-HSE06.inp) In-Reply-To: References: Message-ID: Hi, could you compile the code with the debug symbols (i.e. pdbg versin, or alternative with -g)? My suspicious is that there is a mismatch in the angular momentum used in libderiv and CP2K. >From your output CP2K uses libderiv_max_am1=5 libint_max_am=6, could you check what are the values used to compile the library? You can check your include/libint/libint.h in libint to see if it matches. Cheers, Alfio Il giorno gioved? 18 maggio 2017 17:39:21 UTC+2, zhj... at gmail.com ha scritto: > > Dear all, > I am trying to run the test of QS/regtest-hfx-wfn-fitting/CH4-HSE06.inp, > but an Error message appeared immediately after starting this calculation: > > *forrtl: severe (174): SIGSEGV, segmentation fault occurred* > *Image PC Routine Line > Source* > *cp2k.popt 00000000076355A1 Unknown Unknown > Unknown* > *cp2k.popt 0000000007633CF7 Unknown Unknown > Unknown* > *cp2k.popt 00000000075EF624 Unknown Unknown > Unknown* > *cp2k.popt 00000000075EF436 Unknown Unknown > Unknown* > *cp2k.popt 000000000759E2FF Unknown Unknown > Unknown* > *cp2k.popt 00000000075A561D Unknown Unknown > Unknown* > *libpthread.so.0 00007F7F9B26E100 Unknown Unknown > Unknown* > *cp2k.popt 000000000132A4BE Unknown Unknown > Unknown* > *cp2k.popt 000000000084877E Unknown Unknown > Unknown* > *cp2k.popt 0000000000843CA5 Unknown Unknown > Unknown* > *cp2k.popt 0000000000A33524 Unknown Unknown > Unknown* > *cp2k.popt 0000000000A31563 Unknown Unknown > Unknown* > *cp2k.popt 00000000009A9289 Unknown Unknown > Unknown* > *cp2k.popt 00000000016F6EB8 Unknown Unknown > Unknown* > *cp2k.popt 00000000016F5619 Unknown Unknown > Unknown* > *cp2k.popt 0000000000E16383 Unknown Unknown > Unknown* > *cp2k.popt 000000000041326D Unknown Unknown > Unknown* > *cp2k.popt 00000000004085B2 Unknown Unknown > Unknown* > *cp2k.popt 0000000000407B1E Unknown Unknown > Unknown* > *libc.so.6 00007F7F99A94B15 Unknown Unknown > Unknown* > *cp2k.popt 0000000000407A29 Unknown Unknown > Unknown* > > If the section of *ADMM* and* AUX_FIT_BASIS_SET* is removed, then the > test will run without error occurred. > Can anyone tell me how to solve this proplem ? Thanks ! > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Fri May 19 08:06:23 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Fri, 19 May 2017 10:06:23 +0200 Subject: [CP2K:9014] BLYP functional and smoothing In-Reply-To: References: Message-ID: Hi a few comments, but unfortunately no real solution to your problem - BLYP is not easy to converge on a regular grid - Smoothing works fine for constant volume but requires very high cutoffs for pressure calculations - I'm not aware that MD with ALMO is possible 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: Yifei Shi Sent by: cp... at googlegroups.com Date: 05/17/2017 10:54PM Subject: [CP2K:9014] BLYP functional and smoothing Dear cp2k users, I'm trying to run a MD simulation with NPT_I ensemble of liquid water with BLYP XC functional and dispersion. Without XC functional smoothing there's a small energy drift, but the density is very close to well established values(~1.04). But when I added smoothing, although the conserved quantity is constant, the density then changed to a substantially value(~1.2). The only difference between the 2 runs is the second one has the smoothing section: ?????? &XC_GRID ???????? XC_SMOOTH_RHO? NN10 ???????? XC_DERIV? SPLINE2_SMOOTH ?????? &END XC_GRID I'm wondering if the smoothing I used was inappropriate. I also attached the input file with smoothing. Thanks very much for any suggestions! Best, Yifei -- 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 "BLYP_smoothing.inp" removed by J?rg Hutter/at/UZH] From syf.ta... at gmail.com Fri May 19 19:39:51 2017 From: syf.ta... at gmail.com (Yifei Shi) Date: Fri, 19 May 2017 12:39:51 -0700 (PDT) Subject: [CP2K:9014] BLYP functional and smoothing In-Reply-To: References: Message-ID: Hi Juerg, Thanks very much for the information. I also did NVT calculation which didn't seem to have such problem. I forgot that ALMO MD was our local development with Rustam Khaliullin and is not updated to the trunk yet. Best, Yifei On Friday, May 19, 2017 at 4:06:30 AM UTC-4, jgh wrote: > > Hi > > a few comments, but unfortunately no real solution to your problem > > - BLYP is not easy to converge on a regular grid > - Smoothing works fine for constant volume but requires very high cutoffs > for pressure calculations > > - I'm not aware that MD with ALMO is possible > > 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: Yifei Shi > Sent by: cp... at googlegroups.com > Date: 05/17/2017 10:54PM > Subject: [CP2K:9014] BLYP functional and smoothing > > Dear cp2k users, > > I'm trying to run a MD simulation with NPT_I ensemble of liquid water with > BLYP XC functional and dispersion. Without XC functional smoothing there's > a small energy drift, but the density is very close to well established > values(~1.04). But when I added smoothing, although the conserved quantity > is constant, the density then changed to a substantially value(~1.2). The > only difference between the 2 runs is the second one has the smoothing > section: > &XC_GRID > XC_SMOOTH_RHO NN10 > XC_DERIV SPLINE2_SMOOTH > &END XC_GRID > > I'm wondering if the smoothing I used was inappropriate. I also attached > the input file with smoothing. Thanks very much for any suggestions! > > Best, > Yifei > > > > > -- > > 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 "BLYP_smoothing.inp" removed by J?rg Hutter/at/UZH] > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhj... at gmail.com Sat May 20 07:45:24 2017 From: zhj... at gmail.com (zhj... at gmail.com) Date: Sat, 20 May 2017 00:45:24 -0700 (PDT) Subject: Run cp2k test error for ADMM (QS/regtest-hfx-wfn-fitting/CH4-HSE06.inp) In-Reply-To: References: Message-ID: <14e1e7fd-ad74-4dca-8365-2759b9754341@googlegroups.com> Hi, Alfio Lazzaro, Thank you for your response. The angular momentum parameters in libint.h and libderiv.h are: *#define LIBINT_MAX_AM 6* *#define LIBINT_OPT_AM 5* *#define LIBDERIV_MAX_AM1 5#define LIBDERIV_MAX_AM12 4* The configure parameters of libint are: *./configure --prefix=/opt/libint-1.4.4 --with-ar=ar FC=ifort F77=ifort **F90=ifort FCFLAGS="-O3 -xHost" CC=icc CFLAGS="-O3 -xHost" \* *CXX=icpc CXXFLAGS="-O3 -xHost" --with-cc-optflags="-O2 -xHost" **--with-cxx-optflags="-O2 -xHost" --with-libint-max-am=5 --with-libint-opt-am=4 \* *--with-libderiv-max-am1=4* I met some strange things: 1. when the "*-xHost*" optflag is removed, then the test "QS/regtest-hfx-wfn-fitting/CH4-HSE06.inp" will run successfully(but has a warning of "SCF run NOT converged"); 2. When I use the cp2k version in 1 to calculate my example, then the error is occurred: *application called MPI_Abort(MPI_COMM_WORLD, -10) - process 0* I will attach some files to you. Thank you for your help!! Best regards, Zhjs ? 2017?5?19???? UTC+8??4:01:08?Alfio Lazzaro??? > > Hi, > could you compile the code with the debug symbols (i.e. pdbg versin, or > alternative with -g)? > My suspicious is that there is a mismatch in the angular momentum used in > libderiv and CP2K. > From your output CP2K uses libderiv_max_am1=5 libint_max_am=6, could you > check what are the values used to compile the library? > You can check your include/libint/libint.h in libint to see if it matches. > > Cheers, > > Alfio > > > > Il giorno gioved? 18 maggio 2017 17:39:21 UTC+2, zhj... at gmail.com ha > scritto: >> >> Dear all, >> I am trying to run the test of QS/regtest-hfx-wfn-fitting/CH4-HSE06.inp, >> but an Error message appeared immediately after starting this calculation: >> >> *forrtl: severe (174): SIGSEGV, segmentation fault occurred* >> *Image PC Routine Line >> Source* >> *cp2k.popt 00000000076355A1 Unknown Unknown >> Unknown* >> *cp2k.popt 0000000007633CF7 Unknown Unknown >> Unknown* >> *cp2k.popt 00000000075EF624 Unknown Unknown >> Unknown* >> *cp2k.popt 00000000075EF436 Unknown Unknown >> Unknown* >> *cp2k.popt 000000000759E2FF Unknown Unknown >> Unknown* >> *cp2k.popt 00000000075A561D Unknown Unknown >> Unknown* >> *libpthread.so.0 00007F7F9B26E100 Unknown Unknown >> Unknown* >> *cp2k.popt 000000000132A4BE Unknown Unknown >> Unknown* >> *cp2k.popt 000000000084877E Unknown Unknown >> Unknown* >> *cp2k.popt 0000000000843CA5 Unknown Unknown >> Unknown* >> *cp2k.popt 0000000000A33524 Unknown Unknown >> Unknown* >> *cp2k.popt 0000000000A31563 Unknown Unknown >> Unknown* >> *cp2k.popt 00000000009A9289 Unknown Unknown >> Unknown* >> *cp2k.popt 00000000016F6EB8 Unknown Unknown >> Unknown* >> *cp2k.popt 00000000016F5619 Unknown Unknown >> Unknown* >> *cp2k.popt 0000000000E16383 Unknown Unknown >> Unknown* >> *cp2k.popt 000000000041326D Unknown Unknown >> Unknown* >> *cp2k.popt 00000000004085B2 Unknown Unknown >> Unknown* >> *cp2k.popt 0000000000407B1E Unknown Unknown >> Unknown* >> *libc.so.6 00007F7F99A94B15 Unknown Unknown >> Unknown* >> *cp2k.popt 0000000000407A29 Unknown Unknown >> Unknown* >> >> If the section of *ADMM* and* AUX_FIT_BASIS_SET* is removed, then the >> test will run without error occurred. >> Can anyone tell me how to solve this proplem ? Thanks ! >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Linux-x86-64-intel-mic.psmp Type: application/octet-stream Size: 11169 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: display_cp2ktest_with_DBUG1 Type: application/octet-stream Size: 120101 