From mayan... at gmail.com Mon Jun 1 05:01:17 2020 From: mayan... at gmail.com (Mayank Dodia) Date: Sun, 31 May 2020 22:01:17 -0700 (PDT) Subject: [CP2K-user] Bond sequences error Message-ID: <398f3bb5-93c8-458e-bb47-2cd1de56873c@googlegroups.com> Hi, Has anyone experienced this sort of error? ******************************************************************************* * ___ * * / \ * * [ABORT] different sequence of bonds for same molecule kind molecule type = * * \___/ 1 molecule number= 634 NOT FOUND! Check the connectivity of * * | your system. * * O/| * * /| | * * / \ topology_util.F:1117 * ******************************************************************************* ===== Routine Calling Stack ===== 4 topology_molecules_check 3 connectivity_control 2 topology_control 1 CP2K application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor I was running a QMMM file and this failure occurred after a restarted calculation which ran without any issues before. I tried rerunning the calculation by simplifying it to plain MM input with just solvent water molecules, without success, and I am not really sure where the error is. Can someone help me understand what exactly the error is and how should I resolve it? Best Regards, MayankDodia -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: test.inp Type: chemical/x-gamess-input Size: 703931 bytes Desc: not available URL: From fsai... at gmail.com Mon Jun 1 08:54:26 2020 From: fsai... at gmail.com (Fernan Saiz) Date: Mon, 1 Jun 2020 01:54:26 -0700 (PDT) Subject: [CP2K-user] contribution of atomic orbitals to molecular orbitals Message-ID: Dear all, I would like to know if CP2k can print the contribution of every atomic orbital to each molecular orbital in a given system. Plotting molecular orbitals in cube files can give a qualitatively idea if electrons are localised, but it can be inaccurate if these particles are delocalised in condensed systems. From the manual, it might look like MAO might be able to do this job. Best regards, - Fernan Saiz, PhD Marie Sk?odowska-Curie individual fellow Institut de Ci?ncia de Materials de Barcelona (ICMAB) Spanish National Research Council (CSIC) Campus de la UAB Bellaterra, 08193, Spain -------------- next part -------------- An HTML attachment was scrubbed... URL: From suns... at gmail.com Mon Jun 1 12:19:36 2020 From: suns... at gmail.com (shixun sun) Date: Mon, 1 Jun 2020 05:19:36 -0700 (PDT) Subject: [CP2K-user] questions about section of bsse input Message-ID: Dear CP2K communities, I search the google group for BSSE problems and found the inp of BSSE(OH-H2O) in the data dictionary under the guidance. and I attached it with this letter. There are somethings that still confused me. 1. As for the system of OH-H2O which already demonstrated by the developer of CP2K, the configurations are four. but in the input, it's only 2 fragments. And I was confused with the GLB_CONF (1 0) and SUB_CONF 1 0, Could someone explain the meanings of 1 and 0 in the glb_conf for me? And what's the rule to set 1 and 0 in the glb_conf and sub_conf and the quantity of configuration part? 2. the OH seems to be charged when importing the coordination into some visualized software. But in the input, they all 0. And the OH seems to have odd electrons but in the multiplicity they all 2. &CONFIGURATION GLB_CONF 1 0 SUB_CONF 1 0 CHARGE 0 MULTIPLICITY 2 &END &CONFIGURATION GLB_CONF 1 1 SUB_CONF 1 0 CHARGE 0 MULTIPLICITY 2 &END &CONFIGURATION GLB_CONF 1 1 SUB_CONF 0 1 CHARGE 0 MULTIPLICITY 0 &END &CONFIGURATION GLB_CONF 1 1 SUB_CONF 1 1 CHARGE 0 MULTIPLICITY 2 Can anyone help me? Any answer will be appreciated Millions of thanks for your reply??? BEST -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: OH-H2O-bsse.inp Type: chemical/x-gamess-input Size: 1889 bytes Desc: not available URL: From maxime.cp.... at gmail.com Tue Jun 2 08:49:43 2020 From: maxime.cp.... at gmail.com (Maxime Van den Bossche) Date: Tue, 2 Jun 2020 01:49:43 -0700 (PDT) Subject: [CP2K-user] Memory usage in hybrid DFT calculations Message-ID: <75628087-7b70-4e74-8fca-b6f396908315@googlegroups.com> Dear CP2K developers, I have started to benchmark CP2K on our clusters, and there are a few things that I don't fully understand about the memory consumption of hybrid DFT calculations. 1. What needs to be considered in setting MAX_MEMORY , so as to use as much RAM as possible? MAX_MEMORY being the maximal amount of memory per MPI rank, in MiB, that the HFX module is allowed to use. At first, I thought it would simply involve dividing the amount of RAM per (multi-core) compute node by the number of MPI ranks per node, and then subtracting a modest amount that will be needed by the rest of the program. In the attached down-scaled version of the LiH-HFX benchmark, for example, the GGA prerun on a 28-core node utilizes circa 250 MiB per MPI rank. In a subsequent HFX calculation on the same node with MAX_MEMORY = 1500 MiB, the HFX module uses all of its allowed memory, which is fine. But the job's total memory usage amounts to around 3000 MiB per MPI rank, as given by CP2K's "max memory usage/rank" output and a check with "htop". This is quite larger than the 1500+250=1750 MiB per MPI rank that I naively expected. So is there a more sophisticated "rule of thumb" for predicting the total memory usage? Or is this not even how CP2K is supposed to behave? 2. What should I expect from using multiple OpenMP threads per MPI rank in terms of memory consumption? Suppose that MAX_MEMORY is such that 50% of the ERIs cannot be stored and need to be (re)calculated on-the-fly, for OMP_NUM_THREADS=1. Suppose then that I set OMP_NUM_THREADS=2, use half the number of MPI ranks, and double the MAX_MEMORY, to arrive at the same memory usage by the HFX module. Should this then allow all ERIs to be stored in memory? Best, Maxime -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: inputs.zip Type: application/zip Size: 5419481 bytes Desc: not available URL: From rybk... at gmail.com Tue Jun 2 11:53:07 2020 From: rybk... at gmail.com (Vladimir Rybkin) Date: Tue, 2 Jun 2020 04:53:07 -0700 (PDT) Subject: [CP2K-user] contribution of atomic orbitals to molecular orbitals In-Reply-To: References: Message-ID: <78e618ca-2a57-4c39-ae69-86b318f18718@googlegroups.com> Dear Fernan, the MO coefficients - that's what you ask for - are huge matrices. Looking at them will barely give you an idea of the degree of localisation. So, if you want local orbitals, you can do MAO, or else, you can do Wannier localization. Electron localisation function can be an option as well. It depends on what exactly you want. Yours, Vladimir ???????????, 1 ???? 2020 ?., 10:54:26 UTC+2 ???????????? Fernan Saiz ???????: > > Dear all, > I would like to know if CP2k can print the contribution of every atomic > orbital to each molecular orbital in a given system. Plotting molecular > orbitals in cube files can give a qualitatively idea if electrons are > localised, but it can be inaccurate if these particles are delocalised in > condensed systems. From the manual, it might look like MAO might be able to > do this job. > > > Best regards, > - Fernan Saiz, PhD > Marie Sk?odowska-Curie individual fellow > Institut de Ci?ncia de Materials de Barcelona (ICMAB) > Spanish National Research Council (CSIC) > Campus de la UAB > Bellaterra, 08193, Spain > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eluni... at gmail.com Wed Jun 3 01:00:09 2020 From: eluni... at gmail.com (Lucas Lodeiro) Date: Tue, 2 Jun 2020 21:00:09 -0400 Subject: [CP2K-user] FFT PLANNING Message-ID: Hello, I am running water box AIMD in CP2K 7.0. I read about the FFT plan routine to accelerate the calculation about 10-15% using the following commands. FFTW_PLAN_TYPE EXHAUSTIVE FFTW_WISDOM_FILE_NAME WISDOM.dat I probe using EXHAUSTIVE, MEASURE, PATIENT, and ESTIMATE... but in all cases the speed up is the same. MEASURE is the only slower case. Also the WISDOM.dat file does not appear in the calculation folder. Somebody can give me some advices about that? Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From janel... at gmail.com Wed Jun 3 12:46:06 2020 From: janel... at gmail.com (Jan Elsner) Date: Wed, 3 Jun 2020 05:46:06 -0700 (PDT) Subject: [CP2K-user] Problem with large CUTOFFs for non-local vdW functionals Message-ID: <61ad6acc-bede-4c61-9cb8-127d49d0c823@googlegroups.com> Dear all, When I try to use a large CUTOFF (MGRID section) with non-local vdW functionals (I have tried optPBE, optB88 and vdW-DF2), the program seems unable to calculate the vdW energy and I get a CPASSERT failed error. For my particular system (periodic rubrene molecular crystal), the program runs fine with CUTOFF 1100 Ry, but fails for CUTOFF 1200 Ry. I note that the CUTOFF at which the program crashes is cell-size dependent e.g. if I use a smaller CELL_REF (or no CELL_REF), I can go to higher CUTOFFs before the program crashes. I attach input and output files using optPBE for the cases: (i) CUTOFF 1100 Ry, run succeeds and (ii) CUTOFF 1200 Ry, run fails. It would be great to know why these functionals cannot cope with large CUTOFFs. Best wishes, Jan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: fail-cutoff-1200.inp Type: chemical/x-gamess-input Size: 1767 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: fail-cutoff-1200.out Type: application/octet-stream Size: 69971 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: subsys.include Type: application/octet-stream Size: 23612 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: success-cutoff-1100.inp Type: chemical/x-gamess-input Size: 1767 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: success-cutoff-1100.out Type: application/octet-stream Size: 128202 bytes Desc: not available URL: From hut... at chem.uzh.ch Wed Jun 3 12:57:00 2020 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Wed, 3 Jun 2020 14:57:00 +0200 Subject: [CP2K-user] [CP2K:13438] Problem with large CUTOFFs for non-local vdW functionals In-Reply-To: <61ad6acc-bede-4c61-9cb8-127d49d0c823@googlegroups.com> References: <61ad6acc-bede-4c61-9cb8-127d49d0c823@googlegroups.com> Message-ID: Hi Nonlocal vdW functionals make use of the precomputed kernel table. This table was calculated with a maximum cutoff and this is checked in CP2K to avoid unphysical extrapolation. If you need such high cutoffs, you have to generate another kernel file. This is a file that was generated from Quantum Espresso. regards Juerg Hutter -------------------------------------------------------------- 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: "Jan Elsner" Sent by: cp... at googlegroups.com Date: 06/03/2020 02:46PM Subject: [CP2K:13438] Problem with large CUTOFFs for non-local vdW functionals Dear all, When I try to use a large CUTOFF (MGRID section) with non-local vdW functionals (I have tried optPBE, optB88 and vdW-DF2), the program seems unable to calculate the vdW energy and I get a CPASSERT failed error. For my particular system (periodic rubrene molecular crystal), the program runs fine with CUTOFF 1100 Ry, but fails for CUTOFF 1200 Ry. I note that the CUTOFF at which the program crashes is cell-size dependent e.g. if I use a smaller CELL_REF (or no CELL_REF), I can go to higher CUTOFFs before the program crashes. I attach input and output files using optPBE for the cases: (i) CUTOFF 1100 Ry, run succeeds and (ii) CUTOFF 1200 Ry, run fails. It would be great to know why these functionals cannot cope with large CUTOFFs. Best wishes, Jan -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/61ad6acc-bede-4c61-9cb8-127d49d0c823%40googlegroups.com. [attachment "fail-cutoff-1200.inp" removed by J?rg Hutter/at/UZH] [attachment "fail-cutoff-1200.out" removed by J?rg Hutter/at/UZH] [attachment "subsys.include" removed by J?rg Hutter/at/UZH] [attachment "success-cutoff-1100.inp" removed by J?rg Hutter/at/UZH] [attachment "success-cutoff-1100.out" removed by J?rg Hutter/at/UZH] From dev.... at gmail.com Wed Jun 3 14:15:12 2020 From: dev.... at gmail.com (Dev Rana) Date: Wed, 3 Jun 2020 07:15:12 -0700 (PDT) Subject: [CP2K-user] [CP2K:13327] SCCS Solvation Model Implementation - Molecule Radii Explodes In-Reply-To: References: <551872ac-a740-47b3-ac9c-5cea80d803ec@googlegroups.com> <7a4d3962-41cd-475c-9a0f-79c9ffa59b7f@googlegroups.com> <99722c46-cf0e-427f-a7f5-bd6eba017cd3@googlegroups.com> Message-ID: <9dcf8abb-1318-4c6a-ac5c-0727be6f9ca3@googlegroups.com> Hi Matthias, Thank you for your help! I was able to go to 200 without it crashing. My rationale for going above 100+ is that in the COSMO model the dielectric constant has a range that goes towards infinity because of metals. A dielectric constant of 80, is good for water but does not accurately represent an infinity model which COSMO does for metals. But I'm pushing forward with the capabilities that we have with CP2K, as I do not have access to the COSMO model. Best Regards, Dev On Monday, May 18, 2020 at 2:52:54 AM UTC-4, Matthias Krack wrote: > > Hi Dev > > > > Never tried such large dielectric constants of 100-1000. Values much > larger than 80 for a solvent seem to me unusual. > > > > Matthias > > > > *From:* c... at googlegroups.com > *On Behalf Of *Dev Rana > *Sent:* Sonntag, 17. Mai 2020 18:02 > *To:* cp2k > > *Subject:* Re: [CP2K:13327] SCCS Solvation Model Implementation - > Molecule Radii Explodes > > > > Hi Matthias, > > > > Thank you so much! This worked. However, when I go beyond a dieletric > constant of 300 i.e. 300, 400, 500, 1000+, with no other changes to the > input file. The convergence starts to go beyond 1 again. Do you have a > reference that might help me understand what input parameters I should be > using to offset my changing conditions? I'm going to try and print a cube > file as you suggested and visualize it in VMD, I'm assuming with the newer > higher dieletric constants the surface might be too close to the molecule > and I will have to change my rho min/max to adjust for it. however I'm not > sure by how much and I hate to keep troubling you. > > > > Best Regards, > > Dev > > On Friday, May 15, 2020 at 1:16:45 PM UTC-4, Matthias Krack wrote: > > Hi Dev > > > > The attached revised input converged after a few steps using SCCS with a > dielectric constant of 80. I changed the method and adapted the rho_min and > rho_max values which define the surface of the cavity and thus they are > system dependent to some extent. If rho_max is chosen too large for > instance, the surface might be too close to the molecule. It is often > helpful to plot the cavity, e.g. with VMD, using a cube file dump of the dielectric > function > > . > > HTH > > > > Matthias > > > > *From:* c... at googlegroups.com *On Behalf Of *Dev > Rana > *Sent:* Freitag, 15. Mai 2020 17:47 > *To:* cp2k > *Subject:* Re: [CP2K:13314] SCCS Solvation Model Implementation - > Molecule Radii Explodes > > > > Hi Matthias, > > > > Thank you again for all your help. I went a bit beyond your suggestion and > changed EPS_SCF to 1E-12 and changed cell size to 10 x 10 x 10 A3. To > answer your questions: > > > > 1.) I was able to run GEO_OPT without SCCS and the simulation completed. > > 2.) I was able to converge and complete a SCCS GEO_OPT simulation with a > dielectric constant of 1. > > > > I then took the dieletric constant back up to 80 (with no other changes), > and the convergence fails - in fact the convergence Hartree's are trending > greater than 1. > > > > I'm going to do a small ramp up in dielectric constant: 2, 5, 10, etc. To > see what happens. But I should be able to use 80+ as the dielectric > constant without issues. > > > > What do you think? Am I missing something? > > > > Again input, output, and XYZ attached. > > > > &GLOBAL > > PROJECT SCCS > > RUN_TYPE geo_opt > > PRINT_LEVEL medium > > SAVE_MEM TRUE > > &END GLOBAL > > > > > > &FORCE_EVAL > > METHOD Quickstep > > # STRESS_TENSOR analytical > > &DFT > > BASIS_SET_FILE_NAME /shared/centos7/cp2k/cp2k-6.1.0/data/BASIS_MOLOPT > > POTENTIAL_FILE_NAME /shared/centos7/cp2k/cp2k-6.1.0/data/POTENTIAL > > > > &QS > > METHOD GPW > > EPS_DEFAULT 1.0E-12 > > EXTRAPOLATION ASPC > > &END QS > > > > &MGRID > > NGRIDS 5 > > CUTOFF [Ry] 600 > > &END MGRID > > > > &SCCS > > ALPHA [N*m^-1] 0.0 > > BETA [GPa] 0.0 > > DELTA_RHO 2.0E-5 > > DERIVATIVE_METHOD fft > > DIELECTRIC_CONSTANT 80 > > GAMMA 0.0 > > EPS_SCCS 1.0E-12 > > ! EPS_SCF 1.0E-10 > > MAX_ITER 100 > > ! METHOD Andreussi > > METHOD Fattebert-Gygi > > MIXING 0.6 > > ! &ANDREUSSI > > ! RHO_MAX 0.008 > > ! RHO_MIN 0.00015 > > ! &END ANDREUSSI > > &FATTEBERT-GYGI > > BETA 1.3 > > RHO_ZERO 0.00078 > > &END FATTEBERT-GYGI > > &END SCCS > > > > &SCF > > SCF_GUESS ATOMIC > > MAX_SCF 300 > > EPS_SCF 1.0E-12 > > &DIAGONALIZATION ON > > ALGORITHM STANDARD > > &END DIAGONALIZATION > > ! &OT on > > ! MINIMIZER DIIS > > ! PRECONDITIONER FULL_ALL > > ! ENERGY_GAP 0.002 > > ! &END OT > > &OUTER_SCF > > EPS_SCF 1e-12 > > MAX_SCF 30 > > &END OUTER_SCF > > &END SCF > > > > &XC > > &XC_FUNCTIONAL PBE > > &END XC_FUNCTIONAL > > &END XC > > > > &PRINT > > &PDOS > > &EACH > > GEO_OPT 1 > > &END EACH > > APPEND TRUE > > &END PDOS > > &SCCS ON > > &EACH > > GEO_OPT 10 > > &END EACH > > &DENSITY_GRADIENT off > > &EACH > > GEO_OPT 10 > > &END EACH > > APPEND > > &END DENSITY_GRADIENT > > &DIELECTRIC_FUNCTION off > > &EACH > > GEO_OPT 10 > > &END EACH > > APPEND > > &END DIELECTRIC_FUNCTION > > &POLARISATION_POTENTIAL off > > &EACH > > GEO_OPT 10 > > &END EACH > > APPEND > > &END POLARISATION_POTENTIAL > > &END SCCS > > &END PRINT > > > > &END DFT > > > > &SUBSYS > > &CELL > > ABC [angstrom] 10 10 10 > > ! PERIODIC XYZ > > ! MULTIPLE_UNIT_CELL 1 1 1 > > &END CELL > > &TOPOLOGY > > COORD_FILE_NAME Al4C.xyz > > COORD_FILE_FORMAT XYZ > > ! MULTIPLE_UNIT_CELL 1 1 1 > > &END > > &KIND C > > ELEMENT C > > BASIS_SET DZVP-MOLOPT-GTH > > POTENTIAL GTH-PBE-q4 > > &END KIND > > &KIND Al > > ELEMENT Al > > BASIS_SET DZVP-MOLOPT-SR-GTH > > POTENTIAL GTH-PBE-q3 > > &END KIND > > &END SUBSYS > > > > &END FORCE_EVAL > > > > &MOTION > > &GEO_OPT > > TYPE MINIMIZATION > > OPTIMIZER BFGS > > MAX_ITER 100 > > &END GEO_OPT > > &CONSTRAINT > > &FIXED_ATOMS > > COMPONENTS_TO_FIX XYZ > > LIST 1 > > &END FIXED_ATOMS > > &END CONSTRAINT > > &PRINT > > &STRUCTURE_DATA > > DISTANCE 1 2 > > DISTANCE 1 3 > > DISTANCE 1 4 > > DISTANCE 1 5 > > DISTANCE 2 3 > > DISTANCE 2 4 > > DISTANCE 2 5 > > DISTANCE 3 4 > > DISTANCE 3 5 > > DISTANCE 4 5 > > ANGLE 1 2 3 > > ANGLE 1 2 4 > > ANGLE 1 2 5 > > ANGLE 1 3 2 > > ANGLE 1 3 4 > > ANGLE 1 3 5 > > ANGLE 1 4 2 > > ANGLE 1 4 3 > > ANGLE 1 4 5 > > ANGLE 1 5 2 > > ANGLE 1 5 3 > > ANGLE 1 5 4 > > &EACH > > GEO_OPT 1 > > &END EACH > > &END STRUCTURE_DATA > > &TRAJECTORY > > &EACH > > GEO_OPT 1 > > &END EACH > > &END TRAJECTORY > > &VELOCITIES > > &EACH > > GEO_OPT 1 > > &END EACH > > &END VELOCITIES > > &FORCES > > &EACH > > GEO_OPT 1 > > &END EACH > > &END FORCES > > &CELL > > &EACH > > GEO_OPT 1 > > &END EACH > > &END CELL > > &RESTART > > &EACH > > GEO_OPT 1 > > &END EACH > > &END RESTART > > &END PRINT > > &END MOTION > > > > > On Wednesday, May 13, 2020 at 8:08:47 PM UTC-4, Matthias Krack wrote: > > Hi Dev > > > > The settings in the regression tests are often physically not meaningful, > since these test runs have to be completed after a few seconds. > > SCCS%EPS_SCF delays the start of the inner SCCS convergence loop only for > values greater zero. Otherwise that value is not considered and the inner > SCCS cycle is activated immediately. > > SCCS%EPS_SCCS, the convergence threshold of the inner SCCS loop for the > polarization charge should be smaller (tighter) than 1.0E-6, at least > 1.0E-8. As soon as the inner SCCS loop is activated, the timings for each > SCF iteration step will increase significantly. Also the implicit solvent > comes not for free. You can reduce the box size to save computer resources, > because your system is small. Does the setup for your system CAl4 > work/converge properly for a geo_opt run in gas phase, i.e. without SCCS? > If that is the case then I would start with a smaller dielectric constant > than 80 for the SCCS and see how the system evolves. The print level medium > provides a detailed SCCS output. > > > > HTH > > > > Matthias > > > > *From:* c... at googlegroups.com *On Behalf Of *Dev > Rana > *Sent:* Donnerstag, 14. Mai 2020 00:29 > *To:* cp2k > *Subject:* Re: [CP2K:13298] SCCS Solvation Model Implementation - > Molecule Radii Explodes > > > > I take back what I previously said. The 0th geo opt step finishes quickly > with SCF steps taking 20-25s each. The 2st geo opt step does not finish and > each SCF step takes 5+ minutes. Here's my input file and output for that. > I'm also running this on GPU. > > > > What do you advise? I've attached the input output files and paste input > below. The convergence values keep increases, rather than decreases. And > Total Energy keep lowering. > > > > &GLOBAL > > PROJECT SCCS > > RUN_TYPE geo_opt > > PRINT_LEVEL low > > SAVE_MEM TRUE > > &END GLOBAL > > > > > > &FORCE_EVAL > > METHOD Quickstep > > # STRESS_TENSOR analytical > > &DFT > > BASIS_SET_FILE_NAME /shared/centos7/cp2k/cp2k-6.1.0/data/BASIS_MOLOPT > > POTENTIAL_FILE_NAME /shared/centos7/cp2k/cp2k-6.1.0/data/POTENTIAL > > > > &QS > > METHOD GPW > > EPS_DEFAULT 1.0E-12 > > EXTRAPOLATION ASPC > > &END QS > > > > &MGRID > > NGRIDS 5 > > CUTOFF [Ry] 600 > > &END MGRID > > > > &SCCS > > ALPHA [N*m^-1] 0.0 > > BETA [GPa] 0.0 > > DELTA_RHO 2.0E-5 > > DERIVATIVE_METHOD cd5 > > DIELECTRIC_CONSTANT 80 > > GAMMA [mN/m] 0.0 > > EPS_SCCS 1.0E-6 > > EPS_SCF 1.0E-7 > > MAX_ITER 100 > > ! METHOD Andreussi > > METHOD Fattebert-Gygi > > MIXING 0.6 > > ! &ANDREUSSI > > ! RHO_MAX 0.001 > > ! RHO_MIN 0.0001 > > ! &END ANDREUSSI > > &FATTEBERT-GYGI > > BETA 1.3 > > RHO_ZERO 0.00078 > > &END FATTEBERT-GYGI > > &END SCCS > > > > &SCF > > SCF_GUESS ATOMIC > > MAX_SCF 300 > > EPS_SCF 1.0E-7 > > &DIAGONALIZATION ON > > ALGORITHM STANDARD > > &END DIAGONALIZATION > > ! &OT on > > ! MINIMIZER DIIS > > ! PRECONDITIONER FULL_ALL > > ! ENERGY_GAP 0.002 > > ! &END OT > > &OUTER_SCF > > EPS_SCF 1e-7 > > MAX_SCF 30 > > &END OUTER_SCF > > &END SCF > > > > &XC > > &XC_FUNCTIONAL PBE > > &END XC_FUNCTIONAL > > &END XC > > > > &PRINT > > &PDOS > > &EACH > > GEO_OPT 1 > > &END EACH > > APPEND TRUE > > &END PDOS > > &SCCS ON > > &EACH > > GEO_OPT 10 > > &END EACH > > &DENSITY_GRADIENT off > > &EACH > > GEO_OPT 10 > > &END EACH > > APPEND > > &END DENSITY_GRADIENT > > &DIELECTRIC_FUNCTION off > > &EACH > > GEO_OPT 10 > > &END EACH > > APPEND > > &END DIELECTRIC_FUNCTION > > &POLARISATION_POTENTIAL off > > &EACH > > GEO_OPT 10 > > &END EACH > > APPEND > > &END POLARISATION_POTENTIAL > > &END SCCS > > &END PRINT > > > > &END DFT > > > > &SUBSYS > > &CELL > > ABC [angstrom] 30 30 30 > > ! PERIODIC XYZ > > ! MULTIPLE_UNIT_CELL 1 1 1 > > &END CELL > > &TOPOLOGY > > COORD_FILE_NAME Al4C.xyz > > COORD_FILE_FORMAT XYZ > > ! MULTIPLE_UNIT_CELL 1 1 1 > > &END > > &KIND C > > ELEMENT C > > BASIS_SET DZVP-MOLOPT-GTH > > POTENTIAL GTH-PBE-q4 > > &END KIND > > &KIND Al > > ELEMENT Al > > BASIS_SET DZVP-MOLOPT-SR-GTH > > POTENTIAL GTH-PBE-q3 > > &END KIND > > &END SUBSYS > > > > &END FORCE_EVAL > > > > &MOTION > > &GEO_OPT > > TYPE MINIMIZATION > > OPTIMIZER BFGS > > MAX_ITER 100 > > &END GEO_OPT > > &CONSTRAINT > > &FIXED_ATOMS > > COMPONENTS_TO_FIX XYZ > > LIST 1 > > &END FIXED_ATOMS > > &END CONSTRAINT > > &PRINT > > &STRUCTURE_DATA > > DISTANCE 1 2 > > DISTANCE 1 3 > > DISTANCE 1 4 > > DISTANCE 1 5 > > DISTANCE 2 3 > > DISTANCE 2 4 > > DISTANCE 2 5 > > DISTANCE 3 4 > > DISTANCE 3 5 > > DISTANCE 4 5 > > ANGLE 1 2 3 > > ANGLE 1 2 4 > > ANGLE 1 2 5 > > ANGLE 1 3 2 > > ANGLE 1 3 4 > > ANGLE 1 3 5 > > ANGLE 1 4 2 > > ANGLE 1 4 3 > > ANGLE 1 4 5 > > ANGLE 1 5 2 > > ANGLE 1 5 3 > > ANGLE 1 5 4 > > &EACH > > GEO_OPT 1 > > &END EACH > > &END STRUCTURE_DATA > > &TRAJECTORY > > &EACH > > GEO_OPT 1 > > &END EACH > > &END TRAJECTORY > > &VELOCITIES > > &EACH > > GEO_OPT 1 > > &END EACH > > &END VELOCITIES > > &FORCES > > &EACH > > GEO_OPT 1 > > &END EACH > > &END FORCES > > &CELL > > &EACH > > GEO_OPT 1 > > &END EACH > > &END CELL > > &RESTART > > &EACH > > GEO_OPT 1 > > &END EACH > > &END RESTART > > &END PRINT > > &END MOTION > > > > > > > > -- > 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 c... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/b0c10452-d528-48da-9f83-07d9b01d5dfb%40googlegroups.com > > . > > -- > 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 c... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/cc63d43c-380a-4575-ac41-5b981251d294%40googlegroups.com > > . > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/99722c46-cf0e-427f-a7f5-bd6eba017cd3%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mayan... at gmail.com Wed Jun 3 15:27:10 2020 From: mayan... at gmail.com (Mayank Dodia) Date: Wed, 3 Jun 2020 08:27:10 -0700 (PDT) Subject: [CP2K-user] Bond sequences error In-Reply-To: <398f3bb5-93c8-458e-bb47-2cd1de56873c@googlegroups.com> References: <398f3bb5-93c8-458e-bb47-2cd1de56873c@googlegroups.com> Message-ID: Hi, Sorry for reposting, but can someone help me understand what exactly the error is and how should I resolve it? On Monday, June 1, 2020 at 7:01:17 AM UTC+2, Mayank Dodia wrote: > > Hi, > > Has anyone experienced this sort of error? > > > ******************************************************************************* > * ___ > * > * / \ > * > * [ABORT] different sequence of bonds for same molecule kind molecule > type = * > * \___/ 1 molecule number= 634 NOT FOUND! Check the > connectivity of * > * | your system. > * > * O/| > * > * /| | > * > * / \ > topology_util.F:1117 * > > ******************************************************************************* > > > ===== Routine Calling Stack ===== > > 4 topology_molecules_check > 3 connectivity_control > 2 topology_control > 1 CP2K > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 > : > system msg for write_line failure : Bad file descriptor > > I was running a QMMM file and this failure occurred after a restarted > calculation which ran without any issues before. I tried rerunning the > calculation by simplifying it to plain MM input with just solvent water > molecules, without success, and I am not really sure where the error is. > Can someone help me understand what exactly the error is and how should I > resolve it? > > Best Regards, > MayankDodia > -------------- next part -------------- An HTML attachment was scrubbed... URL: From janel... at gmail.com Wed Jun 3 15:57:26 2020 From: janel... at gmail.com (Jan Elsner) Date: Wed, 3 Jun 2020 08:57:26 -0700 (PDT) Subject: [CP2K-user] [CP2K:13438] Problem with large CUTOFFs for non-local vdW functionals In-Reply-To: References: <61ad6acc-bede-4c61-9cb8-127d49d0c823@googlegroups.com> Message-ID: Cheers! Jan On Wednesday, June 3, 2020 at 1:57:11 PM UTC+1, jgh wrote: > > Hi > > Nonlocal vdW functionals make use of the precomputed kernel table. > This table was calculated with a maximum cutoff and this is checked > in CP2K to avoid unphysical extrapolation. > If you need such high cutoffs, you have to generate another > kernel file. This is a file that was generated from Quantum Espresso. > > regards > > Juerg Hutter > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: h... at chem.uzh.ch > > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----c... at googlegroups.com wrote: ----- > To: "cp2k" > > From: "Jan Elsner" > Sent by: c... at googlegroups.com > Date: 06/03/2020 02:46PM > Subject: [CP2K:13438] Problem with large CUTOFFs for non-local vdW > functionals > > Dear all, > > When I try to use a large CUTOFF (MGRID section) with non-local vdW > functionals (I have tried optPBE, optB88 and vdW-DF2), the program seems > unable to calculate the vdW energy and I get a CPASSERT failed error. For > my particular system (periodic rubrene molecular crystal), the program runs > fine with CUTOFF 1100 Ry, but fails for CUTOFF 1200 Ry. I note that the > CUTOFF at which the program crashes is cell-size dependent e.g. if I use a > smaller CELL_REF (or no CELL_REF), I can go to higher CUTOFFs before the > program crashes. > > I attach input and output files using optPBE for the cases: (i) CUTOFF > 1100 Ry, run succeeds and (ii) CUTOFF 1200 Ry, run fails. > > It would be great to know why these functionals cannot cope with large > CUTOFFs. > > Best wishes, > > Jan > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/61ad6acc-bede-4c61-9cb8-127d49d0c823%40googlegroups.com. > > > > [attachment "fail-cutoff-1200.inp" removed by J?rg Hutter/at/UZH] > [attachment "fail-cutoff-1200.out" removed by J?rg Hutter/at/UZH] > [attachment "subsys.include" removed by J?rg Hutter/at/UZH] > [attachment "success-cutoff-1100.inp" removed by J?rg Hutter/at/UZH] > [attachment "success-cutoff-1100.out" removed by J?rg Hutter/at/UZH] > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dev.... at gmail.com Wed Jun 3 16:18:35 2020 From: dev.... at gmail.com (Dev Rana) Date: Wed, 3 Jun 2020 09:18:35 -0700 (PDT) Subject: [CP2K-user] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics? Message-ID: <6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e@googlegroups.com> As the question in the subject suggests, is it possible to run a solvation model with MD? -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthi... at psi.ch Wed Jun 3 16:42:28 2020 From: matthi... at psi.ch (Krack Matthias (PSI)) Date: Wed, 3 Jun 2020 16:42:28 +0000 Subject: [CP2K-user] [CP2K:13443] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics? In-Reply-To: <6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e@googlegroups.com> References: <6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e@googlegroups.com> Message-ID: <33c41f58c1a948209a7ba61ba36574ac@psi.ch> Yes. From: cp... at googlegroups.com On Behalf Of Dev Rana Sent: Mittwoch, 3. Juni 2020 18:19 To: cp2k Subject: [CP2K:13443] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics? As the question in the subject suggests, is it possible to run a solvation model with MD? -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mattwa... at gmail.com Wed Jun 3 18:21:18 2020 From: mattwa... at gmail.com (Matt W) Date: Wed, 3 Jun 2020 11:21:18 -0700 (PDT) Subject: [CP2K-user] Bond sequences error In-Reply-To: References: <398f3bb5-93c8-458e-bb47-2cd1de56873c@googlegroups.com> Message-ID: Maybe check the names of atoms in the restart files. Perhaps H1 etc are only being called H in the restart or similar? Matt On Wednesday, June 3, 2020 at 4:27:11 PM UTC+1, Mayank Dodia wrote: > > Hi, > > Sorry for reposting, but can someone help me understand what exactly the > error is and how should I resolve it? > > On Monday, June 1, 2020 at 7:01:17 AM UTC+2, Mayank Dodia wrote: >> >> Hi, >> >> Has anyone experienced this sort of error? >> >> >> ******************************************************************************* >> * ___ >> * >> * / \ >> * >> * [ABORT] different sequence of bonds for same molecule kind molecule >> type = * >> * \___/ 1 molecule number= 634 NOT FOUND! Check the >> connectivity of * >> * | your system. >> * >> * O/| >> * >> * /| | >> * >> * / \ >> topology_util.F:1117 * >> >> ******************************************************************************* >> >> >> ===== Routine Calling Stack ===== >> >> 4 topology_molecules_check >> 3 connectivity_control >> 2 topology_control >> 1 CP2K >> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 >> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 >> : >> system msg for write_line failure : Bad file descriptor >> >> I was running a QMMM file and this failure occurred after a restarted >> calculation which ran without any issues before. I tried rerunning the >> calculation by simplifying it to plain MM input with just solvent water >> molecules, without success, and I am not really sure where the error is. >> Can someone help me understand what exactly the error is and how should I >> resolve it? >> >> Best Regards, >> MayankDodia >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hasanal... at gmail.com Wed Jun 3 18:48:29 2020 From: hasanal... at gmail.com (Hasan Al-Mahayni) Date: Wed, 3 Jun 2020 11:48:29 -0700 (PDT) Subject: [CP2K-user] Displaying restart file Message-ID: <7b835054-97fb-45d4-a843-da080e161e40@googlegroups.com> Hi, I am running a simple energy calculation on a slab using ASE, with k-points. Usually, I get the projectname-1.restart file outputted but it doesn't appear here. Is there a tag or something to make it output a .restart file so I can continue the calculations? This is my input file: !!! Generated by ASE !!! &MOTION &PRINT &TRAJECTORY FORMAT XYZ &END TRAJECTORY &CELL &END CELL &END PRINT &END MOTION &FORCE_EVAL METHOD Quickstep STRESS_TENSOR ANALYTICAL &DFT UKS .TRUE. CHARGE 0 MULTIPLICITY 1 WFN_RESTART_FILE_NAME cp2k-RESTART.kp BASIS_SET_FILE_NAME BASIS_MOLOPT POTENTIAL_FILE_NAME POTENTIAL &MGRID NGRIDS 5 RELATIVE_CUTOFF 50 CUTOFF [eV] 8.000000000000000000e+02 &END MGRID &QS EPS_DEFAULT 1.0E-12 METHOD GPW EXTRAPOLATION USE_GUESS &END QS &SCF SCF_GUESS RESTART ADDED_MOS 200 CHOLESKY OFF MAX_SCF 200 &SMEAR T METHOD FERMI_DIRAC ELECTRONIC_TEMPERATURE 3.0000E+2 &END SMEAR &MIXING T METHOD BROYDEN_MIXING ALPHA 4.0000000000000002E-01 BETA 1.5000000000000000E+00 NMIXING 5 NBUFFER 8 &END MIXING &END SCF &POISSON POISSON_SOLVER PERIODIC PERIODIC XYZ &END POISSON &KPOINTS SCHEME MONKHORST-PACK 8 8 8 FULL_GRID .TRUE. &END KPOINTS &LS_SCF MAX_SCF 200 &END LS_SCF &XC &XC_FUNCTIONAL &PBE &END PBE &END XC_FUNCTIONAL &END XC &END DFT &PRINT &STRESS_TENSOR ON &END STRESS_TENSOR &END PRINT &SUBSYS &COORD Cu 2.683164727356096790e+01 1.647377632857454444e+01 1.500000000000000000e+01 Cu 2.938430275364440547e+01 1.647377632857454444e+01 1.500000000000000000e+01 Cu 3.193695823372784304e+01 1.647377632857454444e+01 1.500000000000000000e+01 Cu 3.448961371381128060e+01 1.647377632857454444e+01 1.500000000000000000e+01 Cu 2.810797501360268669e+01 1.868444082143636109e+01 1.500000000000000000e+01 Cu 3.066063049368612425e+01 1.868444082143636109e+01 1.500000000000000000e+01 Cu 3.321328597376955827e+01 1.868444082143636109e+01 1.500000000000000000e+01 Cu 3.576594145385299583e+01 1.868444082143636109e+01 1.500000000000000000e+01 Cu 2.938430275364440547e+01 2.089510531429818130e+01 1.500000000000000000e+01 Cu 3.193695823372784304e+01 2.089510531429818130e+01 1.500000000000000000e+01 Cu 3.448961371381128060e+01 2.089510531429818130e+01 1.500000000000000000e+01 Cu 3.704226919389471107e+01 2.089510531429818130e+01 1.500000000000000000e+01 Cu 3.066063049368612070e+01 2.310576980716000151e+01 1.500000000000000000e+01 Cu 3.321328597376955827e+01 2.310576980716000151e+01 1.500000000000000000e+01 Cu 3.576594145385299583e+01 2.310576980716000151e+01 1.500000000000000000e+01 Cu 3.831859693393643340e+01 2.310576980716000151e+01 1.500000000000000000e+01 Cu 2.683164727356096790e+01 1.500000000000000000e+01 1.708423447177455046e+01 Cu 2.938430275364440547e+01 1.500000000000000000e+01 1.708423447177455046e+01 Cu 3.193695823372784304e+01 1.500000000000000000e+01 1.708423447177455046e+01 Cu 3.448961371381128060e+01 1.500000000000000000e+01 1.708423447177455046e+01 Cu 2.810797501360268669e+01 1.721066449286181665e+01 1.708423447177455046e+01 Cu 3.066063049368612425e+01 1.721066449286181665e+01 1.708423447177455046e+01 Cu 3.321328597376955827e+01 1.721066449286181665e+01 1.708423447177455046e+01 Cu 3.576594145385299583e+01 1.721066449286181665e+01 1.708423447177455046e+01 Cu 2.938430275364440547e+01 1.942132898572363686e+01 1.708423447177455046e+01 Cu 3.193695823372784304e+01 1.942132898572363686e+01 1.708423447177455046e+01 Cu 3.448961371381128060e+01 1.942132898572363686e+01 1.708423447177455046e+01 Cu 3.704226919389471107e+01 1.942132898572363686e+01 1.708423447177455046e+01 Cu 3.066063049368612425e+01 2.163199347858545352e+01 1.708423447177455046e+01 Cu 3.321328597376955827e+01 2.163199347858545352e+01 1.708423447177455046e+01 Cu 3.576594145385299583e+01 2.163199347858545352e+01 1.708423447177455046e+01 Cu 3.831859693393643340e+01 2.163199347858545352e+01 1.708423447177455046e+01 &END COORD &CELL PERIODIC XY A 4.314986775165566257e+01 0.000000000000000000e+00 0.000000000000000000e+00 B 2.200037645584174584e+01 3.810576980716000151e+01 0.000000000000000000e+00 C 0.000000000000000000e+00 0.000000000000000000e+00 3.208423447177455046e+01 &END CELL &KIND Cu BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE &END KIND &END SUBSYS &END FORCE_EVAL &GLOBAL PROJECT cp2k PRINT_LEVEL MEDIUM &END GLOBAL Thanks, Hasan. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- !!! Generated by ASE !!! &MOTION &PRINT &TRAJECTORY FORMAT XYZ &END TRAJECTORY &CELL &END CELL &END PRINT &END MOTION &FORCE_EVAL METHOD Quickstep STRESS_TENSOR ANALYTICAL &DFT UKS .TRUE. CHARGE 0 MULTIPLICITY 1 WFN_RESTART_FILE_NAME cp2k-RESTART.kp BASIS_SET_FILE_NAME BASIS_MOLOPT POTENTIAL_FILE_NAME POTENTIAL &MGRID NGRIDS 5 RELATIVE_CUTOFF 50 CUTOFF [eV] 8.000000000000000000e+02 &END MGRID &QS EPS_DEFAULT 1.0E-12 METHOD GPW EXTRAPOLATION USE_GUESS &END QS &SCF SCF_GUESS RESTART ADDED_MOS 200 CHOLESKY OFF MAX_SCF 200 &SMEAR T METHOD FERMI_DIRAC ELECTRONIC_TEMPERATURE 3.0000E+2 &END SMEAR &MIXING T METHOD BROYDEN_MIXING ALPHA 4.0000000000000002E-01 BETA 1.5000000000000000E+00 NMIXING 5 NBUFFER 8 &END MIXING &END SCF &POISSON POISSON_SOLVER PERIODIC PERIODIC XYZ &END POISSON &KPOINTS SCHEME MONKHORST-PACK 8 8 8 FULL_GRID .TRUE. &END KPOINTS &LS_SCF MAX_SCF 200 &END LS_SCF &XC &XC_FUNCTIONAL &PBE &END PBE &END XC_FUNCTIONAL &END XC &END DFT &PRINT &STRESS_TENSOR ON &END STRESS_TENSOR &END PRINT &SUBSYS &COORD Cu 2.683164727356096790e+01 1.647377632857454444e+01 1.500000000000000000e+01 Cu 2.938430275364440547e+01 1.647377632857454444e+01 1.500000000000000000e+01 Cu 3.193695823372784304e+01 1.647377632857454444e+01 1.500000000000000000e+01 Cu 3.448961371381128060e+01 1.647377632857454444e+01 1.500000000000000000e+01 Cu 2.810797501360268669e+01 1.868444082143636109e+01 1.500000000000000000e+01 Cu 3.066063049368612425e+01 1.868444082143636109e+01 1.500000000000000000e+01 Cu 3.321328597376955827e+01 1.868444082143636109e+01 1.500000000000000000e+01 Cu 3.576594145385299583e+01 1.868444082143636109e+01 1.500000000000000000e+01 Cu 2.938430275364440547e+01 2.089510531429818130e+01 1.500000000000000000e+01 Cu 3.193695823372784304e+01 2.089510531429818130e+01 1.500000000000000000e+01 Cu 3.448961371381128060e+01 2.089510531429818130e+01 1.500000000000000000e+01 Cu 3.704226919389471107e+01 2.089510531429818130e+01 1.500000000000000000e+01 Cu 3.066063049368612070e+01 2.310576980716000151e+01 1.500000000000000000e+01 Cu 3.321328597376955827e+01 2.310576980716000151e+01 1.500000000000000000e+01 Cu 3.576594145385299583e+01 2.310576980716000151e+01 1.500000000000000000e+01 Cu 3.831859693393643340e+01 2.310576980716000151e+01 1.500000000000000000e+01 Cu 2.683164727356096790e+01 1.500000000000000000e+01 1.708423447177455046e+01 Cu 2.938430275364440547e+01 1.500000000000000000e+01 1.708423447177455046e+01 Cu 3.193695823372784304e+01 1.500000000000000000e+01 1.708423447177455046e+01 Cu 3.448961371381128060e+01 1.500000000000000000e+01 1.708423447177455046e+01 Cu 2.810797501360268669e+01 1.721066449286181665e+01 1.708423447177455046e+01 Cu 3.066063049368612425e+01 1.721066449286181665e+01 1.708423447177455046e+01 Cu 3.321328597376955827e+01 1.721066449286181665e+01 1.708423447177455046e+01 Cu 3.576594145385299583e+01 1.721066449286181665e+01 1.708423447177455046e+01 Cu 2.938430275364440547e+01 1.942132898572363686e+01 1.708423447177455046e+01 Cu 3.193695823372784304e+01 1.942132898572363686e+01 1.708423447177455046e+01 Cu 3.448961371381128060e+01 1.942132898572363686e+01 1.708423447177455046e+01 Cu 3.704226919389471107e+01 1.942132898572363686e+01 1.708423447177455046e+01 Cu 3.066063049368612425e+01 2.163199347858545352e+01 1.708423447177455046e+01 Cu 3.321328597376955827e+01 2.163199347858545352e+01 1.708423447177455046e+01 Cu 3.576594145385299583e+01 2.163199347858545352e+01 1.708423447177455046e+01 Cu 3.831859693393643340e+01 2.163199347858545352e+01 1.708423447177455046e+01 &END COORD &CELL PERIODIC XY A 4.314986775165566257e+01 0.000000000000000000e+00 0.000000000000000000e+00 B 2.200037645584174584e+01 3.810576980716000151e+01 0.000000000000000000e+00 C 0.000000000000000000e+00 0.000000000000000000e+00 3.208423447177455046e+01 &END CELL &KIND Cu BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE &END KIND &END SUBSYS &END FORCE_EVAL &GLOBAL PROJECT cp2k PRINT_LEVEL MEDIUM &END GLOBAL From dev.... at gmail.com Wed Jun 3 18:48:38 2020 From: dev.... at gmail.com (Dev Rana) Date: Wed, 3 Jun 2020 11:48:38 -0700 (PDT) Subject: [CP2K-user] [CP2K:13443] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics? In-Reply-To: <33c41f58c1a948209a7ba61ba36574ac@psi.ch> References: <6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e@googlegroups.com> <33c41f58c1a948209a7ba61ba36574ac@psi.ch> Message-ID: <206d8b04-4fb7-4076-8ad6-d7f609f50bf6@googlegroups.com> Thank you for the confirmation Matthias! Would you be able to look at my input file? I'm having trouble with SCF convergence and my Andreussi model set up. I'm trying to simulate 6 carbon atoms randomly placed as they migrate through a molten Al system, using MD. Using the solvation model, I've set up my 6 C atoms and have a dieletric constant of 80. I'm also attaching my latest output file. I was originally using Diagonalization method for the SCF, but the convergence column was migrating over 1. I then tried using OT with minimizer DIIS, Full_ALL preconditioner and 0.001 energy_gap, as recommended for OT, and it stays below 1, however it never converges. I'm also running this simulation without a solvation model using a full system of 256 Al atom and 6 carbon atoms randomly placed in the system for comparison, with no issues of convergence, i.e. each SCF converges within 24-30 steps with each step taking about 22 seconds. Thank you so much for all your help thus far! I really appreciate it! Best Regards, Dev On Wednesday, June 3, 2020 at 12:42:32 PM UTC-4, Matthias Krack wrote: > > Yes. > > > > *From:* c... at googlegroups.com > *On Behalf Of *Dev Rana > *Sent:* Mittwoch, 3. Juni 2020 18:19 > *To:* cp2k > > *Subject:* [CP2K:13443] Is it possible to run a Andressui or Fattebert > Solvation Model with Molecular Dynamics? > > > > As the question in the subject suggests, is it possible to run a solvation > model with MD? > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: C6.out Type: application/octet-stream Size: 22065 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: job.in Type: application/octet-stream Size: 2684 bytes Desc: not available URL: From fabia... at gmail.com Wed Jun 3 18:59:30 2020 From: fabia... at gmail.com (Fabian Ducry) Date: Wed, 3 Jun 2020 11:59:30 -0700 (PDT) Subject: [CP2K-user] Displaying restart file In-Reply-To: <7b835054-97fb-45d4-a843-da080e161e40@googlegroups.com> References: <7b835054-97fb-45d4-a843-da080e161e40@googlegroups.com> Message-ID: Hi Hasan, You can control the printing of the restart file with the MOTION%PRINT%RESTART section. Best, Fabian -------------- next part -------------- An HTML attachment was scrubbed... URL: From hasanal... at gmail.com Wed Jun 3 19:46:01 2020 From: hasanal... at gmail.com (Hasan Al-Mahayni) Date: Wed, 3 Jun 2020 15:46:01 -0400 Subject: [CP2K-user] [CP2K:13448] Re: Displaying restart file In-Reply-To: References: <7b835054-97fb-45d4-a843-da080e161e40@googlegroups.com> Message-ID: Hi, I tried this: &MOTION &PRINT &RESTART HIGH &END RESTART &TRAJECTORY FORMAT XYZ &END TRAJECTORY &CELL &END CELL &END PRINT &END MOTION It still doesn't output anything... On Wed, Jun 3, 2020 at 2:59 PM Fabian Ducry wrote: > Hi Hasan, > > You can control the printing of the restart file with the > MOTION%PRINT%RESTART section. > > Best, > Fabian > > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/a5ec26a6-8a9a-4d0f-8c76-1a22b860c6f3%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hale.m... at live.com Thu Jun 4 03:08:09 2020 From: hale.m... at live.com (Michael Hale) Date: Wed, 3 Jun 2020 20:08:09 -0700 (PDT) Subject: [CP2K-user] Visualize electron density during formation of a water molecule Message-ID: Hey, sorry for the basic question. I've skimmed some computational chemistry books, but I still find the CP2K documentation a bit overwhelming. I'm trying to put two hydrogens an an oxygen atom near each other and watch the spontaneous assembly of a water molecule. I can make the input file and have CP2K output the forces on the atoms and a cube file that I can use to make a 3D visualization of the electron density in Mathematica. Then I update the atom positions with a simple velocity Verlet update and run CP2K again. The resulting animation looks how I want stylistically, but the behavior is clearly not accurate. The atoms come together and bounce off of each other and come back together and bounce off harder. They keep getting more energy and bouncing farther and farther away until they fly apart instead of bonding together. Is the error that the energy calculation for the forces and electron density isn't converging and causing the erratic behavior? Is the error probably in the way I'm updating the atom positions manually? Can I use the CP2K molecular dynamics functionality to do multiple steps of the simulation at once while also outputting the cube file of the electron density for each step? Is this type of simulation of the formation of small molecules within the scope of CP2K? It seems most people typically assume the molecules are already formed and they just want to simulate how those molecules interact, not how atoms come together to form the small molecules. This is all just for fun. I just want to watch the animations and see how "sticky" the atoms and molecules are. Thanks for any help and guidance you might provide. -------------- next part -------------- An HTML attachment was scrubbed... URL: From fabia... at gmail.com Thu Jun 4 05:44:48 2020 From: fabia... at gmail.com (Fabian Ducry) Date: Wed, 3 Jun 2020 22:44:48 -0700 (PDT) Subject: [CP2K-user] [CP2K:13448] Re: Displaying restart file In-Reply-To: References: <7b835054-97fb-45d4-a843-da080e161e40@googlegroups.com> Message-ID: <153ff752-aa0c-4acf-ab64-86f1ce3788bf@googlegroups.com> Are you running just an ENERGY_FORCE calculation with CP2K and perform the optimization/MD in ASE? CP2K does not print a restart file for ENERGY_FORCE calculations, because there is no change in the coordinates. ASE should have all the information to restart the simulation. Fabian -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthi... at psi.ch Thu Jun 4 08:54:06 2020 From: matthi... at psi.ch (Krack Matthias (PSI)) Date: Thu, 4 Jun 2020 08:54:06 +0000 Subject: [CP2K-user] [CP2K:13447] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics? In-Reply-To: <206d8b04-4fb7-4076-8ad6-d7f609f50bf6@googlegroups.com> References: <6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e@googlegroups.com> <33c41f58c1a948209a7ba61ba36574ac@psi.ch> <206d8b04-4fb7-4076-8ad6-d7f609f50bf6@googlegroups.com> Message-ID: Dev, your setup of a system of six separated carbon atoms does not have a band gap and the addition of an implicit solvent won?t change that most likely. The problem should show up already for a single isolated carbon atom which you can converge either as a triplet within a spin polarized run (LSD and MULTIP 3) or with smearing, i.e. with a fractional occupation of 2/3 for the three degenerated C 2p orbitals. The latter approach works only with diagonalization (try broyden_mixing). Matthias From: cp... at googlegroups.com On Behalf Of Dev Rana Sent: Mittwoch, 3. Juni 2020 20:49 To: cp2k Subject: Re: [CP2K:13447] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics? Thank you for the confirmation Matthias! Would you be able to look at my input file? I'm having trouble with SCF convergence and my Andreussi model set up. I'm trying to simulate 6 carbon atoms randomly placed as they migrate through a molten Al system, using MD. Using the solvation model, I've set up my 6 C atoms and have a dieletric constant of 80. I'm also attaching my latest output file. I was originally using Diagonalization method for the SCF, but the convergence column was migrating over 1. I then tried using OT with minimizer DIIS, Full_ALL preconditioner and 0.001 energy_gap, as recommended for OT, and it stays below 1, however it never converges. I'm also running this simulation without a solvation model using a full system of 256 Al atom and 6 carbon atoms randomly placed in the system for comparison, with no issues of convergence, i.e. each SCF converges within 24-30 steps with each step taking about 22 seconds. Thank you so much for all your help thus far! I really appreciate it! Best Regards, Dev On Wednesday, June 3, 2020 at 12:42:32 PM UTC-4, Matthias Krack wrote: Yes. From: c... at googlegroups.com > On Behalf Of Dev Rana Sent: Mittwoch, 3. Juni 2020 18:19 To: cp2k > Subject: [CP2K:13443] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics? As the question in the subject suggests, is it possible to run a solvation model with MD? -- 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 c... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e%40googlegroups.com. -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/206d8b04-4fb7-4076-8ad6-d7f609f50bf6%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhaoxia... at gmail.com Thu Jun 4 09:54:57 2020 From: zhaoxia... at gmail.com (Xiaokun Zhao) Date: Thu, 4 Jun 2020 02:54:57 -0700 (PDT) Subject: [CP2K-user] Abnormal breakdown during the AIMD calculation. Message-ID: <2911f368-1290-4a5c-b69e-d05a90059c69@googlegroups.com> Dear CP2K users, Now I'm running the AIMD simulation at 300K under NVT ensemble. I have two problems: 1) My calculation always breakdown after 200~300 aimd steps. I have changed several HPC to do the calculation, but got the same result. So, I don't think it's a hardware problem. I also check my input file for several times and I am not sure if there are some mistakes in it. 2) Also, I found that my calculation would become slower after dozens of aimd steps. I check the out file, it seems that the calculation needs more minimize step during the scf iterative process. It is strage that once I killed this calculation and make a restart. This scf iterative process becomes very easy to converge, but as the calculation process it become slower soon. I don't know why? I attached my input file cp2k.inp and cp2k-1.ener. Thanks a lot for your help in advance. Best regards, Xiaokun -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cp2k.inp Type: chemical/x-gamess-input Size: 3667 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cp2k.ener Type: application/octet-stream Size: 160606 bytes Desc: not available URL: From nju... at gmail.com Thu Jun 4 10:22:38 2020 From: nju... at gmail.com (Hua Tian) Date: Thu, 4 Jun 2020 03:22:38 -0700 (PDT) Subject: [CP2K-user] [CP2K:13100] SCAN XC density functional: Do we have to use specific PSEUDOPOTENTIALS for SCAN? Are they available? In-Reply-To: References: <43781524-ffdc-45d0-8899-258ace32638e@googlegroups.com> Message-ID: Dear Prof. Hutter and Bryantsev, In my FPMD simulations for aqueous simulation by using SCAN functional (with the MOLOPT-SR basis sets and the GTH pseudopotentials for SCAN from the website in your e-mail.), I found that smoothing methods (e.g., &XC_GRID / XC_DERIV NN10_SMOOTH / XC_SMOOTH_RHO NN10 / &END XC_GRID) was probably important for the convergence of SCF. For a simulation using SCAN functional with CUTOFF 400 that SCF did not converge, adding the &XC_GRID part methoned above made the SCF converge. However, I did not know if this setting would influence the accuracy of simulations. Sincerely, Tian Hua ? 2020?4?10???? UTC+8??6:31:42?jgh??? > > Hi > > 1) Many people have used PBE pp previously. > SCAN optimized pp can be found at > https://github.com/juerghutter/GTH/blob/master/SCAN/POTENTIAL > 2) Newly published SCAN parameters for D3 are available in the current > version of CP2K from Github. For older version you need to > add a line in the input with the parameters. > 3) Use very high cutoffs, depending on your system. If the cutoff is not > high enough SCF will not converge smoothly to a low value (10^-7 in > OT). > I don't have experience if the smoothing methods work to reduce the > cutoff. > > regards > > Juerg Hutter > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: h... at chem.uzh.ch > > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----c... at googlegroups.com wrote: ----- > To: "cp2k" > > From: "Vyacheslav Bryantsev" > Sent by: c... at googlegroups.com > Date: 04/09/2020 04:50PM > Subject: [CP2K:13100] SCAN XC density functional: Do we have to use > specific PSEUDOPOTENTIALS for SCAN? Are they available? > > Dear CP2K Community, > > Is there a set or recommended setting for using SCAN in cp2k? > > More specifically, > 1. Can we use PBE pseudopotentials for SCAN or this is a bad idea? If not, > where one can find specific pseudopotentials reparametrized for SCAN? > 2. Does the D3 correction work automatically now with SCAN. If not, how to > specify it? > 3. Recommendations for grid when using SCAN > > Thank you, > Slava > > > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/43781524-ffdc-45d0-8899-258ace32638e%40googlegroups.com. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nju... at gmail.com Thu Jun 4 10:43:36 2020 From: nju... at gmail.com (Hua Tian) Date: Thu, 4 Jun 2020 03:43:36 -0700 (PDT) Subject: [CP2K-user] How to use the MOLOPT-SR basis sets and GTH pseudopotentials in Gaussian (09 or 16) package Message-ID: <088f8024-83be-4475-bc56-55b045c471c0@googlegroups.com> Dear CP2K developers, I am sorry to bother you for a problem about the use of the feature parameters in CP2K. I wonder if I can use the MOLOPT-SR basis sets and GTH pseudopotentials in Gaussian (09 or 16) package (by using the ?genecp? keyword.). If yes, what should I do to change the format of them (e.g., for the DZVP-MOLOPT-SR basis sets and GTH pseudopotentials for H.)