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: display_cp2ktest_without-xHost_without_DBUG Type: application/octet-stream Size: 120020 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: display_MyExample_WithDBUG1 Type: application/octet-stream Size: 63682 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: display_MyExample_Without-xHost_WithoutDBUG Type: application/octet-stream Size: 63682 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MyExample_sio2.inp Type: chemical/x-gamess-input Size: 3941 bytes Desc: not available URL: From yanfa... at gmail.com Sun May 21 01:24:55 2017 From: yanfa... at gmail.com (Fangyong Yan) Date: Sat, 20 May 2017 21:24:55 -0400 Subject: [CP2K:8746] Re: a question about constrained MD, shake algorithm and the free energy calculation using Lagrange multiplier In-Reply-To: References: <1c9465c2-8cde-4a69-bbee-b900a62b83b6@googlegroups.com> <6cbd29a8-c548-40a7-8227-4301aa6bee3b@googlegroups.com> Message-ID: I think in order to use constrained MD, we need to locate the reaction coordinate, which is not an easy task. I think lots of people have been working on such problems, how to map the free energy surface, not only in ab-initio MD calculations, but also in classical MD calculations, how to locate the reactants, saddle points (transition states), and products. In quantum mechanics calculation, we use potential energy surface, in MD, we use free energy surface. I am still trying to learn all these, but I think in order to understand our problems, we need to have a better understanding of our energy surfaces, which is a very complicated problem. On Fri, Mar 3, 2017 at 12:22 PM, Fangyong Yan wrote: > however, at this moment, I dont think I can find a better way to simulate > high free energy barrier for chemical reactions. Ab-initio constrained MD > seems to be the only choice, with enough sampling and good guess for the > reaction coordinate, the trajectory made up ab-initio constrained MD will > be reasonable. > > On Sun, Feb 26, 2017 at 7:48 PM, Fangyong Yan > wrote: > >> 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 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >> 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/to >> pic/cp2k/yWqahb93_38/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 yanfa... at gmail.com Sun May 21 01:41:43 2017 From: yanfa... at gmail.com (Fangyong Yan) Date: Sat, 20 May 2017 21:41:43 -0400 Subject: [CP2K:8746] Re: a question about constrained MD, shake algorithm and the free energy calculation using Lagrange multiplier In-Reply-To: References: <1c9465c2-8cde-4a69-bbee-b900a62b83b6@googlegroups.com> <6cbd29a8-c548-40a7-8227-4301aa6bee3b@googlegroups.com> Message-ID: I am not talking about using classical MD to do reactions, I am just saying that in classical MD, there are also free energy mapping, which includes local minima, maxima, and saddle points. On Sat, May 20, 2017 at 9:24 PM, Fangyong Yan wrote: > I think in order to use constrained MD, we need to locate the reaction > coordinate, which is not an easy task. I think lots of people have been > working on such problems, how to map the free energy surface, not only in > ab-initio MD calculations, but also in classical MD calculations, how to > locate the reactants, saddle points (transition states), and products. In > quantum mechanics calculation, we use potential energy surface, in MD, we > use free energy surface. > > I am still trying to learn all these, but I think in order to understand > our problems, we need to have a better understanding of our energy > surfaces, which is a very complicated problem. > > On Fri, Mar 3, 2017 at 12:22 PM, Fangyong Yan > wrote: > >> however, at this moment, I dont think I can find a better way to simulate >> high free energy barrier for chemical reactions. Ab-initio constrained MD >> seems to be the only choice, with enough sampling and good guess for the >> reaction coordinate, the trajectory made up ab-initio constrained MD will >> be reasonable. >> >> On Sun, Feb 26, 2017 at 7:48 PM, Fangyong Yan >> wrote: >> >>> 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 >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>> 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/to >>> pic/cp2k/yWqahb93_38/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 ning.zh... at gmail.com Mon May 22 12:34:41 2017 From: ning.zh... at gmail.com (ning.zh... at gmail.com) Date: Mon, 22 May 2017 05:34:41 -0700 (PDT) Subject: Who can download the 1.8GB files from the website: https://www.cp2k.org/exercises:2015_cecam_tutorial:index Message-ID: Hi everyone, I want to study the Exercises of the 4th CP2K tutorial from the website: https://www.cp2k.org/exercises:2015_cecam_tutorial:index But I found that the input files of 1.8G ( http://www.epcc.ed.ac.uk/~ibethune/files/CP2K_CECAM.tar.gz) are not downloaded. The link didn't work. So, Who does have the files? Maybe they are transfered to the new website? Thanks Ning -------------- next part -------------- An HTML attachment was scrubbed... URL: From i.be... at epcc.ed.ac.uk Mon May 22 12:39:09 2017 From: i.be... at epcc.ed.ac.uk (Iain Bethune) Date: Mon, 22 May 2017 13:39:09 +0100 Subject: [CP2K:9022] Who can download the 1.8GB files from the website: https://www.cp2k.org/exercises:2015_cecam_tutorial:index In-Reply-To: References: Message-ID: <6B0E4CAD-35E3-4265-A964-73B47CA1D0A9@epcc.ed.ac.uk> Hi Ning, Not all in one file, but you can obtain copies of the relevant inputs by clicking on the links to the individual exercises e.g. https://www.cp2k.org/exercises:2015_cecam_tutorial:mtd1 contains a link to: http://cp2k.org/static/exercises/2015_cecam_tutorial/MTD1.tar.xz 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 22 May 2017, at 13:34, ning.zh... at gmail.com wrote: > > Hi everyone, > > I want to study the Exercises of the 4th CP2K tutorial from the website: https://www.cp2k.org/exercises:2015_cecam_tutorial:index > > But I found that the input files of 1.8G (http://www.epcc.ed.ac.uk/~ibethune/files/CP2K_CECAM.tar.gz) are not downloaded. The link didn't work. > > So, Who does have the files? Maybe they are transfered to the new website? > > Thanks > > Ning > > > -- > 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 michel... at gmail.com Mon May 22 16:04:24 2017 From: michel... at gmail.com (Michel) Date: Mon, 22 May 2017 09:04:24 -0700 (PDT) Subject: Error: DIPOLE never stored Message-ID: <53a28f75-6c3b-4cbd-86a1-9e67e9f865cb@googlegroups.com> Dear All, I want to perform vibrational analysis and I have checked few input files out there to find out which keywords are necessary. I have first carried out a structural optimization of my periodic system with "CELL_OPT" then used the relaxed atomic positions and lattice parameters in the input file for vibrational analysis. Unfortunately, I encounter the following error message: Trying to access result ([DIPOLE]) which was never stored! Which has already been discussed in this forum a couple of times. The solutions that I could found are still not solving my issue, so I guess there is something wrong in my input file that I cannot see. It would be really helpful if your expert eyes could spot any mistakes in my input file (attached). No other files except the input, atom coordinates, potential and basis sets files are present in the folder of calculation when the calculation starts. Thank you very much for helping me solving this issue. Best, Michel. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TEST_VIB-r-0.out Type: application/octet-stream Size: 11242 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TEST_VIB.out Type: application/octet-stream Size: 10612 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TEST_VIB.inp Type: chemical/x-gamess-input Size: 2553 bytes Desc: not available URL: From ning.zh... at gmail.com Tue May 23 10:36:05 2017 From: ning.zh... at gmail.com (ning.zh... at gmail.com) Date: Tue, 23 May 2017 03:36:05 -0700 (PDT) Subject: [CP2K:9022] Who can download the 1.8GB files from the website: https://www.cp2k.org/exercises:2015_cecam_tutorial:index In-Reply-To: <6B0E4CAD-35E3-4265-A964-73B47CA1D0A9@epcc.ed.ac.uk> References: <6B0E4CAD-35E3-4265-A964-73B47CA1D0A9@epcc.ed.ac.uk> Message-ID: <3aaef13c-7f13-4ab3-8952-74949734817d@googlegroups.com> Hi Bethune, yeap, thanks. ning ? 2017?5?22???? UTC+8??8:39:13?IBethune??? > > Hi Ning, > > Not all in one file, but you can obtain copies of the relevant inputs by > clicking on the links to the individual exercises e.g. > > https://www.cp2k.org/exercises:2015_cecam_tutorial:mtd1 contains a link > to: > > http://cp2k.org/static/exercises/2015_cecam_tutorial/MTD1.tar.xz > > 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 22 May 2017, at 13:34, ning.... at gmail.com wrote: > > > > Hi everyone, > > > > I want to study the Exercises of the 4th CP2K tutorial from the website: > https://www.cp2k.org/exercises:2015_cecam_tutorial:index > > > > But I found that the input files of 1.8G ( > http://www.epcc.ed.ac.uk/~ibethune/files/CP2K_CECAM.tar.gz) are not > downloaded. The link didn't work. > > > > So, Who does have the files? Maybe they are transfered to the new > website? > > > > Thanks > > > > Ning > > > > > > -- > > 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 tuf6... at temple.edu Wed May 24 15:12:32 2017 From: tuf6... at temple.edu (tuf6... at temple.edu) Date: Wed, 24 May 2017 08:12:32 -0700 (PDT) Subject: QMMM setup for alanine in methanol Message-ID: <1954bf39-7ee7-4d33-a21c-acb3108a513f@googlegroups.com> Hello CP2K Users, Here I am attaching my CP2K input file for the QMMM simulation of alanine in methanol where I am interested in treating the alanine and some methanol molecule in QM region and rest of the methanol as MM. I made this input by taking the help from the cp2k website for urea in water example. In urea water example only urea is treated QM and water as MM. My questions are as follows: (1) Is this is the correct input file to start simulations in terms of input parameters? (2) if I am using "The Adaptive Buffered Force" from https://arxiv.org/pdf/1409.5218.pdf , the simulation is very slow. (3) How to deal with the temperature of QM region and total system. Is both should be equal. (4) ECOUPL COULOMB or GEEP which one is preferable for this system. (5) How to deal with the periodicity of the QM region. Thanking you Regards, Vivek (http://astro.temple.edu/~tuf65156) Temple University. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: bkp_qmmm1.inp Type: chemical/x-gamess-input Size: 8285 bytes Desc: not available URL: From kolbuszow... at gmail.com Wed May 24 17:03:39 2017 From: kolbuszow... at gmail.com (Kamil) Date: Wed, 24 May 2017 10:03:39 -0700 (PDT) Subject: MD RESTART WITH EXTERNAL TRAJECTORY Message-ID: <43c2ad1a-8c4b-41a7-b209-ceca2ec2c0db@googlegroups.com> Dear All, I have a question on restarting MD simulations for external trajectory calculations. 1.) I have an external trajectory in xyz format. 2.) I want to recalculate wannier centers, so I use REFTRAJ and it works well. The problems is due to the time limits in the queue system at the computer centre. Let's say that my calculations end at the step no 1499. 3.) Is it possible to restart the MD calculations for the frame no. 1500 from my external xyz trajectory? Each time when I try to do it CP2K comes back to the first frame. 4.) Should I delete all the frames up to 1500 manually and ask CP2K to start REFTRAJ again? I would really appreciate your kind help! All the best, Kamil -------------- next part -------------- An HTML attachment was scrubbed... URL: From loktar.... at gmail.com Wed May 24 19:33:41 2017 From: loktar.... at gmail.com (Xiaoliu) Date: Wed, 24 May 2017 12:33:41 -0700 (PDT) Subject: ERRORL2 in cp_fm_cholesky Message-ID: Dear cp2k users, I'm a beginner in cp2k ab initio simulation. i got an error in localLog_p1.out file: *** Local logger file of MPI task 1 in communicator 0 *** *** PID = 103815 *** Hostname = mike016 ===== Routine Calling Stack ===== 11 cp_fm_cholesky_decompose 10 make_full_inverse_cholesky 9 make_preconditioner 8 prepare_preconditioner 7 init_scf_loop 6 scf_env_do_scf 5 qs_energies_scf 4 qs_forces 3 velocity_verlet 2 qs_mol_dyn_low 1 CP2K ********************************************************************** *** 06:57:10 ERRORL2 in cp_fm_cholesky:cp_fm_cholesky_decompose :: *** *** condition FAILED at line 96 *** ********************************************************************** There's no error in my job.out file, and my simulation didn't fail till the walltime in hpc ran out. I read some previous discussions about the cholesky error,and checked my .soft file in hpc and it seems fine: # # This is the .soft file. # It is used to customize your environment by setting up environment # variables such as PATH and MANPATH. # To learn what can be in this file, use 'man softenv'. +cuda-4.2.9 +fftw-3.3.3-Intel-13.0.0 +Intel-12.1.4 +gaussian-09-D01 +lammps-06Dec12-Intel-13.0.0-openmpi-1.6.2 +openmpi-1.6.2-gcc-4.4.6 # # @default The version of cp2k in the hpc is: packages/cp2k/2.5.1/gcc-4.4.6-openmpi-1.6.2, and here's my input file: &GLOBAL PRINT_LEVEL LOW PROJECT_NAME xiaoliu_nvt_1 RUN_TYPE MD WALLTIME 1.7000000000000000E+05 &END GLOBAL &MOTION &MD ENSEMBLE NVT STEPS 10000 TIMESTEP 0.5 TEMPERATURE 3.2100000000000000E+02 COMVEL_TOL 1.0000000000000001E-05 &THERMOSTAT REGION MASSIVE &NOSE LENGTH 3 YOSHIDA 3 TIMECON 100 MTS 2 &END NOSE &END THERMOSTAT &END MD &PRINT &VELOCITIES SILENT FILENAME =Vel_nvt_1.dat &END VELOCITIES &RESTART SILENT &EACH MD 1 &END EACH &END RESTART &END PRINT &END MOTION &FORCE_EVAL METHOD QS &DFT BASIS_SET_FILE_NAME /work/xzhan91/SA_3MNaCl_H2O/CP2K/BASIS_SETS POTENTIAL_FILE_NAME /work/xzhan91/SA_3MNaCl_H2O/CP2K/POTENTIAL &SCF MAX_SCF 200 EPS_SCF 4.9999999999999998E-07 SCF_GUESS RESTART &OT T MINIMIZER DIIS N_HISTORY_VEC 7 PRECONDITIONER FULL_SINGLE_INVERSE &END OT &OUTER_SCF T EPS_SCF 4.9999999999999998E-07 MAX_SCF 200 &END OUTER_SCF &PRINT &RESTART SILENT BACKUP_COPIES 0 &END RESTART &RESTART_HISTORY SILENT BACKUP_COPIES 0 &END RESTART_HISTORY &END PRINT &END SCF &QS EPS_DEFAULT 9.9999999999999998E-13 EXTRAPOLATION ASPC EXTRAPOLATION_ORDER 3 &END QS &MGRID CUTOFF 4.0000000000000000E+02 &END MGRID &XC DENSITY_CUTOFF 1.0000000000000000E-10 GRADIENT_CUTOFF 1.0000000000000000E-10 TAU_CUTOFF 1.0000000000000000E-10 &XC_GRID XC_DERIV SPLINE2 &END XC_GRID &XC_FUNCTIONAL BLYP &END XC_FUNCTIONAL &VDW_POTENTIAL POTENTIAL_TYPE PAIR_POTENTIAL &PAIR_POTENTIAL R_CUTOFF 1.0000000000000009E+01 TYPE DFTD2 REFERENCE_FUNCTIONAL BLYP &END PAIR_POTENTIAL &END VDW_POTENTIAL &END XC &END DFT &SUBSYS &CELL A 15.035d0 0.0000000000000000E+00 0.0000000000000000E+00 B 0.0000000000000000E+00 15.035d0 0.0000000000000000E+00 C 0.0000000000000000E+00 0.0000000000000000E+00 15.035d0 MULTIPLE_UNIT_CELL 1 1 1 &END CELL &COORD C 14.47500 9.08300 -0.27400 O 13.46100 8.72200 -0.98500 O 15.29700 9.92600 -0.70800 C 14.65500 8.47300 1.07400 H 15.65500 8.41500 1.53400 H 14.14000 7.49900 1.09800 H 14.03300 9.16000 1.66800 Na 7.39400 15.40500 7.48500 Cl 7.75600 3.73500 -4.85000 Cl 20.37100 14.26700 -0.18800 Cl 22.22800 12.23100 -4.60000 Cl 9.35100 1.82500 0.65000 Cl 14.06200 8.00600 -7.44000 Cl 11.73700 6.61900 4.02100 Na 15.53000 2.22700 -1.71800 Na 17.57900 10.98700 -6.77700 Na 18.91400 11.69400 -0.47200 Na 9.68300 5.25300 -6.77700 Na 12.62600 2.06600 -6.46300 Na 9.61100 10.19400 0.51100 O 10.83200 7.37000 -2.76300 H 10.34600 7.09600 -3.50500 H 11.71600 7.61800 -3.08800 O 10.60500 8.31800 1.52500 H 11.36700 8.21400 2.15500 H 10.33200 7.40800 1.34600 O 12.72400 13.02300 2.83900 H 13.40200 12.91800 2.13900 H 11.95100 13.08700 2.28600 O 13.80800 15.15300 4.89300 H 13.43400 14.57200 4.22400 H 13.26500 14.91900 5.66200 O 9.32500 13.63700 -5.15400 H 8.47100 13.47900 -4.84500 H 9.85000 13.08400 -4.56000 O 9.10700 1.85500 4.06400 H 9.26500 2.81100 4.30500 H 8.66100 1.96800 3.19800 O 13.43000 1.66600 -2.73600 H 12.62300 1.47600 -2.18900 H 13.16700 1.42200 -3.60700 O 7.75800 11.55000 1.65200 H 7.38600 12.39500 1.96400 H 7.26300 10.85800 2.17000 O 21.27400 3.88300 5.20500 H 21.38800 4.81700 5.38200 H 20.71200 3.83100 4.44300 O 13.64000 16.07200 -5.37800 H 13.38800 15.12300 -5.62600 H 14.45000 15.92600 -4.85600 O 21.92500 13.67100 2.56700 H 21.06200 13.27300 2.82600 H 21.60500 13.92900 1.62700 O 12.36400 9.74800 4.41300 H 12.16100 8.80500 4.29700 H 13.24300 9.75600 4.00400 O 12.58300 11.41000 6.56900 H 12.11900 10.75300 7.10400 H 12.77400 10.97600 5.74900 O 15.86200 15.66500 -3.94400 H 16.59800 15.29100 -3.38300 H 16.34100 16.18300 -4.63400 O 12.41900 13.32700 -7.21500 H 12.38500 12.74300 -7.99000 H 11.97500 12.73900 -6.62100 O 16.96100 4.47400 1.35500 H 17.13500 3.68000 1.88900 H 16.04200 4.73300 1.52100 O 17.62200 8.63700 -7.33200 H 18.17600 8.09000 -6.77600 H 16.71600 8.45800 -7.07600 O 12.20500 4.80700 -6.08500 H 12.80200 4.65000 -5.38400 H 12.79000 5.27400 -6.74600 O 12.23800 11.27800 -5.25400 H 12.85300 10.73800 -4.70700 H 11.54000 11.59800 -4.63400 O 17.32400 2.38200 5.75300 H 17.65500 1.43700 5.81200 H 16.47400 2.31500 5.24400 O 18.16700 1.72900 -1.82000 H 18.92400 1.97600 -1.31400 H 18.26100 0.79200 -1.95900 O 21.11500 7.27100 0.76800 H 21.24200 6.32500 1.04500 H 20.22300 7.43500 1.15700 O 18.91200 3.04000 3.48400 H 19.32000 2.27200 2.99600 H 18.49900 2.68100 4.28600 O 21.20900 10.89500 5.46400 H 21.27800 10.53700 4.62500 H 22.08900 11.12200 5.67800 O 10.94500 12.24800 -3.14100 H 11.01900 11.45000 -2.64300 H 10.63600 12.80100 -2.44600 O 7.23400 12.91500 -1.62800 H 6.46100 13.35200 -1.25100 H 7.22800 13.17300 -2.55800 O 12.94200 8.03300 -4.46700 H 13.11500 8.04300 -5.42700 H 13.31800 8.80600 -4.15900 O 17.88700 14.80200 -2.60300 H 18.25100 14.52100 -1.73900 H 18.49200 14.33500 -3.19000 O 12.17200 16.04200 2.21400 H 11.88900 15.93200 3.13000 H 11.38500 16.35400 1.82500 O 15.42400 11.11400 7.88900 H 14.82100 11.74200 7.59000 H 14.75700 10.43800 8.18400 O 9.47400 13.36000 5.14400 H 8.88600 14.10000 5.08900 H 9.37800 12.82400 4.35100 O 10.30900 11.04900 3.56600 H 10.83600 11.70600 3.05600 H 11.07000 10.59800 4.00000 O 9.65500 13.91800 -1.17400 H 9.58700 14.79600 -0.74800 H 8.74000 13.62100 -1.32900 O 10.88600 3.68400 -2.55900 H 11.70900 3.17000 -2.32300 H 10.60200 3.32100 -3.40700 O 14.49800 3.65900 -4.93000 H 14.82100 4.32000 -4.29500 H 15.30800 3.14300 -5.10800 O 14.69000 2.08400 4.96800 H 14.49500 1.12000 4.91000 H 14.25100 2.50800 4.26700 O 13.93500 2.46000 2.26300 H 13.43500 1.62000 2.37900 H 13.19300 3.13300 2.18800 O 17.69900 9.69800 0.60400 H 17.81300 8.80000 1.04700 H 16.84100 9.65000 0.25900 O 14.82600 12.03800 1.43400 H 14.59900 11.59100 0.62700 H 15.71300 12.39400 1.21800 O 6.36300 2.83600 1.70800 H 5.76800 2.19200 2.14400 H 7.12200 2.37200 1.34000 O 6.48000 4.72400 -2.02600 H 7.28300 5.16500 -1.67400 H 6.79500 4.47200 -2.88700 O 9.26400 4.47400 4.96600 H 10.11200 4.92100 4.87600 H 8.73800 4.83700 4.27100 O 7.95800 8.51800 -0.08200 H 7.41300 9.13500 -0.59800 H 7.21300 7.96700 0.37900 O 17.39500 15.57300 2.08700 H 17.75100 14.79100 1.70400 H 16.64100 15.64300 1.46600 O 19.42600 8.58500 -3.02100 H 18.42900 8.43600 -2.97200 H 19.73800 7.69000 -3.02000 O 7.18100 10.25100 -1.93600 H 7.46500 11.12500 -1.66300 H 7.17900 10.37000 -2.90700 O 19.38500 14.29700 -4.73800 H 20.08400 13.67200 -4.48200 H 19.82100 15.15600 -4.61200 O 20.05100 16.86200 2.09300 H 19.24200 16.27200 2.22300 H 20.57500 16.35700 1.44300 O 9.97500 3.13200 7.81600 H 9.14300 2.88700 7.38200 H 10.54700 2.49200 7.46100 O 11.41000 16.41500 -1.37000 H 10.87400 16.75300 -0.58900 H 10.68500 16.35800 -2.01900 O 20.06900 3.99400 -0.95700 H 20.94300 4.19800 -1.40800 H 20.19100 4.39400 -0.10000 O 18.21100 15.51800 5.07800 H 17.86100 14.73700 5.61200 H 17.71900 15.29600 4.22400 O 11.02700 15.79200 4.76100 H 10.47700 15.02100 4.65200 H 10.40200 16.47300 4.48200 O 18.93400 4.38800 -5.68000 H 18.19100 4.81700 -6.18100 H 19.16200 5.05000 -5.10100 O 7.75600 15.34000 5.13900 H 8.01800 16.09900 4.55700 H 6.77300 15.44400 5.08800 O 16.54600 12.20900 -1.12000 H 15.86400 12.57300 -1.73000 H 16.25600 11.26900 -1.03500 O 11.70900 3.74900 1.65600 H 10.85600 3.27300 1.36300 H 11.48000 4.62700 2.00900 O 7.20000 2.14900 6.96400 H 6.98000 2.69600 7.68100 H 6.68200 2.56400 6.26300 O 7.06900 15.95700 -5.57800 H 7.31800 16.87400 -5.34400 H 6.31300 15.85600 -4.99100 O 19.65400 11.24000 -2.85500 H 19.38100 10.30000 -2.97200 H 20.59000 11.38400 -3.15200 O 19.61000 6.62200 4.03900 H 20.38700 6.43900 4.59400 H 18.92300 6.69700 4.68200 O 16.74900 8.07700 -2.87100 H 16.34900 8.32300 -2.02000 H 16.16200 7.34900 -3.09900 O 15.14100 5.35900 -2.82400 H 14.40500 5.56500 -2.26800 H 15.76900 5.13500 -2.13800 O 10.73800 1.96700 -4.91100 H 9.97900 2.60300 -5.10700 H 10.39600 1.28000 -4.33400 O 14.48500 5.11800 2.79400 H 14.57400 4.84300 3.69600 H 13.57600 5.48800 2.77600 O 16.28400 9.99400 -4.77600 H 15.40400 10.28900 -4.36300 H 16.38900 9.19200 -4.24900 O 19.87300 5.66000 -3.04400 H 20.63300 5.45300 -2.44900 H 19.14200 5.32800 -2.53500 O 9.16300 7.20900 -5.21800 H 8.24200 6.87000 -5.07900 H 8.96900 8.10900 -5.51800 O 6.36300 8.34000 -7.35300 H 6.11600 7.57500 -6.83400 H 7.21200 8.67800 -6.98800 O 17.56900 4.69200 -1.41800 H 17.55200 4.65800 -0.42700 H 18.38500 4.18300 -1.43200 O 8.02800 7.73600 3.07700 H 7.90900 6.75400 3.19900 H 8.93900 7.87500 3.30900 O 14.17900 10.54700 -3.21900 H 14.51600 11.35800 -2.79600 H 13.98800 10.08900 -2.36100 O 11.22800 9.80100 -7.60400 H 10.42700 9.40300 -7.95100 H 11.77200 9.15700 -7.21600 O 15.11100 0.59900 0.61200 H 15.24100 1.25600 1.36000 H 14.17700 0.48500 0.72800 O 9.38100 11.85300 7.42200 H 9.48300 12.23300 6.56600 H 10.12300 11.22500 7.50600 O 8.86300 14.62200 2.27500 H 8.03500 14.33700 2.72000 H 8.63300 15.52400 2.08900 O 7.52100 1.66400 -1.90700 H 7.88600 2.50700 -2.19000 H 7.81900 1.72300 -1.02000 O 11.52000 16.55300 7.52200 H 11.03100 15.98100 8.09100 H 11.54300 16.12100 6.63600 O 14.08300 5.43100 6.09800 H 13.47100 5.83700 5.48900 H 14.00100 6.10400 6.81300 O 14.38800 13.29500 -5.33900 H 15.04700 12.89200 -5.92500 H 13.57700 13.19600 -5.83600 O 7.62800 5.01000 2.92900 H 8.27400 5.09600 2.18600 H 6.91100 4.51600 2.49200 O 14.25200 2.81000 7.62200 H 14.37400 2.16300 6.90000 H 14.23400 3.67900 7.18100 O 8.88700 8.90800 7.12200 H 8.54900 9.64000 6.58200 H 8.80300 8.17000 6.52400 O 19.22600 11.93300 7.23200 H 19.80200 11.57000 6.57900 H 19.70900 11.65100 8.08600 O 20.72000 2.27900 -5.78800 H 20.15400 3.07200 -5.70300 H 21.56000 2.62900 -5.45500 O 10.59700 13.03100 1.10000 H 10.80200 13.31800 0.17000 H 10.02100 13.68100 1.51900 O 20.37700 4.70200 1.56100 H 19.97200 4.28200 2.28000 H 21.05700 4.07800 1.40500 O 14.26100 3.74800 -0.25400 H 13.80100 3.56600 0.58000 H 13.95100 4.65000 -0.55400 O 16.94800 2.08300 -5.37100 H 17.19700 1.89800 -6.29600 H 17.78200 2.45000 -5.04900 O 21.70600 9.70100 2.86400 H 21.35000 9.66200 1.94600 H 21.98200 8.74200 2.90500 O 17.01100 9.61800 5.27500 H 16.97200 9.42600 6.19500 H 16.21200 9.14200 5.03200 O 19.35300 12.54800 3.88900 H 19.66400 12.60900 4.81200 H 19.54300 11.59600 3.69600 O 14.67800 11.55100 4.17400 H 14.03800 12.18100 4.46400 H 14.70600 11.83100 3.23600 O 17.10600 13.31600 6.16400 H 17.65300 12.84900 6.83400 H 16.68200 12.55300 5.71100 O 14.97300 8.09200 4.90100 H 14.70000 7.17400 4.82900 H 14.50200 8.38000 5.69800 O 16.69500 5.81800 -6.50800 H 16.04800 6.50500 -6.35900 H 16.54200 5.54600 -7.44400 O 17.86600 12.11900 1.87300 H 17.85000 11.12600 1.92400 H 18.10200 12.33400 2.82400 O 9.42000 16.15500 -3.13800 H 8.62000 16.59200 -2.85400 H 9.05300 15.39400 -3.65300 O 16.67900 4.76800 6.87000 H 15.81100 5.00000 6.53700 H 16.79100 3.83500 6.57500 O 11.27800 6.86100 7.40800 H 11.40500 6.83800 6.41900 H 12.07800 7.38500 7.71500 O 17.29000 13.48900 -6.16800 H 17.86400 13.94800 -5.47300 H 17.09100 14.13600 -6.80000 O 18.72000 6.45600 6.83300 H 18.11800 5.75500 6.60100 H 18.08000 7.17200 7.06100 O 21.29200 6.60700 6.37900 H 21.67800 7.39200 6.83600 H 20.46900 6.66100 6.74400 O 14.65300 13.18600 -2.72500 H 14.71000 14.16700 -2.66200 H 14.54600 12.97300 -3.65400 O 9.61600 14.78700 -7.38700 H 9.38300 14.47300 -6.48100 H 10.00500 13.92800 -7.68700 O 20.83200 16.12800 -7.53900 H 20.88000 16.78200 -6.78600 H 20.57300 15.32500 -7.03200 O 8.60800 9.89500 -5.72600 H 9.13500 10.42000 -6.20300 H 8.15100 10.65200 -5.34600 O 7.94300 10.40600 4.97600 H 7.45300 9.79100 4.38600 H 8.73800 10.62600 4.46900 O 18.42500 7.03200 1.54100 H 18.76200 6.76400 2.41400 H 18.09600 6.14700 1.23600 O 9.03400 5.45100 -2.08600 H 9.49900 6.25800 -2.27600 H 9.77500 4.82000 -2.12600 O 22.09400 6.67900 -5.17300 H 22.31900 5.76400 -5.05700 H 21.37400 6.71100 -4.49700 O 6.80600 13.06000 -7.81500 H 7.60700 12.47300 -7.86800 H 6.45000 13.04400 -6.91000 O 18.91500 9.76600 3.46300 H 18.78500 8.94000 2.95000 H 18.20200 9.71400 4.17600 O 11.11700 9.84400 -1.48600 H 10.59600 9.18700 -1.87900 H 11.93700 9.34700 -1.30500 O 20.15700 10.51900 -6.38200 H 20.67300 10.95900 -5.67700 H 20.77400 9.91700 -6.84900 O 20.88400 15.90900 5.48100 H 20.69900 16.11000 6.41000 H 19.95200 15.84500 5.21100 O 13.09900 6.04400 -0.94600 H 13.10200 7.01300 -0.70100 H 12.16600 5.86600 -1.18000 O 20.90700 10.03800 -0.11900 H 21.58200 10.21700 -0.77000 H 20.61100 9.14300 -0.36200 O 7.77700 5.74600 7.41500 H 6.91700 6.17700 7.38400 H 7.79500 5.29800 6.55300 O 9.20300 5.50700 0.75600 H 8.88800 6.20600 0.13000 H 9.42300 4.75100 0.20200 O 21.46200 15.92200 -3.04600 H 21.03900 15.37300 -2.34300 H 21.97700 16.48500 -2.46700 &END COORD &KIND H BASIS_SET TZV2P-GTH POTENTIAL GTH-BLYP-q1 &END KIND &KIND O BASIS_SET TZV2P-GTH POTENTIAL GTH-BLYP-q6 &END KIND &KIND C BASIS_SET TZV2P-GTH POTENTIAL GTH-BLYP-q4 &END KIND &KIND Na BASIS_SET TZV2P-GTH POTENTIAL GTH-BLYP-q9 &END KIND &KIND Cl BASIS_SET TZV2P-GTH POTENTIAL GTH-BLYP-q7 &END KIND &END SUBSYS &PRINT &FORCES SILENT FILENAME =Frc_nvt_1.dat &END FORCES &END PRINT &END FORCE_EVAL Is there any idea about this error? I'm really appreciated. Thanks, Xiaoliu -------------- next part -------------- An HTML attachment was scrubbed... URL: From anu... at gmail.com Wed May 24 21:04:38 2017 From: anu... at gmail.com (anurag vohra) Date: Wed, 24 May 2017 14:04:38 -0700 (PDT) Subject: Considering charge on vacancies in cp2k Message-ID: <51b1cb35-bf8c-4796-9897-0e4784016e4e@googlegroups.com> Hi, I wonder if charge on vacancies (singly or doubly negatively charged) can be considered in bulk Ge using cp2k. As far as I know charge on the total system can be changed but doesn't it assures charge is localized at vacancy or it is evenly distributed over the system? I would like to study formation energies for vacancies with different charges in bulk Ge system, does anyone has idea how to do this in cp2k? Any sort of help is appreciated. Regards, Anurag -------------- next part -------------- An HTML attachment was scrubbed... URL: From olive... at gmail.com Wed May 24 23:39:48 2017 From: olive... at gmail.com (Luiz Fernando Lopes Oliveira) Date: Wed, 24 May 2017 16:39:48 -0700 (PDT) Subject: Regtest Message-ID: <6f345b2d-07c2-4ad1-bdac-91e32365ecde@googlegroups.com> Hi. I successfully compiled CP2K, and made some initial tests with my own input files, which worked just fine. However, when I run a regtest I got all tests failed > Number of FAILED tests 2573 > Number of WRONG tests 0 > Number of CORRECT tests 0 > Number of NEW tests 0 > Total number of tests 2573 > GREPME 2573 0 0 0 2573 X > I ran the regtest using "make ARCH=Linux-x86-64-intel-host VERSION=psmp test" from the makefiles folder. I took some of the input files from cp2k/tests that generated the RUNTIME FAILS and, as my own input files, I haven't had any issue with them. Anyway I'm surprised that regtests failed, and would like very much some advises on it. -------------- next part -------------- An HTML attachment was scrubbed... URL: From taosun... at gmail.com Thu May 25 17:09:31 2017 From: taosun... at gmail.com (Sun Tao) Date: Thu, 25 May 2017 10:09:31 -0700 (PDT) Subject: confusion about QM/MM setup in CP2k Message-ID: <988d807c-e79f-414f-a380-ecb8b3833088@googlegroups.com> Dear experts: I am confused about some settings of the QMMM portion of CP2K. In the section QMMM/CELL we need to set up the QM region. Then in QMMM/QM_KIND section, there is a keyword MM_INDEX, for which my understanding is to tell the program the index of the MM atoms that would be treated in QM fashion. Here is the question: does CP2K allow MM atoms inside QM regions? Or say in the QM region some atoms could be treated in QM and others could still be treated in MM? If CP2K does allow this, how do these two different kinds of atoms (QM atoms and MM atoms) interact with each other inside the QM box? Is there any papers/books I could refer to if this is the case? Before I only know that the coupling happens between QM region and MM region and the boundary between QM and MM is important to treat. Thanks very much for your help. Look forward to your reply! Tao -------------- next part -------------- An HTML attachment was scrubbed... URL: From alfio.... at gmail.com Thu May 25 17:50:53 2017 From: alfio.... at gmail.com (Alfio Lazzaro) Date: Thu, 25 May 2017 10:50:53 -0700 (PDT) Subject: Regtest In-Reply-To: <6f345b2d-07c2-4ad1-bdac-91e32365ecde@googlegroups.com> References: <6f345b2d-07c2-4ad1-bdac-91e32365ecde@googlegroups.com> Message-ID: <49931f7d-3ec6-4321-89b7-082012229951@googlegroups.com> Could you attach the log of the tests? It can be useful to understand what's wrong... Alfio Il giorno gioved? 25 maggio 2017 01:39:48 UTC+2, Luiz Fernando Lopes Oliveira ha scritto: > > > Hi. I successfully compiled CP2K, and made some initial tests with my own > input files, which worked just fine. However, when I run a regtest I got > all tests failed > >> Number of FAILED tests 2573 >> Number of WRONG tests 0 >> Number of CORRECT tests 0 >> Number of NEW tests 0 >> Total number of tests 2573 >> GREPME 2573 0 0 0 2573 X >> > > I ran the regtest using "make ARCH=Linux-x86-64-intel-host VERSION=psmp > test" from the makefiles folder. I took some of the input files from > cp2k/tests that generated the RUNTIME FAILS and, as my own input files, I > haven't had any issue with them. Anyway I'm surprised that regtests failed, > and would like very much some advises on it. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mattwa... at gmail.com Thu May 25 21:25:27 2017 From: mattwa... at gmail.com (Matt W) Date: Thu, 25 May 2017 14:25:27 -0700 (PDT) Subject: confusion about QM/MM setup in CP2k In-Reply-To: <988d807c-e79f-414f-a380-ecb8b3833088@googlegroups.com> References: <988d807c-e79f-414f-a380-ecb8b3833088@googlegroups.com> Message-ID: <6e81e560-704b-4bea-bbf9-f3142f813a0e@googlegroups.com> Hi Tao, The boxes are used essentially for electrostatic calculations. The interface between the QM and MM atoms is the real region where they connect, not really anything to do with the cells. You should see a list of relevant references at the end of the output file - there are two particular to CP2K by Laio and co-workers that you should try and read. Matt On Thursday, May 25, 2017 at 6:09:31 PM UTC+1, Sun Tao wrote: > > Dear experts: > > I am confused about some settings of the QMMM portion of CP2K. In the > section QMMM/CELL we need to set up the QM region. Then in QMMM/QM_KIND > section, there is a keyword MM_INDEX, for which my understanding is to tell > the program the index of the MM atoms that would be treated in QM fashion. > > Here is the question: does CP2K allow MM atoms inside QM regions? Or say > in the QM region some atoms could be treated in QM and others could still > be treated in MM? If CP2K does allow this, how do these two different kinds > of atoms (QM atoms and MM atoms) interact with each other inside the QM > box? Is there any papers/books I could refer to if this is the case? Before > I only know that the coupling happens between QM region and MM region and > the boundary between QM and MM is important to treat. > > Thanks very much for your help. Look forward to your reply! > > Tao > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mattwa... at gmail.com Thu May 25 21:40:46 2017 From: mattwa... at gmail.com (Matt W) Date: Thu, 25 May 2017 14:40:46 -0700 (PDT) Subject: Considering charge on vacancies in cp2k In-Reply-To: <51b1cb35-bf8c-4796-9897-0e4784016e4e@googlegroups.com> References: <51b1cb35-bf8c-4796-9897-0e4784016e4e@googlegroups.com> Message-ID: <24f9ee64-df9f-4be6-adb7-fcba5f78785c@googlegroups.com> Hi, generally in DFT codes you cannot specify particular distributions of electrons, merely find the lowest energy total electron density. What you can do is provide an initial geometry that would favour the 'excess' charge being where you want it to go. Matt On Wednesday, May 24, 2017 at 10:04:38 PM UTC+1, anurag vohra wrote: > > Hi, > > I wonder if charge on vacancies (singly or doubly negatively charged) can > be considered in bulk Ge using cp2k. As far as I know charge on the total > system can be changed but doesn't it assures charge is localized at vacancy > or it is evenly distributed over the system? > > I would like to study formation energies for vacancies with different > charges in bulk Ge system, does anyone has idea how to do this in cp2k? Any > sort of help is appreciated. > > Regards, > Anurag > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mattwa... at gmail.com Thu May 25 21:48:02 2017 From: mattwa... at gmail.com (Matt W) Date: Thu, 25 May 2017 14:48:02 -0700 (PDT) Subject: ERRORL2 in cp_fm_cholesky In-Reply-To: References: Message-ID: <700fce76-e839-4e09-b3f9-8cd9c7af8d19@googlegroups.com> Hi, probably means there is a near linear dependency in you basis set. Try using the MOLOPT basis sets (available in BASIS_MOLOPT or BASIS_MOLOPT_UCL) to see if they cure the problem. The issue, is probably the Na atoms - likely you'll need a _much_ highter cutoff too. Matt On Wednesday, May 24, 2017 at 8:33:41 PM UTC+1, Xiaoliu wrote: > > Dear cp2k users, > > I'm a beginner in cp2k ab initio simulation. i got an error > in localLog_p1.out file: > > *** Local logger file of MPI task 1 in communicator 0 *** > *** PID = 103815 > *** Hostname = mike016 > > > ===== Routine Calling Stack ===== > > 11 cp_fm_cholesky_decompose > 10 make_full_inverse_cholesky > 9 make_preconditioner > 8 prepare_preconditioner > 7 init_scf_loop > 6 scf_env_do_scf > 5 qs_energies_scf > 4 qs_forces > 3 velocity_verlet > 2 qs_mol_dyn_low > 1 CP2K > > ********************************************************************** > *** 06:57:10 ERRORL2 in cp_fm_cholesky:cp_fm_cholesky_decompose :: *** > *** condition FAILED at line 96 *** > ********************************************************************** > > There's no error in my job.out file, and my simulation didn't fail till > the walltime in hpc ran out. > > I read some previous discussions about the cholesky error,and checked my > .soft file in hpc and it seems fine: > > # > # This is the .soft file. > # It is used to customize your environment by setting up environment > # variables such as PATH and MANPATH. > # To learn what can be in this file, use 'man softenv'. > +cuda-4.2.9 > +fftw-3.3.3-Intel-13.0.0 > +Intel-12.1.4 > +gaussian-09-D01 > +lammps-06Dec12-Intel-13.0.0-openmpi-1.6.2 > +openmpi-1.6.2-gcc-4.4.6 > # > # > @default > > The version of cp2k in the hpc is: packages/cp2k/2.5.1/gcc-4.4.6-openmpi-1.6.2, > and here's my input file: > > &GLOBAL > PRINT_LEVEL LOW > PROJECT_NAME xiaoliu_nvt_1 > RUN_TYPE MD > WALLTIME 1.7000000000000000E+05 > &END GLOBAL > &MOTION > &MD > ENSEMBLE NVT > STEPS 10000 > TIMESTEP 0.5 > TEMPERATURE 3.2100000000000000E+02 > COMVEL_TOL 1.0000000000000001E-05 > &THERMOSTAT > REGION MASSIVE > &NOSE > LENGTH 3 > YOSHIDA 3 > TIMECON 100 > MTS 2 > &END NOSE > &END THERMOSTAT > &END MD > &PRINT > &VELOCITIES SILENT > FILENAME =Vel_nvt_1.dat > &END VELOCITIES > &RESTART SILENT > &EACH > MD 1 > &END EACH > &END RESTART > &END PRINT > &END MOTION > &FORCE_EVAL > METHOD QS > &DFT > BASIS_SET_FILE_NAME /work/xzhan91/SA_3MNaCl_H2O/CP2K/BASIS_SETS > POTENTIAL_FILE_NAME /work/xzhan91/SA_3MNaCl_H2O/CP2K/POTENTIAL > &SCF > MAX_SCF 200 > EPS_SCF 4.9999999999999998E-07 > SCF_GUESS RESTART > &OT T > MINIMIZER DIIS > N_HISTORY_VEC 7 > PRECONDITIONER FULL_SINGLE_INVERSE > &END OT > &OUTER_SCF T > EPS_SCF 4.9999999999999998E-07 > MAX_SCF 200 > &END OUTER_SCF > &PRINT > &RESTART SILENT > BACKUP_COPIES 0 > &END RESTART > &RESTART_HISTORY SILENT > BACKUP_COPIES 0 > &END RESTART_HISTORY > &END PRINT > &END SCF > &QS > EPS_DEFAULT 9.9999999999999998E-13 > EXTRAPOLATION ASPC > EXTRAPOLATION_ORDER 3 > &END QS > &MGRID > CUTOFF 4.0000000000000000E+02 > &END MGRID > &XC > DENSITY_CUTOFF 1.0000000000000000E-10 > GRADIENT_CUTOFF 1.0000000000000000E-10 > TAU_CUTOFF 1.0000000000000000E-10 > &XC_GRID > XC_DERIV SPLINE2 > &END XC_GRID > &XC_FUNCTIONAL BLYP > &END XC_FUNCTIONAL > &VDW_POTENTIAL > POTENTIAL_TYPE PAIR_POTENTIAL > &PAIR_POTENTIAL > R_CUTOFF 1.0000000000000009E+01 > TYPE DFTD2 > REFERENCE_FUNCTIONAL BLYP > &END PAIR_POTENTIAL > &END VDW_POTENTIAL > &END XC > &END DFT > &SUBSYS > &CELL > A 15.035d0 0.0000000000000000E+00 0.0000000000000000E+00 > B 0.0000000000000000E+00 15.035d0 0.0000000000000000E+00 > C 0.0000000000000000E+00 0.0000000000000000E+00 15.035d0 > MULTIPLE_UNIT_CELL 1 1 1 > &END CELL > &COORD > C 14.47500 9.08300 -0.27400 > O 13.46100 8.72200 -0.98500 > O 15.29700 9.92600 -0.70800 > C 14.65500 8.47300 1.07400 > H 15.65500 8.41500 1.53400 > H 14.14000 7.49900 1.09800 > H 14.03300 9.16000 1.66800 > Na 7.39400 15.40500 7.48500 > Cl 7.75600 3.73500 -4.85000 > Cl 20.37100 14.26700 -0.18800 > Cl 22.22800 12.23100 -4.60000 > Cl 9.35100 1.82500 0.65000 > Cl 