? Thank you for your attention to my consultations. Sincerely, Tian Hua H DZVP-MOLOPT-SR-GTH DZVP-MOLOPT-SR-GTH-q1 1 2 0 1 5 2 1 10.068468228533 -0.033917444900 0.059193775500 0.009905134400 2.680222868089 -0.122202212100 0.843318328900 0.122449566500 0.791501539122 -0.443818861200 -1.155707115500 0.477183240900 0.239116150487 -0.453182186600 0.049479621200 0.547919678200 0.082193184441 -0.131612861500 0.522708738000 0.869031854000 H GTH-PBE-q1 GTH-PBE 1 0.20000000 2 -4.17890044 0.72446331 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Thu Jun 4 13:16:27 2020 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Thu, 4 Jun 2020 15:16:27 +0200 Subject: [CP2K-user] [CP2K:13455] How to use the MOLOPT-SR basis sets and GTH pseudopotentials in Gaussian (09 or 16) package In-Reply-To: <088f8024-83be-4475-bc56-55b045c471c0@googlegroups.com> References: <088f8024-83be-4475-bc56-55b045c471c0@googlegroups.com> Message-ID: Hi This option is, afaik, in G16 not available. They use another type of pseudopotentials. regards Juerg Hutter -------------------------------------------------------------- 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: "Hua Tian" Sent by: cp... at googlegroups.com Date: 06/04/2020 12:43PM Subject: [CP2K:13455] How to use the MOLOPT-SR basis sets and GTH pseudopotentials in Gaussian (09 or 16) package Dear CP2K developers, I am sorry to bother you for a problem about the use of the feature parameters in CP2K. I wonder if I can use the MOLOPT-SR basis sets and GTH pseudopotentials in Gaussian (09 or 16) package (by using the ?genecp? keyword.). If yes, what should I do to change the format of them (e.g., for the DZVP-MOLOPT-SR basis sets and GTH pseudopotentials for H.)? Thank you for your attention to my consultations. Sincerely, Tian Hua H DZVP-MOLOPT-SR-GTH DZVP-MOLOPT-SR-GTH-q1 1 2 0 1 5 2 1 10.068468228533 -0.033917444900 0.059193775500 0.009905134400 2.680222868089 -0.122202212100 0.843318328900 0.122449566500 0.791501539122 -0.443818861200 -1.155707115500 0.477183240900 0.239116150487 -0.453182186600 0.049479621200 0.547919678200 0.082193184441 -0.131612861500 0.522708738000 0.869031854000 H GTH-PBE-q1 GTH-PBE 1 0.20000000 2 -4.17890044 0.72446331 0 -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/088f8024-83be-4475-bc56-55b045c471c0%40googlegroups.com. From hut... at chem.uzh.ch Thu Jun 4 13:26:15 2020 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Thu, 4 Jun 2020 15:26:15 +0200 Subject: [CP2K-user] [CP2K:13450] Visualize electron density during formation of a water molecule In-Reply-To: References: Message-ID: Hi What I would do: Small basis e.g. DZVP LSD SCF with Diagonalization and Broyden mixing, use all MOs Fermi-Dirac Smearing with high temperature NVT MD with velocity rescaling to get rid of excessive energy Print CUBE file automatically during MD regards Juerg Hutter -------------------------------------------------------------- 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: "Michael Hale" Sent by: cp... at googlegroups.com Date: 06/04/2020 05:08AM Subject: [CP2K:13450] Visualize electron density during formation of a water molecule Hey, sorry for the basic question. I've skimmed some computational chemistry books, but I still find the CP2K documentation a bit overwhelming. I'm trying to put two hydrogens an an oxygen atom near each other and watch the spontaneous assembly of a water molecule. I can make the input file and have CP2K output the forces on the atoms and a cube file that I can use to make a 3D visualization of the electron density in Mathematica. Then I update the atom positions with a simple velocity Verlet update and run CP2K again. The resulting animation looks how I want stylistically, but the behavior is clearly not accurate. The atoms come together and bounce off of each other and come back together and bounce off harder. They keep getting more energy and bouncing farther and farther away until they fly apart instead of bonding together. Is the error that the energy calculation for the forces and electron density isn't converging and causing the erratic behavior? Is the error probably in the way I'm updating the atom positions manually? Can I use the CP2K molecular dynamics functionality to do multiple steps of the simulation at once while also outputting the cube file of the electron density for each step? Is this type of simulation of the formation of small molecules within the scope of CP2K? It seems most people typically assume the molecules are already formed and they just want to simulate how those molecules interact, not how atoms come together to form the small molecules. This is all just for fun. I just want to watch the animations and see how "sticky" the atoms and molecules are. Thanks for any help and guidance you might provide. -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/e90450de-cd30-4bad-ae96-96779a50764e%40googlegroups.com. From nju... at gmail.com Thu Jun 4 13:34:36 2020 From: nju... at gmail.com (Hua Tian) Date: Thu, 4 Jun 2020 06:34:36 -0700 (PDT) Subject: [CP2K-user] [CP2K:13455] How to use the MOLOPT-SR basis sets and GTH pseudopotentials in Gaussian (09 or 16) package In-Reply-To: References: <088f8024-83be-4475-bc56-55b045c471c0@googlegroups.com> Message-ID: <651cbadc-9b81-4586-9cb5-fe7d5d022da2@googlegroups.com> Dear Prof. Hutter, Thank you very much for your early reply and guidance. I will trying using other double-zeta basis sets in Gaussian. Sincerely, Tian Hua ? 2020?6?4???? UTC+8??9:16:38?jgh??? > > Hi > > This option is, afaik, in G16 not available. They use another type > of pseudopotentials. > > regards > > Juerg Hutter > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: h... at chem.uzh.ch > > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----c... at googlegroups.com wrote: ----- > To: "cp2k" > > From: "Hua Tian" > Sent by: c... at googlegroups.com > Date: 06/04/2020 12:43PM > Subject: [CP2K:13455] How to use the MOLOPT-SR basis sets and GTH > pseudopotentials in Gaussian (09 or 16) package > > Dear CP2K developers, > I am sorry to bother you for a problem about the use of the feature > parameters in CP2K. I wonder if I can use the MOLOPT-SR basis sets and GTH > pseudopotentials in Gaussian (09 or 16) package (by using the ?genecp? > keyword.). If yes, what should I do to change the format of them (e.g., for > the DZVP-MOLOPT-SR basis sets and GTH pseudopotentials for H.)? > Thank you for your attention to my consultations. > Sincerely, > Tian Hua > > H DZVP-MOLOPT-SR-GTH DZVP-MOLOPT-SR-GTH-q1 > 1 > 2 0 1 5 2 1 > 10.068468228533 -0.033917444900 0.059193775500 0.009905134400 > 2.680222868089 -0.122202212100 0.843318328900 0.122449566500 > 0.791501539122 -0.443818861200 -1.155707115500 0.477183240900 > 0.239116150487 -0.453182186600 0.049479621200 0.547919678200 > 0.082193184441 -0.131612861500 0.522708738000 0.869031854000 > > H GTH-PBE-q1 GTH-PBE > 1 > 0.20000000 2 -4.17890044 0.72446331 > 0 > > > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/088f8024-83be-4475-bc56-55b045c471c0%40googlegroups.com. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hale.m... at live.com Thu Jun 4 14:10:05 2020 From: hale.m... at live.com (Michael Hale) Date: Thu, 4 Jun 2020 07:10:05 -0700 (PDT) Subject: [CP2K-user] [CP2K:13450] Visualize electron density during formation of a water molecule In-Reply-To: References: Message-ID: <533942f6-e28d-402b-992e-bdc724ec9e6f@googlegroups.com> Great! Thank you. I'll look into those options and hopefully mess with it some more this weekend. Is there much of a hobbyist community around computational chemistry? I'm a pretty experienced software developer, but still new to this. I know there are projects like Folding at Home which don't give you much control, and Chemistry Stack Exchange which is more just traditional Q&A. But I'd love to find community projects to help enhance digital chemistry textbooks with ab initio quantum MD animations of common reactions and such. I actually first tried this during a weekend a couple of years ago. Here was the result: https://www.youtube.com/watch?v=foG5LgFYb2o I finally revisited it a week or two ago. I thought maybe just my initial conditions needed to be tweaked, but then I realized my simulation set up had deeper problems, haha. Thanks again for your help. I hope to post an update again soon. On Thursday, June 4, 2020 at 9:26:25 AM UTC-4, jgh wrote: > > Hi > > What I would do: > > Small basis e.g. DZVP > LSD > SCF with Diagonalization and Broyden mixing, use all MOs > Fermi-Dirac Smearing with high temperature > NVT MD with velocity rescaling to get rid of excessive energy > Print CUBE file automatically during MD > > regards > > Juerg Hutter > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: h... at chem.uzh.ch > > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----c... at googlegroups.com wrote: ----- > To: "cp2k" > > From: "Michael Hale" > Sent by: c... at googlegroups.com > Date: 06/04/2020 05:08AM > Subject: [CP2K:13450] Visualize electron density during formation of a > water molecule > > Hey, sorry for the basic question. I've skimmed some computational > chemistry books, but I still find the CP2K documentation a bit > overwhelming. I'm trying to put two hydrogens an an oxygen atom near each > other and watch the spontaneous assembly of a water molecule. I can make > the input file and have CP2K output the forces on the atoms and a cube file > that I can use to make a 3D visualization of the electron density in > Mathematica. Then I update the atom positions with a simple velocity Verlet > update and run CP2K again. The resulting animation looks how I want > stylistically, but the behavior is clearly not accurate. The atoms come > together and bounce off of each other and come back together and bounce off > harder. They keep getting more energy and bouncing farther and farther away > until they fly apart instead of bonding together. > > Is the error that the energy calculation for the forces and electron > density isn't converging and causing the erratic behavior? Is the error > probably in the way I'm updating the atom positions manually? Can I use the > CP2K molecular dynamics functionality to do multiple steps of the > simulation at once while also outputting the cube file of the electron > density for each step? Is this type of simulation of the formation of small > molecules within the scope of CP2K? It seems most people typically assume > the molecules are already formed and they just want to simulate how those > molecules interact, not how atoms come together to form the small > molecules. > > This is all just for fun. I just want to watch the animations and see how > "sticky" the atoms and molecules are. Thanks for any help and guidance you > might provide. > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/e90450de-cd30-4bad-ae96-96779a50764e%40googlegroups.com. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jerry1... at hotmail.com Thu Jun 4 14:44:03 2020 From: jerry1... at hotmail.com (Tzu-Yao HSU) Date: Thu, 4 Jun 2020 07:44:03 -0700 (PDT) Subject: [CP2K-user] [CP2K:12697] energy jump in SCCS In-Reply-To: <16b1636efad847d0962ed6ba7fdb6361@psi.ch> References: <16b1636efad847d0962ed6ba7fdb6361@psi.ch> Message-ID: <9ba5de66-d129-4f24-8c09-139d9f834286@googlegroups.com> Hi all, I got similar problem as Geng, but my calculation is pure DFT energy evaluation. During the SCF run, the polarisation energy abruptly jumped up to a positive value and the SCF convergence jumped down at certain convergence level . Then the polarisation energy always stayed positive until the SCF run converged. Here are my input file (.inp) and reduced output file (.out, grep 'Diag.' and 'Polarisation energy' then paste) . My molecular structure (optimized.dat) was obtained by performing GEO_OPT in vacuum. Further increasing the MGRID CUTOFF, EPS_SCF in SCCS section, simulation box size, and decreasing CUTOFFs in XC section do not change the converged energy. Since the converged polarisation energy is always positive, I still wonder how may I improve my input file? I appreciate any response to this problem. Thank you very much Best regards Tzu-Yao Matthias Krack? 2020?1?7???? UTC+1??7?40?51???? > > Hi Geng > > > > Such fluctuations are usually caused by numerical noise. A larger cutoff, > e.g. 800 instead of 400Ry, will most likely resolve that issue. > > > > HTH > > > > Matthias > > > > *From:* c... at googlegroups.com > *On Behalf Of *Geng Sun > *Sent:* Dienstag, 31. Dezember 2019 18:26 > *To:* cp2k > > *Subject:* [CP2K:12697] energy jump in SCCS > > > > Dear CP2K users, > > > > I am trying to use the SCCS solvent model to optimize a H2O molecule in > solvent and calculate the solvation energy. > > I found that during the structure optimization, the total energy jumps up > almost 3 eV, but the structure of H2O still looks good. > > Finally, with the energy obtained in solvent ( -17.07615353442375 a.u.) > and energy in vacuum (-17.22203206260123), the solvation energy is positive. > > Therefore, there must be something wrong in the calculations, but I can > not figure it out. > > > > > > grep "Total energy:" cp2k.out gives: > > > > Total energy: - > 17.22994560779211 > Total energy: - > 17.23016218028583 > Total energy: - > 17.23052945533816 > Total energy: - > 17.23057483762070 > Total energy: - > 17.23059795728501 > Total energy: - > 17.23061684603447 > Total energy: - > 17.23062875959604 > Total energy: - > 17.23063230147527 > Total energy: - > 17.23063606787884 > Total energy: - > 17.23458599053544 > Total energy: - > 17.07789974445440 > Total energy: - > 17.23050622895307 > Total energy: - > 17.23059409756609 > Total energy: - > 17.23153569898144 > Total energy: - > 17.23062905094530 > Total energy: - > 17.23063896643257 > Total energy: - > 17.06258564479369 > Total energy: - > 17.23061553671926 > Total energy: - > 17.23064419320881 > Total energy: - > 17.23017384159302 > Total energy: - > 17.09997174618866 > Total energy: - > 17.23053249119082 > Total energy: - > 17.23061888501270 > Total energy: - > 17.23062632201262 > Total energy: - > 17.10641501376824 > Total energy: - > 17.23063629047595 > Total energy: - > 17.23099984646603 > Total energy: - > 17.11100171504137 > Total energy: - > 17.10215507558170 > Total energy: - > 17.13946950681089 > Total energy: - > 17.05320236101690 > Total energy: - > 17.23214150951693 > Total energy: - > 17.14172122406513 > Total energy: - > 17.05319840556444 > Total energy: - > 17.06170695684858 > Total energy: - > 17.11231720859150 > Total energy: - > 17.07455263629729 > Total energy: - > 17.07623660559768 > Total energy: - > 17.07963295606425 > Total energy: - > 17.07859069368490 > Total energy: - > 17.07694563368373 > Total energy: - > 17.07637515123947 > Total energy: - > 17.07632103460653 > Total energy: - > 17.07605114342309 > Total energy: - > 17.07615353442375 > > > > Here is the input file: > > &FORCE_EVAL > &DFT > UKS > BASIS_SET_FILE_NAME BASIS_MOLOPT_UCL > BASIS_SET_FILE_NAME BASIS_MOLOPT > POTENTIAL_FILE_NAME GTH_POTENTIALS > &MGRID > CUTOFF 400 > COMMENSURATE > &END MGRID > &QS > EXTRAPOLATION PS > EXTRAPOLATION_ORDER 3 > EPS_DEFAULT 1.0E-12 > MAP_CONSISTENT T > &END QS > &PRINT > &SCCS ON > &EACH > QS_SCF 1 > &END EACH > &END SCCS > &END PRINT > &SCCS > ALPHA [N*m^-1] 0.02 > GAMMA [mN/m] 0.0 > BETA [GPa] -0.08 > DELTA_RHO 2.0E-5 > DERIVATIVE_METHOD CD5 > DIELECTRIC_CONSTANT 6.02 > EPS_SCCS 1.0E-10 > EPS_SCF 0.03 > MAX_ITER 100 > METHOD Andreussi > MIXING 0.6 > &ANDREUSSI > RHO_MAX 0.003 > RHO_MIN 0.0003 > &END ANDREUSSI > &END SCCS > &SCF > EPS_SCF 1.0E-7 > MAX_SCF 31 > SCF_GUESS RESTART > &OT > ENERGY_GAP 0.002 > LINESEARCH 2PNT > PRECONDITIONER FULL_ALL > MINIMIZER DIIS > &END OT > &OUTER_SCF > EPS_SCF 1.0E-7 > MAX_SCF 20 > &END OUTER_SCF > &END SCF > &XC > &XC_FUNCTIONAL PBE > &END XC_FUNCTIONAL > &END XC > &END DFT > &SUBSYS > &KIND H > BASIS_SET TZVP-MOLOPT-GTH > POTENTIAL GTH-PBE-q1 > &END KIND > &KIND O > BASIS_SET TZVP-MOLOPT-GTH > POTENTIAL GTH-PBE-q6 > &END KIND > &COORD > O 7.424704500000000706e+00 9.621645000000000891e+00 > 1.106072519999999848e+01 > H 7.912573799999999657e+00 1.000790999999999897e+01 > 1.180680414000000056e+01 > H 6.473416799999999860e+00 9.760409999999998476e+00 > 1.119866495999999856e+01 > &END COORD > &CELL > PERIODIC XYZ > A 1.641000000000000014e+01 0.000000000000000000e+00 > 0.000000000000000000e+00 > B 0.000000000000000000e+00 1.650000000000000000e+01 > 0.000000000000000000e+00 > C 0.000000000000000000e+00 0.000000000000000000e+00 > 1.824599999999999866e+01 > &END CELL > &END SUBSYS > &PRINT > &FORCES ON > LOG_PRINT_KEY T > &END FORCES > &END PRINT > &END FORCE_EVAL > > > > I greatly appreciate any suggestions on fixing this. > > > > Thank you very much. > > > Best Regards, > > > > Geng > > > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/be04892b-30f6-4654-b51a-5acc8228e885%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: neutral_L30_e1500.inp Type: chemical/x-gamess-input Size: 4186 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: neutral_L30_e1500.out Type: application/octet-stream Size: 8668 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: optimized.dat Type: application/octet-stream Size: 780 bytes Desc: not available URL: From dev.... at gmail.com Thu Jun 4 16:26:35 2020 From: dev.... at gmail.com (Dev Rana) Date: Thu, 4 Jun 2020 09:26:35 -0700 (PDT) Subject: [CP2K-user] [CP2K:13447] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics? In-Reply-To: References: <6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e@googlegroups.com> <33c41f58c1a948209a7ba61ba36574ac@psi.ch> <206d8b04-4fb7-4076-8ad6-d7f609f50bf6@googlegroups.com> Message-ID: <461f1bb0-1c1e-4841-94c4-99731983785d@googlegroups.com> Hi Matthias, Thank you for your input. I understand that as the distance from C1 (carbon #1) to C2 (carbon #2) increases, the band gap decreases until only the valence electrons remains. When the distance between atoms becomes short, the electrons converge into the conduction band which allows a bond to form with overlapping electrons. Therefore, since my electrons were so far apart, they had no band gap to overcome. I understand your rationale for using a spin polarized run or smearing, and I have tried this using a 6 membered carbon ring, instead. i.e. all 6 atoms are close. Using SCCS & MD, it tells me that I need a stress tensor enabled. So I turn it on, then it says that SCCS is not configured for using the stress tensor. Therefore, I can't really run SCCS with MD, unless I use a SCF OT method. I guess I just don't understand how to run SCCS and MD with my system in which I'd like to see a reaction occurring between the 6 carbon atoms as they react into a ring or chain. What would you suggest? I apologize for the many questions, I'm a complete newbie with this stuff, with very little guidance as I am self-teaching these topics. Best Regards, Dev On Thursday, June 4, 2020 at 4:54:09 AM UTC-4, Matthias Krack wrote: > > Dev, > > > > your setup of a system of six separated carbon atoms does not have a band > gap and the addition of an implicit solvent won?t change that most likely. > The problem should show up already for a single isolated carbon atom which > you can converge either as a triplet within a spin polarized run (LSD and > MULTIP 3) or with smearing, i.e. with a fractional occupation of 2/3 for > the three degenerated C 2p orbitals. The latter approach works only with > diagonalization (try broyden_mixing). > > > > Matthias > > > > *From:* c... at googlegroups.com *On Behalf Of *Dev > Rana > *Sent:* Mittwoch, 3. Juni 2020 20:49 > *To:* cp2k > *Subject:* Re: [CP2K:13447] Is it possible to run a Andressui or > Fattebert Solvation Model with Molecular Dynamics? > > > > Thank you for the confirmation Matthias! Would you be able to look at my > input file? I'm having trouble with SCF convergence and my Andreussi model > set up. > > > > I'm trying to simulate 6 carbon atoms randomly placed as they migrate > through a molten Al system, using MD. Using the solvation model, I've set > up my 6 C atoms and have a dieletric constant of 80. I'm also attaching my > latest output file. > > > > I was originally using Diagonalization method for the SCF, but the > convergence column was migrating over 1. > > I then tried using OT with minimizer DIIS, Full_ALL preconditioner and > 0.001 energy_gap, as recommended for OT, and it stays below 1, however it > never converges. > > > > I'm also running this simulation without a solvation model using a full > system of 256 Al atom and 6 carbon atoms randomly placed in the system for > comparison, with no issues of convergence, i.e. each SCF converges within > 24-30 steps with each step taking about 22 seconds. > > > > Thank you so much for all your help thus far! I really appreciate it! > > > > Best Regards, > > Dev > > On Wednesday, June 3, 2020 at 12:42:32 PM UTC-4, Matthias Krack wrote: > > Yes. > > > > *From:* c... at googlegroups.com *On Behalf Of *Dev > Rana > *Sent:* Mittwoch, 3. Juni 2020 18:19 > *To:* cp2k > *Subject:* [CP2K:13443] Is it possible to run a Andressui or Fattebert > Solvation Model with Molecular Dynamics? > > > > As the question in the subject suggests, is it possible to run a solvation > model with MD? > > -- > 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 c... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e%40googlegroups.com > > . > > -- > 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 c... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/206d8b04-4fb7-4076-8ad6-d7f609f50bf6%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mshakiba.... at gmail.com Thu Jun 4 19:39:02 2020 From: mshakiba.... at gmail.com (Mohammad Shakiba) Date: Thu, 4 Jun 2020 12:39:02 -0700 (PDT) Subject: [CP2K-user] Can we obtain excited-states forces in TDDFPT using CP2K? Message-ID: <06aa203c-6b24-4f68-9428-d659b91a4338o@googlegroups.com> Hello everyone, My question is that is there a way to obtain the excited-states forces using CP2K? Thank you so much. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthi... at psi.ch Thu Jun 4 20:39:08 2020 From: matthi... at psi.ch (Krack Matthias (PSI)) Date: Thu, 4 Jun 2020 20:39:08 +0000 Subject: [CP2K-user] [CP2K:13460] energy jump in SCCS In-Reply-To: <9ba5de66-d129-4f24-8c09-139d9f834286@googlegroups.com> References: <16b1636efad847d0962ed6ba7fdb6361@psi.ch> <9ba5de66-d129-4f24-8c09-139d9f834286@googlegroups.com> Message-ID: Hi Tzu-Yao You may try smaller values for RHO_MAX and RHO_MIN. A cut-off of 600 Ry (maybe even 400 Ry) should large enough. HTH Matthias From: cp... at googlegroups.com On Behalf Of Tzu-Yao HSU Sent: Donnerstag, 4. Juni 2020 16:44 To: cp2k Subject: Re: [CP2K:13460] energy jump in SCCS Hi all, I got similar problem as Geng, but my calculation is pure DFT energy evaluation. During the SCF run, the polarisation energy abruptly jumped up to a positive value and the SCF convergence jumped down at certain convergence level . Then the polarisation energy always stayed positive until the SCF run converged. Here are my input file (.inp) and reduced output file (.out, grep 'Diag.' and 'Polarisation energy' then paste) . My molecular structure (optimized.dat) was obtained by performing GEO_OPT in vacuum. Further increasing the MGRID CUTOFF, EPS_SCF in SCCS section, simulation box size, and decreasing CUTOFFs in XC section do not change the converged energy. Since the converged polarisation energy is always positive, I still wonder how may I improve my input file? I appreciate any response to this problem. Thank you very much Best regards Tzu-Yao Matthias Krack? 2020?1?7???? UTC+1??7?40?51???? Hi Geng Such fluctuations are usually caused by numerical noise. A larger cutoff, e.g. 800 instead of 400Ry, will most likely resolve that issue. HTH Matthias From: c... at googlegroups.com > On Behalf Of Geng Sun Sent: Dienstag, 31. Dezember 2019 18:26 To: cp2k > Subject: [CP2K:12697] energy jump in SCCS Dear CP2K users, I am trying to use the SCCS solvent model to optimize a H2O molecule in solvent and calculate the solvation energy. I found that during the structure optimization, the total energy jumps up almost 3 eV, but the structure of H2O still looks good. Finally, with the energy obtained in solvent ( -17.07615353442375 a.u.) and energy in vacuum (-17.22203206260123), the solvation energy is positive. Therefore, there must be something wrong in the calculations, but I can not figure it out. grep "Total energy:" cp2k.out gives: Total energy: -17.22994560779211 Total energy: -17.23016218028583 Total energy: -17.23052945533816 Total energy: -17.23057483762070 Total energy: -17.23059795728501 Total energy: -17.23061684603447 Total energy: -17.23062875959604 Total energy: -17.23063230147527 Total energy: -17.23063606787884 Total energy: -17.23458599053544 Total energy: -17.07789974445440 Total energy: -17.23050622895307 Total energy: -17.23059409756609 Total energy: -17.23153569898144 Total energy: -17.23062905094530 Total energy: -17.23063896643257 Total energy: -17.06258564479369 Total energy: -17.23061553671926 Total energy: -17.23064419320881 Total energy: -17.23017384159302 Total energy: -17.09997174618866 Total energy: -17.23053249119082 Total energy: -17.23061888501270 Total energy: -17.23062632201262 Total energy: -17.10641501376824 Total energy: -17.23063629047595 Total energy: -17.23099984646603 Total energy: -17.11100171504137 Total energy: -17.10215507558170 Total energy: -17.13946950681089 Total energy: -17.05320236101690 Total energy: -17.23214150951693 Total energy: -17.14172122406513 Total energy: -17.05319840556444 Total energy: -17.06170695684858 Total energy: -17.11231720859150 Total energy: -17.07455263629729 Total energy: -17.07623660559768 Total energy: -17.07963295606425 Total energy: -17.07859069368490 Total energy: -17.07694563368373 Total energy: -17.07637515123947 Total energy: -17.07632103460653 Total energy: -17.07605114342309 Total energy: -17.07615353442375 Here is the input file: &FORCE_EVAL &DFT UKS BASIS_SET_FILE_NAME BASIS_MOLOPT_UCL BASIS_SET_FILE_NAME BASIS_MOLOPT POTENTIAL_FILE_NAME GTH_POTENTIALS &MGRID CUTOFF 400 COMMENSURATE &END MGRID &QS EXTRAPOLATION PS EXTRAPOLATION_ORDER 3 EPS_DEFAULT 1.0E-12 MAP_CONSISTENT T &END QS &PRINT &SCCS ON &EACH QS_SCF 1 &END EACH &END SCCS &END PRINT &SCCS ALPHA [N*m^-1] 0.02 GAMMA [mN/m] 0.0 BETA [GPa] -0.08 DELTA_RHO 2.0E-5 DERIVATIVE_METHOD CD5 DIELECTRIC_CONSTANT 6.02 EPS_SCCS 1.0E-10 EPS_SCF 0.03 MAX_ITER 100 METHOD Andreussi MIXING 0.6 &ANDREUSSI RHO_MAX 0.003 RHO_MIN 0.0003 &END ANDREUSSI &END SCCS &SCF EPS_SCF 1.0E-7 MAX_SCF 31 SCF_GUESS RESTART &OT ENERGY_GAP 0.002 LINESEARCH 2PNT PRECONDITIONER FULL_ALL MINIMIZER DIIS &END OT &OUTER_SCF EPS_SCF 1.0E-7 MAX_SCF 20 &END OUTER_SCF &END SCF &XC &XC_FUNCTIONAL PBE &END XC_FUNCTIONAL &END XC &END DFT &SUBSYS &KIND H BASIS_SET TZVP-MOLOPT-GTH POTENTIAL GTH-PBE-q1 &END KIND &KIND O BASIS_SET TZVP-MOLOPT-GTH POTENTIAL GTH-PBE-q6 &END KIND &COORD O 7.424704500000000706e+00 9.621645000000000891e+00 1.106072519999999848e+01 H 7.912573799999999657e+00 1.000790999999999897e+01 1.180680414000000056e+01 H 6.473416799999999860e+00 9.760409999999998476e+00 1.119866495999999856e+01 &END COORD &CELL PERIODIC XYZ A 1.641000000000000014e+01 0.000000000000000000e+00 0.000000000000000000e+00 B 0.000000000000000000e+00 1.650000000000000000e+01 0.000000000000000000e+00 C 0.000000000000000000e+00 0.000000000000000000e+00 1.824599999999999866e+01 &END CELL &END SUBSYS &PRINT &FORCES ON LOG_PRINT_KEY T &END FORCES &END PRINT &END FORCE_EVAL I greatly appreciate any suggestions on fixing this. Thank you very much. Best Regards, Geng -- 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 c... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/be04892b-30f6-4654-b51a-5acc8228e885%40googlegroups.com. -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/9ba5de66-d129-4f24-8c09-139d9f834286%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthi... at psi.ch Thu Jun 4 20:53:34 2020 From: matthi... at psi.ch (Krack Matthias (PSI)) Date: Thu, 4 Jun 2020 20:53:34 +0000 Subject: [CP2K-user] [CP2K:13461] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics? In-Reply-To: <461f1bb0-1c1e-4841-94c4-99731983785d@googlegroups.com> References: <6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e@googlegroups.com> <33c41f58c1a948209a7ba61ba36574ac@psi.ch> <206d8b04-4fb7-4076-8ad6-d7f609f50bf6@googlegroups.com> <461f1bb0-1c1e-4841-94c4-99731983785d@googlegroups.com> Message-ID: <46fb58f32aaf47ab9733b1d985ae62f9@psi.ch> Hi Dev a stress tensor is available with SCCS only in the current development version of CP2K and not in any earlier version including the release version 7.1. Note, that the stress tensor is only needed for MD ensembles with a barostat like NpT, i.e. NVT or NVE should work also with earlier versions. HTH Matthias From: cp... at googlegroups.com On Behalf Of Dev Rana Sent: Donnerstag, 4. Juni 2020 18:26 To: cp2k Subject: Re: [CP2K:13461] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics? Hi Matthias, Thank you for your input. I understand that as the distance from C1 (carbon #1) to C2 (carbon #2) increases, the band gap decreases until only the valence electrons remains. When the distance between atoms becomes short, the electrons converge into the conduction band which allows a bond to form with overlapping electrons. Therefore, since my electrons were so far apart, they had no band gap to overcome. I understand your rationale for using a spin polarized run or smearing, and I have tried this using a 6 membered carbon ring, instead. i.e. all 6 atoms are close. Using SCCS & MD, it tells me that I need a stress tensor enabled. So I turn it on, then it says that SCCS is not configured for using the stress tensor. Therefore, I can't really run SCCS with MD, unless I use a SCF OT method. I guess I just don't understand how to run SCCS and MD with my system in which I'd like to see a reaction occurring between the 6 carbon atoms as they react into a ring or chain. I apologize for the many questions, I'm a complete newbie with this stuff, with very little guidance as I am self-teaching these topics. Best Regards, Dev On Thursday, June 4, 2020 at 4:54:09 AM UTC-4, Matthias Krack wrote: Dev, your setup of a system of six separated carbon atoms does not have a band gap and the addition of an implicit solvent won?t change that most likely. The problem should show up already for a single isolated carbon atom which you can converge either as a triplet within a spin polarized run (LSD and MULTIP 3) or with smearing, i.e. with a fractional occupation of 2/3 for the three degenerated C 2p orbitals. The latter approach works only with diagonalization (try broyden_mixing). Matthias From: c... at googlegroups.com > On Behalf Of Dev Rana Sent: Mittwoch, 3. Juni 2020 20:49 To: cp2k > Subject: Re: [CP2K:13447] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics? Thank you for the confirmation Matthias! Would you be able to look at my input file? I'm having trouble with SCF convergence and my Andreussi model set up. I'm trying to simulate 6 carbon atoms randomly placed as they migrate through a molten Al system, using MD. Using the solvation model, I've set up my 6 C atoms and have a dieletric constant of 80. I'm also attaching my latest output file. I was originally using Diagonalization method for the SCF, but the convergence column was migrating over 1. I then tried using OT with minimizer DIIS, Full_ALL preconditioner and 0.001 energy_gap, as recommended for OT, and it stays below 1, however it never converges. I'm also running this simulation without a solvation model using a full system of 256 Al atom and 6 carbon atoms randomly placed in the system for comparison, with no issues of convergence, i.e. each SCF converges within 24-30 steps with each step taking about 22 seconds. Thank you so much for all your help thus far! I really appreciate it! Best Regards, Dev On Wednesday, June 3, 2020 at 12:42:32 PM UTC-4, Matthias Krack wrote: Yes. From: c... at googlegroups.com > On Behalf Of Dev Rana Sent: Mittwoch, 3. Juni 2020 18:19 To: cp2k > Subject: [CP2K:13443] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics? As the question in the subject suggests, is it possible to run a solvation model with MD? -- 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 c... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e%40googlegroups.com. -- 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 c... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/206d8b04-4fb7-4076-8ad6-d7f609f50bf6%40googlegroups.com. -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/461f1bb0-1c1e-4841-94c4-99731983785d%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chen... at gmail.com Fri Jun 5 07:35:39 2020 From: chen... at gmail.com (Chn) Date: Fri, 5 Jun 2020 00:35:39 -0700 (PDT) Subject: [CP2K-user] Question about vibrational analysis Message-ID: Dear experts in CP2K, I am a beginner of CP2K package and I am really thankful if my naive question can be explained. The model is PdCd (111) with small molecule adsorbed on it. When performing a GEO_OPT calculation, I added the keyword "UKS" for spin-polarized calculation in the section "DFT", due to the transition metals that are Pd and Cd atoms in the system according to the tutorials online. However it requires me about three times higher times for the calculation. For the vibrational analysis of the adsorbed molecule, a very tight threshold is needed for "EPS_SCF" to get accurate low frequencies, it will take me too much time. I do not know weather the keyword "UKS" is still necessary here. Many thanks in advance! Regards, chn -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Fri Jun 5 11:42:00 2020 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Fri, 5 Jun 2020 13:42:00 +0200 Subject: [CP2K-user] [CP2K:13462] Can we obtain excited-states forces in TDDFPT using CP2K? In-Reply-To: <06aa203c-6b24-4f68-9428-d659b91a4338o@googlegroups.com> References: <06aa203c-6b24-4f68-9428-d659b91a4338o@googlegroups.com> Message-ID: Hi this functionality is not available in CP2K. There is work in progress on this, but no immediate release anticipated. regards Juerg Hutter -------------------------------------------------------------- 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: "Mohammad Shakiba" Sent by: cp... at googlegroups.com Date: 06/04/2020 09:39PM Subject: [CP2K:13462] Can we obtain excited-states forces in TDDFPT using CP2K? Hello everyone, My question is that is there a way to obtain the excited-states forces using CP2K? Thank you so much. -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/06aa203c-6b24-4f68-9428-d659b91a4338o%40googlegroups.com. From sergi... at gmail.com Fri Jun 5 11:49:50 2020 From: sergi... at gmail.com (Sergiu C) Date: Fri, 5 Jun 2020 04:49:50 -0700 (PDT) Subject: [CP2K-user] [CP2K:10523] Re: reference position bug during dipole moment calculation? In-Reply-To: References: ,> Message-ID: <68ddedd5-2f8d-4425-b2de-a04fe3a78515o@googlegroups.com> Dear CP2K developers, does the printed electric dipole moment sign correspond to normal convention for electric dipole (from negative pole to positive pole)? Thank you. Sergiu On Friday, July 13, 2018 at 6:22:01 PM UTC+2, jgh wrote: > > Hi > > have you checked that the reference point in the output is just > a periodic image of your input value? > Internally we do: > r_val = PBC(r_val) > > 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: h... at chem.uzh.ch > > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----"'Phil G.' via cp2k" > wrote: > ----- > To: "cp2k" > > From: "'Phil G.' via cp2k" > > Date: 07/13/2018 11:51AM > Subject: [CP2K:10523] Re: reference position bug during dipole moment > calculation? > > Dear Matt and Juergen, > > thank you for your replies and hints. > > @Matt: because I want to calculate the bulk polarization, I have to use > the periodic system. So the Berry phase method was used (in the DFT/PRINT > section under MOMENTS I used PERIODIC .TRUE.). Do you think that the result > would be different if I use non-periodic setup as you suggested? > > @Juerg: yes, exactly I get the same results (with very small distinctions > of the dipole moments after using different reference points). But why is > the value of the polarization (as calculated by the dipole moment per slab > volume) much smaller than the experimentally obtained value? > I would like to add a remark (as in my first mail above) that the sign of > Y-value of the reference point is opposite than I gave it (e.g. if I write > Y=a_y /2 (user defined value), then in the dipole moment output file it > looks so: Y= - a_y / 2 , with an opposite sign). Is there a bug? > > Kind regards, > > Phil > > > Am Donnerstag, 12. Juli 2018 16:33:06 UTC+2 schrieb Phil G.: > Dear all, > > in order to get a bulk polarization of a ferroelectric slab system (2x2x1 > slab with 3D periodic boundary condition) I let CP2K start to calculate the > dipole moments of the slab system (in fact the unit cell has the hexagonal > shape, but it does not matter if I cut off a piece of the large system of > the duplicates of the unit cell in xyz coordinate system and this cut piece > satisfy the 3D pbc in the xyz coordinate system?). In order to check the > influence of the choice of a reference point on the dipole moment > calculation, I let start several calculations with different reference > points, e.g. COAC, ZERO, user_defined -> reference_point x y z. > > If using the reference_point ZERO, then I notice an non-explainable > difference between the quantity of the dipole moments for up-polarized slab > and down-polarized slab (the slabs are the same, but are only 180 degree > rotated to each other) and it seems to be the false choice for the dipole > moment calculation. > If I use COAC as the reference point, then the both dipole moment values > are almost of the same quantity (absolute value) in z direction, but of > opposite sign (which is correct). If using COM as the reference point, then > I am wondering why not really the center of the slab was used as expected > (consider the slab system with lengths a_x, a_y, and c_z along the three > x,y,z coordinate axes, so I expect the COM to be nearly at {a_x / 2, a_y / > 2, c_z / 2}, but in the dipole moment file the reference point lies outside > of the slab system. Why? > If using the reference_point USER_DEFINED, REFERENCE_POINT X Y Z , in > which X, Y, and Z are of an arbitrary choice, for example at the center of > the top slab surface (X=a_x / 2 , Y=a_y / 2, Z=0) and the z=0 is exactly > the surface and below it there is the 2x2x1 slab system (i.e. with negative > c_z lying in the bottom slab surface), then after calculation I get the > info from dipole moment file that the y value has the opposite sign. Is > there a bug in the cp2k during the dipole moment calculation? > > After obtaining the calculated dipole moment values, I am able to > calculate the bulk polarization if the z-dipole moment (which is much > larger than in x- and y- directions) is divided by the slab volume (2x2x1 > unit cells in the x,y,z coordinate system). Is that correct? If yes, why > the value is much smaller compared to the experimental value at room > temperature? (e.g. the experimental value of the polarization is 0.71 C/m^2 > [APL 12 (2009), 209] and the calculated value is 0.042 C/m^2 , i.e. it is > at least one order of magnitude smaller). > Is there any mistake I have calculated or should I take account anything > for correct polarization calculation? > > The input file, output and dipole moment file after 200 geometry > optimization steps are attached here below. > > Kind regards, > > Phil > > > -- > 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 c... at googlegroups.com . > To post to this group, send email to c... 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 mshakiba.... at gmail.com Fri Jun 5 19:15:41 2020 From: mshakiba.... at gmail.com (Mohammad Shakiba) Date: Fri, 5 Jun 2020 12:15:41 -0700 (PDT) Subject: [CP2K-user] [CP2K:13462] Can we obtain excited-states forces in TDDFPT using CP2K? In-Reply-To: References: <06aa203c-6b24-4f68-9428-d659b91a4338o@googlegroups.com> Message-ID: <8a4308d6-5f95-4e13-91db-304478168964o@googlegroups.com> Dear Prof. Hutter, Thank you so much for your reply. On Friday, June 5, 2020 at 4:12:11 PM UTC+4:30, jgh wrote: > > Hi > > this functionality is not available in CP2K. There is work in progress > on this, but no immediate release anticipated. > > regards > > Juerg Hutter > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: h... at chem.uzh.ch > > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----c... at googlegroups.com wrote: ----- > To: "cp2k" > > From: "Mohammad Shakiba" > Sent by: c... at googlegroups.com > Date: 06/04/2020 09:39PM > Subject: [CP2K:13462] Can we obtain excited-states forces in TDDFPT using > CP2K? > > Hello everyone, > > My question is that is there a way to obtain the excited-states forces > using CP2K? > > Thank you so much. > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/06aa203c-6b24-4f68-9428-d659b91a4338o%40googlegroups.com. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From k501... at gmail.com Sat Jun 6 00:48:37 2020 From: k501... at gmail.com (Shao-Chun Lee) Date: Fri, 5 Jun 2020 17:48:37 -0700 (PDT) Subject: [CP2K-user] What is the default unit of dipole for ions? Message-ID: <440835be-6fa1-40d8-986a-3e394dafbed4o@googlegroups.com> Hi, When using CP2K_INPUT / FORCE_EVAL / SUBSYS / MULTIPOLES / DIPOLES to specify the dipole of each ion, what unit should I assume? Is it Debye, atomic unit (e*bohr), or e*Angstrom? Thanks, Lee, Shao-Chun -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikhail19... at gmail.com Sat Jun 6 12:36:26 2020 From: mikhail19... at gmail.com (Ref) Date: Sat, 6 Jun 2020 05:36:26 -0700 (PDT) Subject: [CP2K-user] Calculation of PDOS Message-ID: <34a4b50b-0556-43e5-a25e-3285a486aee0o@googlegroups.com> Hello, I want to plot PDOS of some compound. I want to understand in which units of measurement PDOS is given after the algorithm &PDOS # print all projected DOS available: NLUMO -1 # split the density by quantum number: COMPONENTS &END PDOS is executed and the received data is processed by a script https://wiki.wpi.edu/deskinsgroup/Density_of_States_-_CP2K, a link to which is recorded on the CP2K website. I set the cell, followed by multiplication. Does the script give the number of states per unit cell or supercell? Is the number of states normalized to one unit of volume? The initial data PDOS before processing by scripts consist of numbers less than 1. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hale.m... at live.com Sat Jun 6 17:01:22 2020 From: hale.m... at live.com (Michael Hale) Date: Sat, 6 Jun 2020 10:01:22 -0700 (PDT) Subject: [CP2K-user] [CP2K:13450] Visualize electron density during formation of a water molecule In-Reply-To: <533942f6-e28d-402b-992e-bdc724ec9e6f@googlegroups.com> References: <533942f6-e28d-402b-992e-bdc724ec9e6f@googlegroups.com> Message-ID: <59156e08-bd00-4591-b2c1-878ac6010be5o@googlegroups.com> Well I filled out the input file as well as I could figure out from your tips. CP2K runs for a few minutes and then aborts with the error "KS energy is an abnormal value (NaN/Inf)". I tried setting a small MAX_SCF value, but it still hits that error. Any other tips? Here is my input file: &GLOBAL PROJECT water-formation RUN_TYPE MD PRINT_LEVEL LOW &END GLOBAL &MOTION &MD ENSEMBLE NVT &THERMOSTAT TYPE CSVR &END THERMOSTAT &END MD &END MOTION &FORCE_EVAL &SUBSYS &KIND H BASIS_SET DZVP-GTH-PADE POTENTIAL GTH-PADE-q1 &END KIND &KIND O BASIS_SET DZVP-GTH-PADE POTENTIAL GTH-PADE-q6 &END KIND &CELL ABC 10 10 10 PERIODIC NONE &END CELL &COORD H 4.0 4.0 4.66667 H 6.0 6.0 4.66667 O 5.0 5.0 5.66667 &END COORD &END SUBSYS &DFT BASIS_SET_FILE_NAME data/BASIS_SET POTENTIAL_FILE_NAME data/POTENTIAL LSD &SCF ADDED_MOS 10 &DIAGONALIZATION &END DIAGONALIZATION &MIXING METHOD BROYDEN_MIXING &END MIXING &SMEAR METHOD FERMI_DIRAC &END SMEAR &END SCF &XC &XC_FUNCTIONAL PADE &END XC_FUNCTIONAL &END XC &PRINT &E_DENSITY_CUBE &EACH MD 1 &END EACH FILENAME CUBE &END E_DENSITY_CUBE &END PRINT &END DFT &END FORCE_EVAL On Thursday, June 4, 2020 at 10:10:06 AM UTC-4, Michael Hale wrote: > > Great! Thank you. I'll look into those options and hopefully mess with it > some more this weekend. > > Is there much of a hobbyist community around computational chemistry? I'm > a pretty experienced software developer, but still new to this. I know > there are projects like Folding at Home which don't give you much control, and > Chemistry Stack Exchange which is more just traditional Q&A. But I'd love > to find community projects to help enhance digital chemistry textbooks with > ab initio quantum MD animations of common reactions and such. > > I actually first tried this during a weekend a couple of years ago. Here > was the result: > https://www.youtube.com/watch?v=foG5LgFYb2o > > I finally revisited it a week or two ago. I thought maybe just my initial > conditions needed to be tweaked, but then I realized my simulation set up > had deeper problems, haha. Thanks again for your help. I hope to post an > update again soon. > > On Thursday, June 4, 2020 at 9:26:25 AM UTC-4, jgh wrote: >> >> Hi >> >> What I would do: >> >> Small basis e.g. DZVP >> LSD >> SCF with Diagonalization and Broyden mixing, use all MOs >> Fermi-Dirac Smearing with high temperature >> NVT MD with velocity rescaling to get rid of excessive energy >> Print CUBE file automatically during MD >> >> regards >> >> Juerg Hutter >> -------------------------------------------------------------- >> Juerg Hutter Phone : ++41 44 635 4491 >> Institut f?r Chemie C FAX : ++41 44 635 6838 >> Universit?t Z?rich E-mail: h... at chem.uzh.ch >> Winterthurerstrasse 190 >> CH-8057 Z?rich, Switzerland >> --------------------------------------------------------------- >> >> -----c... at googlegroups.com wrote: ----- >> To: "cp2k" >> From: "Michael Hale" >> Sent by: c... at googlegroups.com >> Date: 06/04/2020 05:08AM >> Subject: [CP2K:13450] Visualize electron density during formation of a >> water molecule >> >> Hey, sorry for the basic question. I've skimmed some computational >> chemistry books, but I still find the CP2K documentation a bit >> overwhelming. I'm trying to put two hydrogens an an oxygen atom near each >> other and watch the spontaneous assembly of a water molecule. I can make >> the input file and have CP2K output the forces on the atoms and a cube file >> that I can use to make a 3D visualization of the electron density in >> Mathematica. Then I update the atom positions with a simple velocity Verlet >> update and run CP2K again. The resulting animation looks how I want >> stylistically, but the behavior is clearly not accurate. The atoms come >> together and bounce off of each other and come back together and bounce off >> harder. They keep getting more energy and bouncing farther and farther away >> until they fly apart instead of bonding together. >> >> Is the error that the energy calculation for the forces and electron >> density isn't converging and causing the erratic behavior? Is the error >> probably in the way I'm updating the atom positions manually? Can I use the >> CP2K molecular dynamics functionality to do multiple steps of the >> simulation at once while also outputting the cube file of the electron >> density for each step? Is this type of simulation of the formation of small >> molecules within the scope of CP2K? It seems most people typically assume >> the molecules are already formed and they just want to simulate how those >> molecules interact, not how atoms come together to form the small >> molecules. >> >> This is all just for fun. I just want to watch the animations and see how >> "sticky" the atoms and molecules are. Thanks for any help and guidance you >> might provide. >> -- >> 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 c... at googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/cp2k/e90450de-cd30-4bad-ae96-96779a50764e%40googlegroups.com. >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dev.... at gmail.com Sat Jun 6 20:03:49 2020 From: dev.... at gmail.com (Dev Rana) Date: Sat, 6 Jun 2020 13:03:49 -0700 (PDT) Subject: [CP2K-user] [CP2K:13461] Is it possible to run a Andressui or Fattebert Solvation Model with Molecular Dynamics? In-Reply-To: <46fb58f32aaf47ab9733b1d985ae62f9@psi.ch> References: <6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e@googlegroups.com> <33c41f58c1a948209a7ba61ba36574ac@psi.ch> <206d8b04-4fb7-4076-8ad6-d7f609f50bf6@googlegroups.com> <461f1bb0-1c1e-4841-94c4-99731983785d@googlegroups.com> <46fb58f32aaf47ab9733b1d985ae62f9@psi.ch> Message-ID: <60867d7d-83e5-4a6e-a4a7-72b570f3666do@googlegroups.com> Hi Matthias, Ahh! Ok, this makes sense. I was trying to use NPT_F as the simulation we are trying to accomplish is for a real world system in which P (pressure at atmosphere) and T are actually held constant. Therefore I was using a thermostat and barostat with a large enough cell that it would not contribute to excessive pressures. I can try running NVT or NVE. On Thursday, June 4, 2020 at 4:53:37 PM UTC-4, Matthias Krack wrote: > > Hi Dev > > > > a stress tensor is available with SCCS only in the current development > version of CP2K and not in any earlier version including the release > version 7.1. Note, that the stress tensor is only needed for MD ensembles > with a barostat like NpT, i.e. NVT or NVE should work also with earlier > versions. > > > > HTH > > > > Matthias > > > > *From:* c... at googlegroups.com > *On Behalf Of *Dev Rana > *Sent:* Donnerstag, 4. Juni 2020 18:26 > *To:* cp2k > > *Subject:* Re: [CP2K:13461] Is it possible to run a Andressui or > Fattebert Solvation Model with Molecular Dynamics? > > > > Hi Matthias, > > > > Thank you for your input. I understand that as the distance from C1 > (carbon #1) to C2 (carbon #2) increases, the band gap decreases until only > the valence electrons remains. When the distance between atoms becomes > short, the electrons converge into the conduction band which allows a bond > to form with overlapping electrons. Therefore, since my electrons were so > far apart, they had no band gap to overcome. I understand your rationale > for using a spin polarized run or smearing, and I have tried this using a 6 > membered carbon ring, instead. i.e. all 6 atoms are close. Using SCCS & MD, > it tells me that I need a stress tensor enabled. So I turn it on, then it > says that SCCS is not configured for using the stress tensor. Therefore, I > can't really run SCCS with MD, unless I use a SCF OT method. > > > > I guess I just don't understand how to run SCCS and MD with my system in > which I'd like to see a reaction occurring between the 6 carbon atoms as > they react into a ring or chain. > > > > I apologize for the many questions, I'm a complete newbie with this stuff, > with very little guidance as I am self-teaching these topics. > > > > Best Regards, > > Dev > > On Thursday, June 4, 2020 at 4:54:09 AM UTC-4, Matthias Krack wrote: > > Dev, > > > > your setup of a system of six separated carbon atoms does not have a band > gap and the addition of an implicit solvent won?t change that most likely. > The problem should show up already for a single isolated carbon atom which > you can converge either as a triplet within a spin polarized run (LSD and > MULTIP 3) or with smearing, i.e. with a fractional occupation of 2/3 for > the three degenerated C 2p orbitals. The latter approach works only with > diagonalization (try broyden_mixing). > > > > Matthias > > > > *From:* c... at googlegroups.com *On Behalf Of *Dev > Rana > *Sent:* Mittwoch, 3. Juni 2020 20:49 > *To:* cp2k > *Subject:* Re: [CP2K:13447] Is it possible to run a Andressui or > Fattebert Solvation Model with Molecular Dynamics? > > > > Thank you for the confirmation Matthias! Would you be able to look at my > input file? I'm having trouble with SCF convergence and my Andreussi model > set up. > > > > I'm trying to simulate 6 carbon atoms randomly placed as they migrate > through a molten Al system, using MD. Using the solvation model, I've set > up my 6 C atoms and have a dieletric constant of 80. I'm also attaching my > latest output file. > > > > I was originally using Diagonalization method for the SCF, but the > convergence column was migrating over 1. > > I then tried using OT with minimizer DIIS, Full_ALL preconditioner and > 0.001 energy_gap, as recommended for OT, and it stays below 1, however it > never converges. > > > > I'm also running this simulation without a solvation model using a full > system of 256 Al atom and 6 carbon atoms randomly placed in the system for > comparison, with no issues of convergence, i.e. each SCF converges within > 24-30 steps with each step taking about 22 seconds. > > > > Thank you so much for all your help thus far! I really appreciate it! > > > > Best Regards, > > Dev > > On Wednesday, June 3, 2020 at 12:42:32 PM UTC-4, Matthias Krack wrote: > > Yes. > > > > *From:* c... at googlegroups.com *On Behalf Of *Dev > Rana > *Sent:* Mittwoch, 3. Juni 2020 18:19 > *To:* cp2k > *Subject:* [CP2K:13443] Is it possible to run a Andressui or Fattebert > Solvation Model with Molecular Dynamics? > > > > As the question in the subject suggests, is it possible to run a solvation > model with MD? > > -- > 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 c... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/6b67935a-b8b5-4e7d-b2b7-75b03cfbd73e%40googlegroups.com > > . > > -- > 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 c... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/206d8b04-4fb7-4076-8ad6-d7f609f50bf6%40googlegroups.com > > . > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/461f1bb0-1c1e-4841-94c4-99731983785d%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eluni... at gmail.com Sun Jun 7 02:09:20 2020 From: eluni... at gmail.com (Lucas Lodeiro) Date: Sat, 6 Jun 2020 22:09:20 -0400 Subject: [CP2K-user] Restart NVT Message-ID: Hi all, I am running NVT water box AIMD in CP2K 7.0. The run stopped this morning due to node problem, but I can restart it using the restart file. But I see some differences that I can not understand. I use the same input data to do the restart, but I added: &EXT_RESTART EXTERNAL_FILE WATER-1.restart RESTART_THERMOSTAT .FALSE. &END EXT_RESTART To restart the calculation and to not restart the thermostat. I guess this is the correct way to restart a MD without changing the thermostat behaviour. But in the first step I see some weird data in *.ener file. I see in the first new step, the Cons Qty[a.u.] change a little, respect the last step after MD stopped. Also for the n-last steps after MD stopped, the temperature oscillates just +-10?C around the objective temperature and the average temperature was the correct objective temperature. In the first n-steps of the restart MD, the temperature starts oscillating more than 10 ?C (in cases 30?C), but the average temperature was correct respect the last average temperature and objective temperature. This is a part of the data (step 28945 is the first step of restart MD): 28925 14462.500000 0.524397237 292.822905020 -2167.386128946 -2166.788489113 9.942549903 28926 14463.000000 0.523902002 292.546366555 -2167.385787588 -2166.788513509 18.580139473 28927 14463.500000 0.521503538 291.207066513 -2167.383420424 -2166.788416738 15.250579394 28928 14464.000000 0.518609792 289.591201566 -2167.380528831 -2166.788292618 17.792272486 28929 14464.500000 0.517109605 288.753498602 -2167.379085941 -2166.788225441 10.424001478 28930 14465.000000 0.518164941 289.342797441 -2167.380271236 -2166.788232301 9.924992632 28931 14465.500000 0.521824007 291.386016117 -2167.384120605 -2166.788300216 15.055006087 28932 14466.000000 0.527128166 294.347853254 -2167.389667610 -2166.788420716 10.627952956 28933 14466.500000 0.532342877 297.259742512 -2167.395139856 -2166.788555528 14.917385891 28934 14467.000000 0.535600841 299.078986930 -2167.398592480 -2166.788627084 10.879262459 28935 14467.500000 0.535936944 299.266666470 -2167.399018273 -2166.788593698 10.006427173 28936 14468.000000 0.533834852 298.092860267 -2167.396936550 -2166.788491610 9.977815259 28937 14468.500000 0.530754526 296.372809252 -2167.393877604 -2166.788391632 10.085333489 28938 14469.000000 0.528128677 294.906537823 -2167.391326816 -2166.788346629 10.028149899 28939 14469.500000 0.526585940 294.045074707 -2167.389919732 -2166.788363449 9.960049219 28940 14470.000000 0.525859267 293.639301105 -2167.389345953 -2166.788398597 14.496977419 28941 14470.500000 0.525379287 293.371280876 -2167.388985539 -2166.788401415 14.967396073 28942 14471.000000 0.524959273 293.136745417 -2167.388649341 -2166.788369463 10.315914560 28943 14471.500000 0.524874770 293.089558993 -2167.388653910 -2166.788343715 16.983571853 28944 14472.000000 0.525392050 293.378407716 -2167.389290137 -2166.788348686 12.119731613 28945 14472.500000 0.526406871 293.945083066 -2167.390481370 -2166.863446252 47.022801183 28946 14473.000000 0.527734481 294.686419018 -2167.391978869 -2166.863459996 11.051850852 28947 14473.500000 0.529255279 295.535631285 -2167.393652283 -2166.863456336 10.006576888 28948 14474.000000 0.531086126 296.557974111 -2167.395616229 -2166.863432883 9.709443437 28949 14474.500000 0.533577404 297.949101425 -2167.398244277 -2166.863412585 9.787318693 28950 14475.000000 0.537016875 299.869698620 -2167.401858321 -2166.863429212 9.785394795 28951 14475.500000 0.541258217 302.238060033 -2167.406305123 -2166.863475419 9.731476160 28952 14476.000000 0.545774333 304.759854865 -2167.411027429 -2166.863520675 9.752394203 28953 14476.500000 0.549990896 307.114379332 -2167.415448002 -2166.863561837 9.763660893 28954 14477.000000 0.553359699 308.995515632 -2167.419028509 -2166.863608727 9.769082915 28955 14477.500000 0.555299389 310.078636660 -2167.421167132 -2166.863641041 9.809159193 28956 14478.000000 0.555434584 310.154129550 -2167.421461446 -2166.863632113 9.759279175 28957 14478.500000 0.553874622 309.283048227 -2167.420037090 -2166.863598770 9.749239432 28958 14479.000000 0.551014039 307.685701343 -2167.417323889 -2166.863576839 9.767714364 28959 14479.500000 0.547123637 305.513304502 -2167.413592074 -2166.863566261 9.815094918 28960 14480.000000 0.542330631 302.836894640 -2167.408945453 -2166.863544138 9.748038203 28961 14480.500000 0.536899528 299.804172240 -2167.403638144 -2166.863500571 10.112055471 28962 14481.000000 0.531402812 296.734811186 -2167.398244733 -2166.863438049 9.841474611 28963 14481.500000 0.526676227 294.095490925 -2167.393620245 -2166.863376014 9.819765911 28964 14482.000000 0.523490986 292.316855534 -2167.390580350 -2166.863358790 9.816407133 28965 14482.500000 0.521971605 291.468434880 -2167.389273875 -2166.863410344 9.819614979 28966 14483.000000 0.521357575 291.125560959 -2167.388891848 -2166.863481893 9.822640346 Why is happening this step shift in the conserved quantity, and the change in the temperature MD behaviour? Is this normal for a restart MD? Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From nju... at gmail.com Sun Jun 7 10:08:35 2020 From: nju... at gmail.com (Hua Tian) Date: Sun, 7 Jun 2020 03:08:35 -0700 (PDT) Subject: [CP2K-user] Has CP2K supported the analytical stress tensor for meta-GGA functionals? Message-ID: <05646988-c84f-4c12-9020-d3128507385bo@googlegroups.com> Dear CP2K developers, In the past versions of CP2K, the analytical stress tensor for meta-GGA functionals was not supported because of the using of laplacian of the density, as mentioned by Prof. Hutter. That made some researchers have to turn to other softwares to perform the FPMD simulations in NPT ensemble, e.g., DOI: 10.1039/c6sc04711d. In recent years, meta-GGA functionals progress rapidly, and have played an increasingly important role in DFT calculations. I am wondering if the analytical stress tensor for meta-GGA functionals has been supported in the newest version of CP2K, or this problem can be solved in the near future? Sincerely, Tian Hua -------------- next part -------------- An HTML attachment was scrubbed... URL: From tku... at gmail.com Sun Jun 7 10:34:49 2020 From: tku... at gmail.com (=?utf-8?Q?Thomas_K=C3=BChne?=) Date: Sun, 7 Jun 2020 12:34:49 +0200 Subject: [CP2K-user] [CP2K:13472] Restart NVT In-Reply-To: References: Message-ID: Dear Lucas simply set RESTART_THERMOSTAT TRUE (or remove the line since this is the default) to restart the state of the thermostat. The behavior you observe is an artifact due to restarting positions and velocities but resetting the thermostat ? Cheers, Thomas > Am 07.06.2020 um 04:09 schrieb Lucas Lodeiro : > > Hi all, > > I am running NVT water box AIMD in CP2K 7.0. > The run stopped this morning due to node problem, but I can restart it using the restart file. > But I see some differences that I can not understand. > > I use the same input data to do the restart, but I added: > > &EXT_RESTART > EXTERNAL_FILE WATER-1.restart > RESTART_THERMOSTAT .FALSE. > &END EXT_RESTART > > To restart the calculation and to not restart the thermostat. I guess this is the correct way to restart a MD without changing the thermostat behaviour. > But in the first step I see some weird data in *.ener file. > I see in the first new step, the Cons Qty[a.u.] change a little, respect the last step after MD stopped. > Also for the n-last steps after MD stopped, the temperature oscillates just +-10?C around the objective temperature and the average temperature was the correct objective temperature. In the first n-steps of the restart MD, the temperature starts oscillating more than 10 ?C (in cases 30?C), but the average temperature was correct respect the last average temperature and objective temperature. > This is a part of the data (step 28945 is the first step of restart MD): > > 28925 14462.500000 0.524397237 292.822905020 -2167.386128946 -2166.788489113 9.942549903 > 28926 14463.000000 0.523902002 292.546366555 -2167.385787588 -2166.788513509 18.580139473 > 28927 14463.500000 0.521503538 291.207066513 -2167.383420424 -2166.788416738 15.250579394 > 28928 14464.000000 0.518609792 289.591201566 -2167.380528831 -2166.788292618 17.792272486 > 28929 14464.500000 0.517109605 288.753498602 -2167.379085941 -2166.788225441 10.424001478 > 28930 14465.000000 0.518164941 289.342797441 -2167.380271236 -2166.788232301 9.924992632 > 28931 14465.500000 0.521824007 291.386016117 -2167.384120605 -2166.788300216 15.055006087 > 28932 14466.000000 0.527128166 294.347853254 -2167.389667610 -2166.788420716 10.627952956 > 28933 14466.500000 0.532342877 297.259742512 -2167.395139856 -2166.788555528 14.917385891 > 28934 14467.000000 0.535600841 299.078986930 -2167.398592480 -2166.788627084 10.879262459 > 28935 14467.500000 0.535936944 299.266666470 -2167.399018273 -2166.788593698 10.006427173 > 28936 14468.000000 0.533834852 298.092860267 -2167.396936550 -2166.788491610 9.977815259 > 28937 14468.500000 0.530754526 296.372809252 -2167.393877604 -2166.788391632 10.085333489 > 28938 14469.000000 0.528128677 294.906537823 -2167.391326816 -2166.788346629 10.028149899 > 28939 14469.500000 0.526585940 294.045074707 -2167.389919732 -2166.788363449 9.960049219 > 28940 14470.000000 0.525859267 293.639301105 -2167.389345953 -2166.788398597 14.496977419 > 28941 14470.500000 0.525379287 293.371280876 -2167.388985539 -2166.788401415 14.967396073 > 28942 14471.000000 0.524959273 293.136745417 -2167.388649341 -2166.788369463 10.315914560 > 28943 14471.500000 0.524874770 293.089558993 -2167.388653910 -2166.788343715 16.983571853 > 28944 14472.000000 0.525392050 293.378407716 -2167.389290137 -2166.788348686 12.119731613 > 28945 14472.500000 0.526406871 293.945083066 -2167.390481370 -2166.863446252 47.022801183 > 28946 14473.000000 0.527734481 294.686419018 -2167.391978869 -2166.863459996 11.051850852 > 28947 14473.500000 0.529255279 295.535631285 -2167.393652283 -2166.863456336 10.006576888 > 28948 14474.000000 0.531086126 296.557974111 -2167.395616229 -2166.863432883 9.709443437 > 28949 14474.500000 0.533577404 297.949101425 -2167.398244277 -2166.863412585 9.787318693 > 28950 14475.000000 0.537016875 299.869698620 -2167.401858321 -2166.863429212 9.785394795 > 28951 14475.500000 0.541258217 302.238060033 -2167.406305123 -2166.863475419 9.731476160 > 28952 14476.000000 0.545774333 304.759854865 -2167.411027429 -2166.863520675 9.752394203 > 28953 14476.500000 0.549990896 307.114379332 -2167.415448002 -2166.863561837 9.763660893 > 28954 14477.000000 0.553359699 308.995515632 -2167.419028509 -2166.863608727 9.769082915 > 28955 14477.500000 0.555299389 310.078636660 -2167.421167132 -2166.863641041 9.809159193 > 28956 14478.000000 0.555434584 310.154129550 -2167.421461446 -2166.863632113 9.759279175 > 28957 14478.500000 0.553874622 309.283048227 -2167.420037090 -2166.863598770 9.749239432 > 28958 14479.000000 0.551014039 307.685701343 -2167.417323889 -2166.863576839 9.767714364 > 28959 14479.500000 0.547123637 305.513304502 -2167.413592074 -2166.863566261 9.815094918 > 28960 14480.000000 0.542330631 302.836894640 -2167.408945453 -2166.863544138 9.748038203 > 28961 14480.500000 0.536899528 299.804172240 -2167.403638144 -2166.863500571 10.112055471 > 28962 14481.000000 0.531402812 296.734811186 -2167.398244733 -2166.863438049 9.841474611 > 28963 14481.500000 0.526676227 294.095490925 -2167.393620245 -2166.863376014 9.819765911 > 28964 14482.000000 0.523490986 292.316855534 -2167.390580350 -2166.863358790 9.816407133 > 28965 14482.500000 0.521971605 291.468434880 -2167.389273875 -2166.863410344 9.819614979 > 28966 14483.000000 0.521357575 291.125560959 -2167.388891848 -2166.863481893 9.822640346 > > Why is happening this step shift in the conserved quantity, and the change in the temperature MD behaviour? Is this normal for a restart MD? > > Regards > > > > -- > 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 cp... at googlegroups.com . > To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/CAOFT4PKAWDVhhAb7ALnuiTVLDVL7-5TB5LdNO80ODRrnDGwWiw%40mail.gmail.com . ============================== Thomas D. K?hne Dynamics of Condensed Matter Chair of Theoretical Chemistry University of Paderborn Warburger Str. 100 D-33098 Paderborn Germany tdku... at mail.upb.de +49/(0)5251/60-5726 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tku... at gmail.com Sun Jun 7 10:41:12 2020 From: tku... at gmail.com (=?utf-8?Q?Thomas_K=C3=BChne?=) Date: Sun, 7 Jun 2020 12:41:12 +0200 Subject: [CP2K-user] [CP2K:13453] Abnormal breakdown during the AIMD calculation. In-Reply-To: <2911f368-1290-4a5c-b69e-d05a90059c69@googlegroups.com> References: <2911f368-1290-4a5c-b69e-d05a90059c69@googlegroups.com> Message-ID: Dear Xiaokun, can you also provide the output file? Cheers, Thomas > Am 04.06.2020 um 11:54 schrieb Xiaokun Zhao : > > Dear CP2K users, > > Now I'm running the AIMD simulation at 300K under NVT ensemble. I have two problems: > > 1) My calculation always breakdown after 200~300 aimd steps. I have changed several HPC to do the calculation, but got the same result. So, I don't think it's a hardware problem. I also check my input file for several times and I am not sure if there are some mistakes in it. > > 2) Also, I found that my calculation would become slower after dozens of aimd steps. I check the out file, it seems that the calculation needs more minimize step during the scf iterative process. It is strage that once I killed this calculation and make a restart. This scf iterative process becomes very easy to converge, but as the calculation process it become slower soon. I don't know why? > > I attached my input file cp2k.inp and cp2k-1.ener. > > Thanks a lot for your help in advance. > > Best regards, > Xiaokun > > > > -- > 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 cp... at googlegroups.com . > To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/2911f368-1290-4a5c-b69e-d05a90059c69%40googlegroups.com . > ============================== Thomas D. K?hne Dynamics of Condensed Matter Chair of Theoretical Chemistry University of Paderborn Warburger Str. 100 D-33098 Paderborn Germany tdku... at mail.upb.de +49/(0)5251/60-5726 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tku... at gmail.com Sun Jun 7 10:45:47 2020 From: tku... at gmail.com (=?utf-8?Q?Thomas_K=C3=BChne?=) Date: Sun, 7 Jun 2020 12:45:47 +0200 Subject: [CP2K-user] [CP2K:13465] Question about vibrational analysis In-Reply-To: References: Message-ID: Dear Can, if not all vibrational modes are necessary, e.g. for the substrate, the best way to save computational time is to use the MODE_SELECTIVE option. Best, Thomas > Am 05.06.2020 um 09:35 schrieb Chn : > > Dear experts in CP2K, > > I am a beginner of CP2K package and I am really thankful if my naive question can be explained. > The model is PdCd (111) with small molecule adsorbed on it. When performing a GEO_OPT calculation, I added the keyword "UKS" for spin-polarized calculation in the section "DFT", due to the transition metals that are Pd and Cd atoms in the system according to the tutorials online. However it requires me about three times higher times for the calculation. For the vibrational analysis of the adsorbed molecule, a very tight threshold is needed for "EPS_SCF" to get accurate low frequencies, it will take me too much time. I do not know weather the keyword "UKS" is still necessary here. > Many thanks in advance! > > Regards, > chn > > -- > 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 cp... at googlegroups.com . > To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/b1960a87-e117-4ac0-a3b0-94da7efea13ao%40googlegroups.com . ============================== Thomas D. K?hne Dynamics of Condensed Matter Chair of Theoretical Chemistry University of Paderborn Warburger Str. 100 D-33098 Paderborn Germany tdku... at mail.upb.de +49/(0)5251/60-5726 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Sun Jun 7 12:34:08 2020 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Sun, 7 Jun 2020 14:34:08 +0200 Subject: [CP2K-user] [CP2K:13471] Visualize electron density during formation of a water molecule In-Reply-To: <59156e08-bd00-4591-b2c1-878ac6010be5o@googlegroups.com> References: <59156e08-bd00-4591-b2c1-878ac6010be5o@googlegroups.com>, <533942f6-e28d-402b-992e-bdc724ec9e6f@googlegroups.com> Message-ID: Hi this worked for me &MOTION &MD ENSEMBLE NVT STEPS 1000 TIMESTEP 0.25 &THERMOSTAT TYPE CSVR &CSVR TIMECON 0.1 &END &END THERMOSTAT &END MD &END MOTION &SCF ADDED_MOS 20 &DIAGONALIZATION &END DIAGONALIZATION &MIXING ALPHA 0.1 &END MIXING &SMEAR METHOD FERMI_DIRAC &END SMEAR MAX_SCF 50 EPS_SCF 1.E-6 &END SCF &MGRID CUTOFF 200 &END Use periodic boundary conditions, it makes the trajectory more smooth. -------------------------------------------------------------- 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: "Michael Hale" Sent by: cp... at googlegroups.com Date: 06/06/2020 07:01PM Subject: Re: [CP2K:13471] Visualize electron density during formation of a water molecule Well I filled out the input file as well as I could figure out from your tips. CP2K runs for a few minutes and then aborts with the error "KS energy is an abnormal value (NaN/Inf)". I tried setting a small MAX_SCF value, but it still hits that error. Any other tips? Here is my input file: &GLOBAL PROJECT water-formation RUN_TYPE MD PRINT_LEVEL LOW &END GLOBAL &MOTION &MD ENSEMBLE NVT &THERMOSTAT TYPE CSVR &END THERMOSTAT &END MD &END MOTION &FORCE_EVAL &SUBSYS &KIND H BASIS_SET DZVP-GTH-PADE POTENTIAL GTH-PADE-q1 &END KIND &KIND O BASIS_SET DZVP-GTH-PADE POTENTIAL GTH-PADE-q6 &END KIND &CELL ABC 10 10 10 PERIODIC NONE &END CELL &COORD H 4.0 4.0 4.66667 H 6.0 6.0 4.66667 O 5.0 5.0 5.66667 &END COORD &END SUBSYS &DFT BASIS_SET_FILE_NAME data/BASIS_SET POTENTIAL_FILE_NAME data/POTENTIAL LSD &SCF ADDED_MOS 10 &DIAGONALIZATION &END DIAGONALIZATION &MIXING METHOD BROYDEN_MIXING &END MIXING &SMEAR METHOD FERMI_DIRAC &END SMEAR &END SCF &XC &XC_FUNCTIONAL PADE &END XC_FUNCTIONAL &END XC &PRINT &E_DENSITY_CUBE &EACH MD 1 &END EACH FILENAME CUBE &END E_DENSITY_CUBE &END PRINT &END DFT &END FORCE_EVAL On Thursday, June 4, 2020 at 10:10:06 AM UTC-4, Michael Hale wrote: Great! Thank you. I'll look into those options and hopefully mess with it some more this weekend. Is there much of a hobbyist community around computational chemistry? I'm a pretty experienced software developer, but still new to this. I know there are projects like Folding at Home which don't give you much control, and Chemistry Stack Exchange which is more just traditional Q&A. But I'd love to find community projects to help enhance digital chemistry textbooks with ab initio quantum MD animations of common reactions and such. I actually first tried this during a weekend a couple of years ago. Here was the result: https://www.youtube.com/watch?v=foG5LgFYb2o I finally revisited it a week or two ago. I thought maybe just my initial conditions needed to be tweaked, but then I realized my simulation set up had deeper problems, haha. Thanks again for your help. I hope to post an update again soon. On Thursday, June 4, 2020 at 9:26:25 AM UTC-4, jgh wrote:Hi What I would do: Small basis e.g. DZVP LSD SCF with Diagonalization and Broyden mixing, use all MOs Fermi-Dirac Smearing with high temperature NVT MD with velocity rescaling to get rid of excessive energy Print CUBE file automatically during MD regards Juerg Hutter -------------------------------------------------------------- Juerg Hutter Phone : ++41 44 635 4491 Institut f?r Chemie C FAX : ++41 44 635 6838 Universit?t Z?rich E-mail: h... at chem.uzh.ch Winterthurerstrasse 190 CH-8057 Z?rich, Switzerland --------------------------------------------------------------- -----c... at googlegroups.com wrote: ----- To: "cp2k" From: "Michael Hale" Sent by: c... at googlegroups.com Date: 06/04/2020 05:08AM Subject: [CP2K:13450] Visualize electron density during formation of a water molecule Hey, sorry for the basic question. I've skimmed some computational chemistry books, but I still find the CP2K documentation a bit overwhelming. I'm trying to put two hydrogens an an oxygen atom near each other and watch the spontaneous assembly of a water molecule. I can make the input file and have CP2K output the forces on the atoms and a cube file that I can use to make a 3D visualization of the electron density in Mathematica. Then I update the atom positions with a simple velocity Verlet update and run CP2K again. The resulting animation looks how I want stylistically, but the behavior is clearly not accurate. The atoms come together and bounce off of each other and come back together and bounce off harder. They keep getting more energy and bouncing farther and farther away until they fly apart instead of bonding together. Is the error that the energy calculation for the forces and electron density isn't converging and causing the erratic behavior? Is the error probably in the way I'm updating the atom positions manually? Can I use the CP2K molecular dynamics functionality to do multiple steps of the simulation at once while also outputting the cube file of the electron density for each step? Is this type of simulation of the formation of small molecules within the scope of CP2K? It seems most people typically assume the molecules are already formed and they just want to simulate how those molecules interact, not how atoms come together to form the small molecules. This is all just for fun. I just want to watch the animations and see how "sticky" the atoms and molecules are. Thanks for any help and guidance you might provide. -- 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 c... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/e90450de-cd30-4bad-ae96-96779a50764e%40googlegroups.com. -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/59156e08-bd00-4591-b2c1-878ac6010be5o%40googlegroups.com. From eluni... at gmail.com Sun Jun 7 15:09:08 2020 From: eluni... at gmail.com (Lucas Lodeiro) Date: Sun, 7 Jun 2020 11:09:08 -0400 Subject: [CP2K-user] [CP2K:13474] Restart NVT In-Reply-To: References: Message-ID: Thanks Thomas, I was a little confused between restart and resetting, now its clear for me :). Regards! El dom., 7 jun. 2020 a las 6:34, Thomas K?hne () escribi?: > Dear Lucas > > simply set RESTART_THERMOSTAT TRUE (or remove the line since this is the > default) > to restart the state of the thermostat. The behavior you observe is an > artifact due to restarting > positions and velocities but resetting the thermostat ? > > Cheers, > Thomas > > Am 07.06.2020 um 04:09 schrieb Lucas Lodeiro : > > Hi all, > > I am running NVT water box AIMD in CP2K 7.0. > The run stopped this morning due to node problem, but I can restart it > using the restart file. > But I see some differences that I can not understand. > > I use the same input data to do the restart, but I added: > > &EXT_RESTART > EXTERNAL_FILE WATER-1.restart > RESTART_THERMOSTAT .FALSE. > &END EXT_RESTART > > To restart the calculation and to not restart the thermostat. I guess this > is the correct way to restart a MD without changing the thermostat > behaviour. > But in the first step I see some weird data in *.ener file. > I see in the first new step, the Cons Qty[a.u.] change a little, respect > the last step after MD stopped. > Also for the n-last steps after MD stopped, the temperature oscillates > just +-10?C around the objective temperature and the average temperature > was the correct objective temperature. In the first n-steps of the restart > MD, the temperature starts oscillating more than 10 ?C (in cases 30?C), but > the average temperature was correct respect the last average temperature > and objective temperature. > This is a part of the data (step 28945 is the first step of restart MD): > > 28925 14462.500000 0.524397237 292.822905020 > -2167.386128946 -2166.788489113 9.942549903 > 28926 14463.000000 0.523902002 292.546366555 > -2167.385787588 -2166.788513509 18.580139473 > 28927 14463.500000 0.521503538 291.207066513 > -2167.383420424 -2166.788416738 15.250579394 > 28928 14464.000000 0.518609792 289.591201566 > -2167.380528831 -2166.788292618 17.792272486 > 28929 14464.500000 0.517109605 288.753498602 > -2167.379085941 -2166.788225441 10.424001478 > 28930 14465.000000 0.518164941 289.342797441 > -2167.380271236 -2166.788232301 9.924992632 > 28931 14465.500000 0.521824007 291.386016117 > -2167.384120605 -2166.788300216 15.055006087 > 28932 14466.000000 0.527128166 294.347853254 > -2167.389667610 -2166.788420716 10.627952956 > 28933 14466.500000 0.532342877 297.259742512 > -2167.395139856 -2166.788555528 14.917385891 > 28934 14467.000000 0.535600841 299.078986930 > -2167.398592480 -2166.788627084 10.879262459 > 28935 14467.500000 0.535936944 299.266666470 > -2167.399018273 -2166.788593698 10.006427173 > 28936 14468.000000 0.533834852 298.092860267 > -2167.396936550 -2166.788491610 9.977815259 > 28937 14468.500000 0.530754526 296.372809252 > -2167.393877604 -2166.788391632 10.085333489 > 28938 14469.000000 0.528128677 294.906537823 > -2167.391326816 -2166.788346629 10.028149899 > 28939 14469.500000 0.526585940 294.045074707 > -2167.389919732 -2166.788363449 9.960049219 > 28940 14470.000000 0.525859267 293.639301105 > -2167.389345953 -2166.788398597 14.496977419 > 28941 14470.500000 0.525379287 293.371280876 > -2167.388985539 -2166.788401415 14.967396073 > 28942 14471.000000 0.524959273 293.136745417 > -2167.388649341 -2166.788369463 10.315914560 > 28943 14471.500000 0.524874770 293.089558993 > -2167.388653910 -2166.788343715 16.983571853 > 28944 14472.000000 0.525392050 293.378407716 > -2167.389290137 -2166.788348686 12.119731613 > 28945 14472.500000 0.526406871 293.945083066 > -2167.390481370 -2166.863446252 47.022801183 > 28946 14473.000000 0.527734481 294.686419018 > -2167.391978869 -2166.863459996 11.051850852 > 28947 14473.500000 0.529255279 295.535631285 > -2167.393652283 -2166.863456336 10.006576888 > 28948 14474.000000 0.531086126 296.557974111 > -2167.395616229 -2166.863432883 9.709443437 > 28949 14474.500000 0.533577404 297.949101425 > -2167.398244277 -2166.863412585 9.787318693 > 28950 14475.000000 0.537016875 299.869698620 > -2167.401858321 -2166.863429212 9.785394795 > 28951 14475.500000 0.541258217 302.238060033 > -2167.406305123 -2166.863475419 9.731476160 > 28952 14476.000000 0.545774333 304.759854865 > -2167.411027429 -2166.863520675 9.752394203 > 28953 14476.500000 0.549990896 307.114379332 > -2167.415448002 -2166.863561837 9.763660893 > 28954 14477.000000 0.553359699 308.995515632 > -2167.419028509 -2166.863608727 9.769082915 > 28955 14477.500000 0.555299389 310.078636660 > -2167.421167132 -2166.863641041 9.809159193 > 28956 14478.000000 0.555434584 310.154129550 > -2167.421461446 -2166.863632113 9.759279175 > 28957 14478.500000 0.553874622 309.283048227 > -2167.420037090 -2166.863598770 9.749239432 > 28958 14479.000000 0.551014039 307.685701343 > -2167.417323889 -2166.863576839 9.767714364 > 28959 14479.500000 0.547123637 305.513304502 > -2167.413592074 -2166.863566261 9.815094918 > 28960 14480.000000 0.542330631 302.836894640 > -2167.408945453 -2166.863544138 9.748038203 > 28961 14480.500000 0.536899528 299.804172240 > -2167.403638144 -2166.863500571 10.112055471 > 28962 14481.000000 0.531402812 296.734811186 > -2167.398244733 -2166.863438049 9.841474611 > 28963 14481.500000 0.526676227 294.095490925 > -2167.393620245 -2166.863376014 9.819765911 > 28964 14482.000000 0.523490986 292.316855534 > -2167.390580350 -2166.863358790 9.816407133 > 28965 14482.500000 0.521971605 291.468434880 > -2167.389273875 -2166.863410344 9.819614979 > 28966 14483.000000 0.521357575 291.125560959 > -2167.388891848 -2166.863481893 9.822640346 > > Why is happening this step shift in the conserved quantity, and the change > in the temperature MD behaviour? Is this normal for a restart MD? > > Regards > > > > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/CAOFT4PKAWDVhhAb7ALnuiTVLDVL7-5TB5LdNO80ODRrnDGwWiw%40mail.gmail.com > > . > > > > > ============================== > Thomas D. K?hne > Dynamics of Condensed Matter > Chair of Theoretical Chemistry > University of Paderborn > Warburger Str. 100 > D-33098 Paderborn > Germany > tdku... at mail.upb.de > +49/(0)5251/60-5726 > > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/F52D1EB6-2425-4A82-8167-AF7DB79B7790%40gmail.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hale.m... at live.com Sun Jun 7 19:19:00 2020 From: hale.m... at live.com (Michael Hale) Date: Sun, 7 Jun 2020 12:19:00 -0700 (PDT) Subject: [CP2K-user] [CP2K:13471] Visualize electron density during formation of a water molecule In-Reply-To: References: <59156e08-bd00-4591-b2c1-878ac6010be5o@googlegroups.com>,> <533942f6-e28d-402b-992e-bdc724ec9e6f@googlegroups.com> Message-ID: <3ca8b617-cb0b-4a61-bb74-2989f4552df1o@googlegroups.com> Worked here too! Thank you. And I put the atoms in a straight line and after bonding they formed the typical bent water molecule shape. Very cool! Next I'll try giving them some initial velocity and add an extra hydrogen to see if it doesn't bond. The bonding seems stronger and the atoms need to be closer together than I would have guessed haha. Interesting. Your book's title and table of contents look interesting, but it seems hard to find on Amazon. But I'll read some more detail into my Essentials of Computational Chemistry book for now and now that you've unblocked my progress I have lots of things to explore! Thanks again! On Sunday, June 7, 2020 at 8:34:19 AM UTC-4, jgh wrote: > > Hi > > this worked for me > > &MOTION > &MD > ENSEMBLE NVT > STEPS 1000 > TIMESTEP 0.25 > &THERMOSTAT > TYPE CSVR > &CSVR > TIMECON 0.1 > &END > &END THERMOSTAT > &END MD > &END MOTION > > &SCF > ADDED_MOS 20 > &DIAGONALIZATION > &END DIAGONALIZATION > &MIXING > ALPHA 0.1 > &END MIXING > &SMEAR > METHOD FERMI_DIRAC > &END SMEAR > MAX_SCF 50 > EPS_SCF 1.E-6 > &END SCF > &MGRID > CUTOFF 200 > &END > > > Use periodic boundary conditions, it makes the trajectory more smooth. > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: h... at chem.uzh.ch > > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----c... at googlegroups.com wrote: ----- > To: "cp2k" > > From: "Michael Hale" > Sent by: c... at googlegroups.com > Date: 06/06/2020 07:01PM > Subject: Re: [CP2K:13471] Visualize electron density during formation of a > water molecule > > Well I filled out the input file as well as I could figure out from your > tips. CP2K runs for a few minutes and then aborts with the error "KS energy > is an abnormal value (NaN/Inf)". I tried setting a small MAX_SCF value, but > it still hits that error. Any other tips? Here is my input file: > > &GLOBAL > PROJECT water-formation > RUN_TYPE MD > PRINT_LEVEL LOW > &END GLOBAL > &MOTION > &MD > ENSEMBLE NVT > &THERMOSTAT > TYPE CSVR > &END THERMOSTAT > &END MD > &END MOTION > &FORCE_EVAL > &SUBSYS > &KIND H > BASIS_SET DZVP-GTH-PADE > POTENTIAL GTH-PADE-q1 > &END KIND > &KIND O > BASIS_SET DZVP-GTH-PADE > POTENTIAL GTH-PADE-q6 > &END KIND > &CELL > ABC 10 10 10 > PERIODIC NONE > &END CELL > &COORD > H 4.0 4.0 4.66667 > H 6.0 6.0 4.66667 > O 5.0 5.0 5.66667 > &END COORD > &END SUBSYS > &DFT > BASIS_SET_FILE_NAME data/BASIS_SET > POTENTIAL_FILE_NAME data/POTENTIAL > LSD > &SCF > ADDED_MOS 10 > &DIAGONALIZATION > &END DIAGONALIZATION > &MIXING > METHOD BROYDEN_MIXING > &END MIXING > &SMEAR > METHOD FERMI_DIRAC > &END SMEAR > &END SCF > &XC > &XC_FUNCTIONAL PADE > &END XC_FUNCTIONAL > &END XC > &PRINT > &E_DENSITY_CUBE > &EACH > MD 1 > &END EACH > FILENAME CUBE > &END E_DENSITY_CUBE > &END PRINT > &END DFT > &END FORCE_EVAL > On Thursday, June 4, 2020 at 10:10:06 AM UTC-4, Michael Hale wrote: > Great! Thank you. I'll look into those options and hopefully mess with it > some more this weekend. > > Is there much of a hobbyist community around computational chemistry? I'm > a pretty experienced software developer, but still new to this. I know > there are projects like Folding at Home which don't give you much control, and > Chemistry Stack Exchange which is more just traditional Q&A. But I'd love > to find community projects to help enhance digital chemistry textbooks with > ab initio quantum MD animations of common reactions and such. > > I actually first tried this during a weekend a couple of years ago. Here > was the result: > https://www.youtube.com/watch?v=foG5LgFYb2o > > I finally revisited it a week or two ago. I thought maybe just my initial > conditions needed to be tweaked, but then I realized my simulation set up > had deeper problems, haha. Thanks again for your help. I hope to post an > update again soon. > > On Thursday, June 4, 2020 at 9:26:25 AM UTC-4, jgh wrote:Hi > > What I would do: > > Small basis e.g. DZVP > LSD > SCF with Diagonalization and Broyden mixing, use all MOs > Fermi-Dirac Smearing with high temperature > NVT MD with velocity rescaling to get rid of excessive energy > Print CUBE file automatically during MD > > regards > > Juerg Hutter > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: h... at chem.uzh.ch > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----c... at googlegroups.com wrote: ----- > To: "cp2k" > From: "Michael Hale" > Sent by: c... at googlegroups.com > Date: 06/04/2020 05:08AM > Subject: [CP2K:13450] Visualize electron density during formation of a > water molecule > > Hey, sorry for the basic question. I've skimmed some computational > chemistry books, but I still find the CP2K documentation a bit > overwhelming. I'm trying to put two hydrogens an an oxygen atom near each > other and watch the spontaneous assembly of a water molecule. I can make > the input file and have CP2K output the forces on the atoms and a cube file > that I can use to make a 3D visualization of the electron density in > Mathematica. Then I update the atom positions with a simple velocity Verlet > update and run CP2K again. The resulting animation looks how I want > stylistically, but the behavior is clearly not accurate. The atoms come > together and bounce off of each other and come back together and bounce off > harder. They keep getting more energy and bouncing farther and farther away > until they fly apart instead of bonding together. > > Is the error that the energy calculation for the forces and electron > density isn't converging and causing the erratic behavior? Is the error > probably in the way I'm updating the atom positions manually? Can I use the > CP2K molecular dynamics functionality to do multiple steps of the > simulation at once while also outputting the cube file of the electron > density for each step? Is this type of simulation of the formation of small > molecules within the scope of CP2K? It seems most people typically assume > the molecules are already formed and they just want to simulate how those > molecules interact, not how atoms come together to form the small > molecules. > > This is all just for fun. I just want to watch the animations and see how > "sticky" the atoms and molecules are. Thanks for any help and guidance you > might provide. > -- > 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 c... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/e90450de-cd30-4bad-ae96-96779a50764e%40googlegroups.com. > > > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/59156e08-bd