14.06200 8.00600 -7.44000 > Cl 11.73700 6.61900 4.02100 > Na 15.53000 2.22700 -1.71800 > Na 17.57900 10.98700 -6.77700 > Na 18.91400 11.69400 -0.47200 > Na 9.68300 5.25300 -6.77700 > Na 12.62600 2.06600 -6.46300 > Na 9.61100 10.19400 0.51100 > O 10.83200 7.37000 -2.76300 > H 10.34600 7.09600 -3.50500 > H 11.71600 7.61800 -3.08800 > O 10.60500 8.31800 1.52500 > H 11.36700 8.21400 2.15500 > H 10.33200 7.40800 1.34600 > O 12.72400 13.02300 2.83900 > H 13.40200 12.91800 2.13900 > H 11.95100 13.08700 2.28600 > O 13.80800 15.15300 4.89300 > H 13.43400 14.57200 4.22400 > H 13.26500 14.91900 5.66200 > O 9.32500 13.63700 -5.15400 > H 8.47100 13.47900 -4.84500 > H 9.85000 13.08400 -4.56000 > O 9.10700 1.85500 4.06400 > H 9.26500 2.81100 4.30500 > H 8.66100 1.96800 3.19800 > O 13.43000 1.66600 -2.73600 > H 12.62300 1.47600 -2.18900 > H 13.16700 1.42200 -3.60700 > O 7.75800 11.55000 1.65200 > H 7.38600 12.39500 1.96400 > H 7.26300 10.85800 2.17000 > O 21.27400 3.88300 5.20500 > H 21.38800 4.81700 5.38200 > H 20.71200 3.83100 4.44300 > O 13.64000 16.07200 -5.37800 > H 13.38800 15.12300 -5.62600 > H 14.45000 15.92600 -4.85600 > O 21.92500 13.67100 2.56700 > H 21.06200 13.27300 2.82600 > H 21.60500 13.92900 1.62700 > O 12.36400 9.74800 4.41300 > H 12.16100 8.80500 4.29700 > H 13.24300 9.75600 4.00400 > O 12.58300 11.41000 6.56900 > H 12.11900 10.75300 7.10400 > H 12.77400 10.97600 5.74900 > O 15.86200 15.66500 -3.94400 > H 16.59800 15.29100 -3.38300 > H 16.34100 16.18300 -4.63400 > O 12.41900 13.32700 -7.21500 > H 12.38500 12.74300 -7.99000 > H 11.97500 12.73900 -6.62100 > O 16.96100 4.47400 1.35500 > H 17.13500 3.68000 1.88900 > H 16.04200 4.73300 1.52100 > O 17.62200 8.63700 -7.33200 > H 18.17600 8.09000 -6.77600 > H 16.71600 8.45800 -7.07600 > O 12.20500 4.80700 -6.08500 > H 12.80200 4.65000 -5.38400 > H 12.79000 5.27400 -6.74600 > O 12.23800 11.27800 -5.25400 > H 12.85300 10.73800 -4.70700 > H 11.54000 11.59800 -4.63400 > O 17.32400 2.38200 5.75300 > H 17.65500 1.43700 5.81200 > H 16.47400 2.31500 5.24400 > O 18.16700 1.72900 -1.82000 > H 18.92400 1.97600 -1.31400 > H 18.26100 0.79200 -1.95900 > O 21.11500 7.27100 0.76800 > H 21.24200 6.32500 1.04500 > H 20.22300 7.43500 1.15700 > O 18.91200 3.04000 3.48400 > H 19.32000 2.27200 2.99600 > H 18.49900 2.68100 4.28600 > O 21.20900 10.89500 5.46400 > H 21.27800 10.53700 4.62500 > H 22.08900 11.12200 5.67800 > O 10.94500 12.24800 -3.14100 > H 11.01900 11.45000 -2.64300 > H 10.63600 12.80100 -2.44600 > O 7.23400 12.91500 -1.62800 > H 6.46100 13.35200 -1.25100 > H 7.22800 13.17300 -2.55800 > O 12.94200 8.03300 -4.46700 > H 13.11500 8.04300 -5.42700 > H 13.31800 8.80600 -4.15900 > O 17.88700 14.80200 -2.60300 > H 18.25100 14.52100 -1.73900 > H 18.49200 14.33500 -3.19000 > O 12.17200 16.04200 2.21400 > H 11.88900 15.93200 3.13000 > H 11.38500 16.35400 1.82500 > O 15.42400 11.11400 7.88900 > H 14.82100 11.74200 7.59000 > H 14.75700 10.43800 8.18400 > O 9.47400 13.36000 5.14400 > H 8.88600 14.10000 5.08900 > H 9.37800 12.82400 4.35100 > O 10.30900 11.04900 3.56600 > H 10.83600 11.70600 3.05600 > H 11.07000 10.59800 4.00000 > O 9.65500 13.91800 -1.17400 > H 9.58700 14.79600 -0.74800 > H 8.74000 13.62100 -1.32900 > O 10.88600 3.68400 -2.55900 > H 11.70900 3.17000 -2.32300 > H 10.60200 3.32100 -3.40700 > O 14.49800 3.65900 -4.93000 > H 14.82100 4.32000 -4.29500 > H 15.30800 3.14300 -5.10800 > O 14.69000 2.08400 4.96800 > H 14.49500 1.12000 4.91000 > H 14.25100 2.50800 4.26700 > O 13.93500 2.46000 2.26300 > H 13.43500 1.62000 2.37900 > H 13.19300 3.13300 2.18800 > O 17.69900 9.69800 0.60400 > H 17.81300 8.80000 1.04700 > H 16.84100 9.65000 0.25900 > O 14.82600 12.03800 1.43400 > H 14.59900 11.59100 0.62700 > H 15.71300 12.39400 1.21800 > O 6.36300 2.83600 1.70800 > H 5.76800 2.19200 2.14400 > H 7.12200 2.37200 1.34000 > O 6.48000 4.72400 -2.02600 > H 7.28300 5.16500 -1.67400 > H 6.79500 4.47200 -2.88700 > O 9.26400 4.47400 4.96600 > H 10.11200 4.92100 4.87600 > H 8.73800 4.83700 4.27100 > O 7.95800 8.51800 -0.08200 > H 7.41300 9.13500 -0.59800 > H 7.21300 7.96700 0.37900 > O 17.39500 15.57300 2.08700 > H 17.75100 14.79100 1.70400 > H 16.64100 15.64300 1.46600 > O 19.42600 8.58500 -3.02100 > H 18.42900 8.43600 -2.97200 > H 19.73800 7.69000 -3.02000 > O 7.18100 10.25100 -1.93600 > H 7.46500 11.12500 -1.66300 > H 7.17900 10.37000 -2.90700 > O 19.38500 14.29700 -4.73800 > H 20.08400 13.67200 -4.48200 > H 19.82100 15.15600 -4.61200 > O 20.05100 16.86200 2.09300 > H 19.24200 16.27200 2.22300 > H 20.57500 16.35700 1.44300 > O 9.97500 3.13200 7.81600 > H 9.14300 2.88700 7.38200 > H 10.54700 2.49200 7.46100 > O 11.41000 16.41500 -1.37000 > H 10.87400 16.75300 -0.58900 > H 10.68500 16.35800 -2.01900 > O 20.06900 3.99400 -0.95700 > H 20.94300 4.19800 -1.40800 > H 20.19100 4.39400 -0.10000 > O 18.21100 15.51800 5.07800 > H 17.86100 14.73700 5.61200 > H 17.71900 15.29600 4.22400 > O 11.02700 15.79200 4.76100 > H 10.47700 15.02100 4.65200 > H 10.40200 16.47300 4.48200 > O 18.93400 4.38800 -5.68000 > H 18.19100 4.81700 -6.18100 > H 19.16200 5.05000 -5.10100 > O 7.75600 15.34000 5.13900 > H 8.01800 16.09900 4.55700 > H 6.77300 15.44400 5.08800 > O 16.54600 12.20900 -1.12000 > H 15.86400 12.57300 -1.73000 > H 16.25600 11.26900 -1.03500 > O 11.70900 3.74900 1.65600 > H 10.85600 3.27300 1.36300 > H 11.48000 4.62700 2.00900 > O 7.20000 2.14900 6.96400 > H 6.98000 2.69600 7.68100 > H 6.68200 2.56400 6.26300 > O 7.06900 15.95700 -5.57800 > H 7.31800 16.87400 -5.34400 > H 6.31300 15.85600 -4.99100 > O 19.65400 11.24000 -2.85500 > H 19.38100 10.30000 -2.97200 > H 20.59000 11.38400 -3.15200 > O 19.61000 6.62200 4.03900 > H 20.38700 6.43900 4.59400 > H 18.92300 6.69700 4.68200 > O 16.74900 8.07700 -2.87100 > H 16.34900 8.32300 -2.02000 > H 16.16200 7.34900 -3.09900 > O 15.14100 5.35900 -2.82400 > H 14.40500 5.56500 -2.26800 > H 15.76900 5.13500 -2.13800 > O 10.73800 1.96700 -4.91100 > H 9.97900 2.60300 -5.10700 > H 10.39600 1.28000 -4.33400 > O 14.48500 5.11800 2.79400 > H 14.57400 4.84300 3.69600 > H 13.57600 5.48800 2.77600 > O 16.28400 9.99400 -4.77600 > H 15.40400 10.28900 -4.36300 > H 16.38900 9.19200 -4.24900 > O 19.87300 5.66000 -3.04400 > H 20.63300 5.45300 -2.44900 > H 19.14200 5.32800 -2.53500 > O 9.16300 7.20900 -5.21800 > H 8.24200 6.87000 -5.07900 > H 8.96900 8.10900 -5.51800 > O 6.36300 8.34000 -7.35300 > H 6.11600 7.57500 -6.83400 > H 7.21200 8.67800 -6.98800 > O 17.56900 4.69200 -1.41800 > H 17.55200 4.65800 -0.42700 > H 18.38500 4.18300 -1.43200 > O 8.02800 7.73600 3.07700 > H 7.90900 6.75400 3.19900 > H 8.93900 7.87500 3.30900 > O 14.17900 10.54700 -3.21900 > H 14.51600 11.35800 -2.79600 > H 13.98800 10.08900 -2.36100 > O 11.22800 9.80100 -7.60400 > H 10.42700 9.40300 -7.95100 > H 11.77200 9.15700 -7.21600 > O 15.11100 0.59900 0.61200 > H 15.24100 1.25600 1.36000 > H 14.17700 0.48500 0.72800 > O 9.38100 11.85300 7.42200 > H 9.48300 12.23300 6.56600 > H 10.12300 11.22500 7.50600 > O 8.86300 14.62200 2.27500 > H 8.03500 14.33700 2.72000 > H 8.63300 15.52400 2.08900 > O 7.52100 1.66400 -1.90700 > H 7.88600 2.50700 -2.19000 > H 7.81900 1.72300 -1.02000 > O 11.52000 16.55300 7.52200 > H 11.03100 15.98100 8.09100 > H 11.54300 16.12100 6.63600 > O 14.08300 5.43100 6.09800 > H 13.47100 5.83700 5.48900 > H 14.00100 6.10400 6.81300 > O 14.38800 13.29500 -5.33900 > H 15.04700 12.89200 -5.92500 > H 13.57700 13.19600 -5.83600 > O 7.62800 5.01000 2.92900 > H 8.27400 5.09600 2.18600 > H 6.91100 4.51600 2.49200 > O 14.25200 2.81000 7.62200 > H 14.37400 2.16300 6.90000 > H 14.23400 3.67900 7.18100 > O 8.88700 8.90800 7.12200 > H 8.54900 9.64000 6.58200 > H 8.80300 8.17000 6.52400 > O 19.22600 11.93300 7.23200 > H 19.80200 11.57000 6.57900 > H 19.70900 11.65100 8.08600 > O 20.72000 2.27900 -5.78800 > H 20.15400 3.07200 -5.70300 > H 21.56000 2.62900 -5.45500 > O 10.59700 13.03100 1.10000 > H 10.80200 13.31800 0.17000 > H 10.02100 13.68100 1.51900 > O 20.37700 4.70200 1.56100 > H 19.97200 4.28200 2.28000 > H 21.05700 4.07800 1.40500 > O 14.26100 3.74800 -0.25400 > H 13.80100 3.56600 0.58000 > H 13.95100 4.65000 -0.55400 > O 16.94800 2.08300 -5.37100 > H 17.19700 1.89800 -6.29600 > H 17.78200 2.45000 -5.04900 > O 21.70600 9.70100 2.86400 > H 21.35000 9.66200 1.94600 > H 21.98200 8.74200 2.90500 > O 17.01100 9.61800 5.27500 > H 16.97200 9.42600 6.19500 > H 16.21200 9.14200 5.03200 > O 19.35300 12.54800 3.88900 > H 19.66400 12.60900 4.81200 > H 19.54300 11.59600 3.69600 > O 14.67800 11.55100 4.17400 > H 14.03800 12.18100 4.46400 > H 14.70600 11.83100 3.23600 > O 17.10600 13.31600 6.16400 > H 17.65300 12.84900 6.83400 > H 16.68200 12.55300 5.71100 > O 14.97300 8.09200 4.90100 > H 14.70000 7.17400 4.82900 > H 14.50200 8.38000 5.69800 > O 16.69500 5.81800 -6.50800 > H 16.04800 6.50500 -6.35900 > H 16.54200 5.54600 -7.44400 > O 17.86600 12.11900 1.87300 > H 17.85000 11.12600 1.92400 > H 18.10200 12.33400 2.82400 > O 9.42000 16.15500 -3.13800 > H 8.62000 16.59200 -2.85400 > H 9.05300 15.39400 -3.65300 > O 16.67900 4.76800 6.87000 > H 15.81100 5.00000 6.53700 > H 16.79100 3.83500 6.57500 > O 11.27800 6.86100 7.40800 > H 11.40500 6.83800 6.41900 > H 12.07800 7.38500 7.71500 > O 17.29000 13.48900 -6.16800 > H 17.86400 13.94800 -5.47300 > H 17.09100 14.13600 -6.80000 > O 18.72000 6.45600 6.83300 > H 18.11800 5.75500 6.60100 > H 18.08000 7.17200 7.06100 > O 21.29200 6.60700 6.37900 > H 21.67800 7.39200 6.83600 > H 20.46900 6.66100 6.74400 > O 14.65300 13.18600 -2.72500 > H 14.71000 14.16700 -2.66200 > H 14.54600 12.97300 -3.65400 > O 9.61600 14.78700 -7.38700 > H 9.38300 14.47300 -6.48100 > H 10.00500 13.92800 -7.68700 > O 20.83200 16.12800 -7.53900 > H 20.88000 16.78200 -6.78600 > H 20.57300 15.32500 -7.03200 > O 8.60800 9.89500 -5.72600 > H 9.13500 10.42000 -6.20300 > H 8.15100 10.65200 -5.34600 > O 7.94300 10.40600 4.97600 > H 7.45300 9.79100 4.38600 > H 8.73800 10.62600 4.46900 > O 18.42500 7.03200 1.54100 > H 18.76200 6.76400 2.41400 > H 18.09600 6.14700 1.23600 > O 9.03400 5.45100 -2.08600 > H 9.49900 6.25800 -2.27600 > H 9.77500 4.82000 -2.12600 > O 22.09400 6.67900 -5.17300 > H 22.31900 5.76400 -5.05700 > H 21.37400 6.71100 -4.49700 > O 6.80600 13.06000 -7.81500 > H 7.60700 12.47300 -7.86800 > H 6.45000 13.04400 -6.91000 > O 18.91500 9.76600 3.46300 > H 18.78500 8.94000 2.95000 > H 18.20200 9.71400 4.17600 > O 11.11700 9.84400 -1.48600 > H 10.59600 9.18700 -1.87900 > H 11.93700 9.34700 -1.30500 > O 20.15700 10.51900 -6.38200 > H 20.67300 10.95900 -5.67700 > H 20.77400 9.91700 -6.84900 > O 20.88400 15.90900 5.48100 > H 20.69900 16.11000 6.41000 > H 19.95200 15.84500 5.21100 > O 13.09900 6.04400 -0.94600 > H 13.10200 7.01300 -0.70100 > H 12.16600 5.86600 -1.18000 > O 20.90700 10.03800 -0.11900 > H 21.58200 10.21700 -0.77000 > H 20.61100 9.14300 -0.36200 > O 7.77700 5.74600 7.41500 > H 6.91700 6.17700 7.38400 > H 7.79500 5.29800 6.55300 > O 9.20300 5.50700 0.75600 > H 8.88800 6.20600 0.13000 > H 9.42300 4.75100 0.20200 > O 21.46200 15.92200 -3.04600 > H 21.03900 15.37300 -2.34300 > H 21.97700 16.48500 -2.46700 > &END COORD > &KIND H > BASIS_SET TZV2P-GTH > POTENTIAL GTH-BLYP-q1 > &END KIND > &KIND O > BASIS_SET TZV2P-GTH > POTENTIAL GTH-BLYP-q6 > &END KIND > &KIND C > BASIS_SET TZV2P-GTH > POTENTIAL GTH-BLYP-q4 > &END KIND > &KIND Na > BASIS_SET TZV2P-GTH > POTENTIAL GTH-BLYP-q9 > &END KIND > &KIND Cl > BASIS_SET TZV2P-GTH > POTENTIAL GTH-BLYP-q7 > &END KIND > > > &END SUBSYS > &PRINT > &FORCES SILENT > FILENAME =Frc_nvt_1.dat > &END FORCES > &END PRINT > &END FORCE_EVAL > > > Is there any idea about this error? I'm really appreciated. > > Thanks, > Xiaoliu > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From taosun... at gmail.com Fri May 26 02:48:25 2017 From: taosun... at gmail.com (Sun Tao) Date: Thu, 25 May 2017 19:48:25 -0700 (PDT) Subject: confusion about QM/MM setup in CP2k In-Reply-To: <6e81e560-704b-4bea-bbf9-f3142f813a0e@googlegroups.com> References: <988d807c-e79f-414f-a380-ecb8b3833088@googlegroups.com> <6e81e560-704b-4bea-bbf9-f3142f813a0e@googlegroups.com> Message-ID: <870e5215-dee6-40bf-82f1-27ea922cb2aa@googlegroups.com> Dear Matt: Thanks very much for your help! I checked the 2 papers, here is my understanding. The 2005 paper about QM/MM electrostatic coupling does allow MM atoms to be inside the QM box. I guess the QM box setup in CP2K is just to apply the scheme in the 2006 paper to calculate the electrostatic interaction within periodic boundary condition. I have some more questions: 1. Does the size of the QM box affect the simulation speed a lot? I could just set up the QM box to be the same as the overall system box, then specify some important part to be treated in QM fasion while other atoms in MM. Is it necessary to set up a smaller QM box? 2. If I set up a smaller QM box, the the box boundary cuts through a covalent bond, do I need to cap the dangling bond with hydrogen atoms as what is usually done for QM/MM? 3. Inside a QM box, for example there is a covalent bond A-B. Now I set atom A to be treated in QM, while atom B to be treated in MM, does this seem to be a correct way? Further more the covalent bond A-B is actually within a piece of solid, and the solid is kept fixed (does not move). Thanks again for your help! Tao ? 2017?5?25???? UTC-5??4:25:27?Matt W??? > > Hi Tao, > > The boxes are used essentially for electrostatic calculations. The > interface between the QM and MM atoms is the real region where they > connect, not really anything to do with the cells. > > You should see a list of relevant references at the end of the output file > - there are two particular to CP2K by Laio and co-workers that you should > try and read. > > Matt > > On Thursday, May 25, 2017 at 6:09:31 PM UTC+1, Sun Tao wrote: >> >> Dear experts: >> >> I am confused about some settings of the QMMM portion of CP2K. In the >> section QMMM/CELL we need to set up the QM region. Then in QMMM/QM_KIND >> section, there is a keyword MM_INDEX, for which my understanding is to tell >> the program the index of the MM atoms that would be treated in QM fashion. >> >> Here is the question: does CP2K allow MM atoms inside QM regions? Or say >> in the QM region some atoms could be treated in QM and others could still >> be treated in MM? If CP2K does allow this, how do these two different kinds >> of atoms (QM atoms and MM atoms) interact with each other inside the QM >> box? Is there any papers/books I could refer to if this is the case? Before >> I only know that the coupling happens between QM region and MM region and >> the boundary between QM and MM is important to treat. >> >> Thanks very much for your help. Look forward to your reply! >> >> Tao >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Fri May 26 07:41:46 2017 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Fri, 26 May 2017 09:41:46 +0200 Subject: [CP2K:9028] MD RESTART WITH EXTERNAL TRAJECTORY In-Reply-To: <43c2ad1a-8c4b-41a7-b209-ceca2ec2c0db@googlegroups.com> References: <43c2ad1a-8c4b-41a7-b209-ceca2ec2c0db@googlegroups.com> Message-ID: Hi maybe CP2K_INPUT / MOTION / MD / REFTRAJ / FIRST_SNAPSHOT helps. 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: Kamil Sent by: cp... at googlegroups.com Date: 05/24/2017 07:03PM Subject: [CP2K:9028] MD RESTART WITH EXTERNAL TRAJECTORY Dear All, I have a question on restarting MD simulations for external trajectory calculations. 1.) I have an external trajectory in xyz format.2.) I want to recalculate wannier centers, so I use REFTRAJ and it works well.? The problems is due to the time limits in the queue system at the computer centre. Let's say that my calculations end at the step no 1499. 3.) Is it possible to restart the MD calculations for the frame no. 1500 from my external xyz trajectory? Each time when I try to do it CP2K comes back to the first frame. 4.) Should I delete all the frames up to 1500 manually and ask CP2K to start REFTRAJ again? I would really appreciate your kind help! All the best,Kamil -- 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 mattwa... at gmail.com Fri May 26 23:07:40 2017 From: mattwa... at gmail.com (Matt W) Date: Fri, 26 May 2017 16:07:40 -0700 (PDT) Subject: confusion about QM/MM setup in CP2k In-Reply-To: <870e5215-dee6-40bf-82f1-27ea922cb2aa@googlegroups.com> References: <988d807c-e79f-414f-a380-ecb8b3833088@googlegroups.com> <6e81e560-704b-4bea-bbf9-f3142f813a0e@googlegroups.com> <870e5215-dee6-40bf-82f1-27ea922cb2aa@googlegroups.com> Message-ID: > > > Thanks very much for your help! I checked the 2 papers, here is my > understanding. The 2005 paper about QM/MM electrostatic coupling does allow > MM atoms to be inside the QM box. I guess the QM box setup in CP2K is just > to apply the scheme in the 2006 paper to calculate the electrostatic > interaction within periodic boundary condition. I have some more questions: > > 1. Does the size of the QM box affect the simulation speed a lot? I could > just set up the QM box to be the same as the overall system box, then > specify some important part to be treated in QM fasion while other atoms in > MM. Is it necessary to set up a smaller QM box? > > Depends on the size/density of your system, for various reasons. You might pay quite a lot for empty space using CP2K in a small system, but negligible for a larger one. > 2. If I set up a smaller QM box, the the box boundary cuts through a > covalent bond, do I need to cap the dangling bond with hydrogen atoms as > what is usually done for QM/MM? > > Yes, you'd need to cap the dangling bonds, entirely as you'd expect. > 3. Inside a QM box, for example there is a covalent bond A-B. Now I set > atom A to be treated in QM, while atom B to be treated in MM, does this > seem to be a correct way? Further more the covalent bond A-B is actually > within a piece of solid, and the solid is kept fixed (does not move). > > As long as you have some forcefield that can describe the interaction. Again, the boxes are pretty much for electrostatics, what really matters is whether there are changes in the bonding of the system. > Thanks again for your help! > > Tao > > ? 2017?5?25???? UTC-5??4:25:27?Matt W??? >> >> Hi Tao, >> >> The boxes are used essentially for electrostatic calculations. The >> interface between the QM and MM atoms is the real region where they >> connect, not really anything to do with the cells. >> >> You should see a list of relevant references at the end of the output >> file - there are two particular to CP2K by Laio and co-workers that you >> should try and read. >> >> Matt >> >> On Thursday, May 25, 2017 at 6:09:31 PM UTC+1, Sun Tao wrote: >>> >>> Dear experts: >>> >>> I am confused about some settings of the QMMM portion of CP2K. In the >>> section QMMM/CELL we need to set up the QM region. Then in QMMM/QM_KIND >>> section, there is a keyword MM_INDEX, for which my understanding is to tell >>> the program the index of the MM atoms that would be treated in QM fashion. >>> >>> Here is the question: does CP2K allow MM atoms inside QM regions? Or say >>> in the QM region some atoms could be treated in QM and others could still >>> be treated in MM? If CP2K does allow this, how do these two different kinds >>> of atoms (QM atoms and MM atoms) interact with each other inside the QM >>> box? Is there any papers/books I could refer to if this is the case? Before >>> I only know that the coupling happens between QM region and MM region and >>> the boundary between QM and MM is important to treat. >>> >>> Thanks very much for your help. Look forward to your reply! >>> >>> Tao >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From yakut... at gmail.com Sun May 28 18:36:25 2017 From: yakut... at gmail.com (yakutovich) Date: Sun, 28 May 2017 11:36:25 -0700 (PDT) Subject: vibrational analysis problem Message-ID: <55d30b33-4813-4b32-9b68-5e9787cec611@googlegroups.com> Dear all, I was trying to perform Vibrational Analysis for my system containing 590 atoms. &VIBRATIONAL_ANALYSIS DX [bohr] 0.04 NPROC_REP 288 FULLY_PERIODIC .TRUE. INTENSITIES .TRUE. &PRINT &PROGRAM_RUN_INFO &END &MOLDEN_VIB FILENAME MOLVIB &END &END PRINT &END VIBRATIONAL_ANALYSIS For this calculation I fixed 324 atoms and let the other 266 to be optimized. &CONSTRAINT &FIXED_ATOMS LIST 1..324 &END FIXED_ATOMS &END CONSTRAINT However instead of 266*6 SCF cycles that I expected cp2k did more than 2500: > grep "SCF WAVEFUNCTION OPTIMIZATION" *-r-*.out | wc -l 2520 At some point the execution reached the WALLTIME 86000 and stopped. What surprised me again that cp2k was still able to compute the normal modes. *So my first question would be: can I trust the results of these calculations, taking into account that the last SCF cycles did not converge due to the time limit?* In order to narrow down the problem I updated cp2k to the latest trunk version(svn:17932). Then I took a water molecule and slightly simplified the VIBRATIONAL_ANALYSIS section. Then I did the same calculations using 1 and 2 replicas. It turned out that in the first case cp2k did 19 scf cycles, while in the second case 24. *So my second question: what cp2k is doing? is it a bug?**1 replica:* VIB_no_intens_1replica> grep "SCF WAVEFUNCTION OPTIMIZATION" *-r-*.out | wc -l 19 VIB_no_intens_1replica> grep "VIB| REPLI" out | wc -l 18 *2 replicas:* ....VIB_no_intens_2replicas> grep "VIB| REPLI" out | wc -l 18 ....VIB_no_intens_2replicas> grep "SCF WAVEFUNCTION OPTIMIZATION" *-r-*.out | wc -l 24 I attached the compressed running directories for the both water cases. I would appreciate any help. Best regards, Sasha -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VIB_no_intens_1replica.tar.gz Type: application/octet-stream Size: 27895 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: VIB_no_intens_2replicas.tar.gz Type: application/octet-stream Size: 37171 bytes Desc: not available URL: From liufe... at gmail.com Mon May 29 10:54:17 2017 From: liufe... at gmail.com (feihu liu) Date: Mon, 29 May 2017 03:54:17 -0700 (PDT) Subject: Density of States In-Reply-To: <1a96b31e-126c-47ee-8ac2-1dd90c3546ec@googlegroups.com> References: <34207dbe-0a3e-4353-9938-ff15772c9aab@googlegroups.com> <988e28d8-3b38-40ec-912b-5f8f470854a9@googlegroups.com> <815a0728-5251-4450-964f-0a55aa92adfa@googlegroups.com> <1a96b31e-126c-47ee-8ac2-1dd90c3546ec@googlegroups.com> Message-ID: Dear Rizwan, I have a similar files with PDOS obtained from cp2k and I don't know how to plot the figure of total DOS and PDOS vs energy. When I use gnuplot, the figure looks very sharp and different with other paper. Would you please suggest me how can I make plot clear and broad? Bests, Feihu ? 2017?3?29???? UTC+8??1:23:27?Rizwan Nabi??? > Dear Yeliz, > Sorry for late response as I was out of the station. Well, I have got the > density of states file but I am not able to get DOS plot similar to that of > already reported in the literature. Would you please suggest me what to do > next? > I also tried with xmgrace visualization software but there seems to be > something wrong with my plot. > I am attaching all the DOS files generated so far, please have a look into > them as for suggesting me what to do. > > > > Regards, > Rizwan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From liufe... at gmail.com Mon May 29 12:04:22 2017 From: liufe... at gmail.com (feihu liu) Date: Mon, 29 May 2017 05:04:22 -0700 (PDT) Subject: How to plot the PDOS In-Reply-To: References: Message-ID: Dear zhendong, I have problems with plotting total DOS and PDOS vs energy. When I load these files(***.pdos) in gnuplot, the figure looks more sharp. Would you please suggest me some possible solution to the said problem, or send me a script-copy if you have one. Bests, Feihu ? 2014?12?10???? UTC+8??5:59:55?Zhendong Guo??? > Dear everyone > I am trying to plot the PDOS of k-Al2O3 > The data I obtained is like this: > # Projected DOS for atomic kind O at iteration step i = 0, E(Fermi) = > 0.228779 a.u. > # MO Eigenvalue [a.u.] Occupation s > py pz px d-2 d-1 > d0 d+1 d+2 > 1 -0.489755 2.000000 0.39864421 > 0.00163451 0.00326415 0.00061696 0.00012282 > 0.00063476 0.00034816 0.00025051 0.00004675 > 2 -0.473240 2.000000 0.40112298 > 0.00723859 0.01714149 0.00081273 0.00010593 > 0.00015517 0.00103264 0.00002880 0.00016156 > 3 -0.465338 2.000000 0.43898799 > 0.00262348 0.00229986 0.01454316 0.00032186 > 0.00058974 0.00054649 0.00054823 0.00068624 > 4 -0.465285 2.000000 0.43909059 > 0.00259368 0.00226564 0.01450073 0.00032261 > 0.00058742 0.00054645 0.00054664 0.00068993 > 5 -0.454790 2.000000 0.46843306 > 0.01670187 0.00153007 0.00185108 0.00016259 > 0.00062377 0.00057248 0.00037747 0.00115138 > 6 -0.453047 2.000000 0.45968147 > 0.00496059 0.01042395 0.00918352 0.00071160 > 0.00032444 0.00037362 0.00092499 0.00046849 > ... > ... > So Could you let me know How can I use this data to plot the PDOS for the > 2s of Oxygen ? > If you have the script to do this, Could you send me one copy? > Best regards. > zhendong > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhj... at gmail.com Tue May 30 13:09:52 2017 From: zhj... at gmail.com (zhj... at gmail.com) Date: Tue, 30 May 2017 06:09:52 -0700 (PDT) Subject: How to plot the PDOS In-Reply-To: References: Message-ID: Hi, I have two files that can obtain the data to plot dos. You can execute like this: [user]# *python get-smearing-pdos.py pdos_file-k1-1.pdos* This will generate a 'smeared.txt' file and you can use this file to plot dos. You can change the value ' *ww=0.09 *' in *python get-smearing-pdos.py* to obtain an appropriate data. ? 2014?12?10???? UTC+8??5:59:55?Zhendong Guo??? > > Dear everyone > I am trying to plot the PDOS of k-Al2O3 > The data I obtained is like this: > # Projected DOS for atomic kind O at iteration step i = 0, E(Fermi) = > 0.228779 a.u. > # MO Eigenvalue [a.u.] Occupation s > py pz px d-2 d-1 > d0 d+1 d+2 > 1 -0.489755 2.000000 0.39864421 > 0.00163451 0.00326415 0.00061696 0.00012282 > 0.00063476 0.00034816 0.00025051 0.00004675 > 2 -0.473240 2.000000 0.40112298 > 0.00723859 0.01714149 0.00081273 0.00010593 > 0.00015517 0.00103264 0.00002880 0.00016156 > 3 -0.465338 2.000000 0.43898799 > 0.00262348 0.00229986 0.01454316 0.00032186 > 0.00058974 0.00054649 0.00054823 0.00068624 > 4 -0.465285 2.000000 0.43909059 > 0.00259368 0.00226564 0.01450073 0.00032261 > 0.00058742 0.00054645 0.00054664 0.00068993 > 5 -0.454790 2.000000 0.46843306 > 0.01670187 0.00153007 0.00185108 0.00016259 > 0.00062377 0.00057248 0.00037747 0.00115138 > 6 -0.453047 2.000000 0.45968147 > 0.00496059 0.01042395 0.00918352 0.00071160 > 0.00032444 0.00037362 0.00092499 0.00046849 > ... > ... > So Could you let me know How can I use this data to plot the PDOS for the > 2s of Oxygen ? > If you have the script to do this, Could you send me one copy? > Best regards. > zhendong > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pdos.py Type: text/x-python Size: 3653 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: get-smearing-pdos.py Type: text/x-python Size: 1948 bytes Desc: not available URL: From g7792... at gmail.com Wed May 31 08:36:11 2017 From: g7792... at gmail.com (=?UTF-8?B?6YOt6IOc5by6?=) Date: Wed, 31 May 2017 01:36:11 -0700 (PDT) Subject: Nanostructures and adsorption on metallic surfaces Message-ID: Dear experts: https://www.cp2k.org/exercises:2015_cecam_tutorial:neb#refnotes:1:note3 I'm learning this exercises and I have a lot of problems. &NONBONDED &GENPOT atoms Cu C FUNCTION A*exp(-av*r)+B*exp(-ac*r)-C/(r^6) VARIABLES r PARAMETERS A av B ac C VALUES 4.13643 1.33747 115.82004 2.206825 75.40708524085266692113 RCUT 15 &END GENPOT VALUES 4.13643 1.33747 115.82004 2.206825 75.40708524085266692113 How are these parameters set? Where can I find it? &LENNARD-JONES atoms C H EPSILON 0.0 SIGMA 3.166 RCUT 15 &END LENNARD-JONES SIGMA 3.166 How are these parameters set? Where can I find it? &EAM atoms Cu Cu PARM_FILE_NAME ../../Files/CU.pot &END EAM CU.pot 29 63.550 3.6030 0.9981995681300759E-03 0.5001000317861326E-04 0.4949999809265137E+01 5000 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 What's in the document? What's the meaning of these numbers? Thanks very much for your help. Look forward to your reply! Shengqiang -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: CU.pot Type: application/vnd.ms-powerpoint Size: 1560149 bytes Desc: not available URL: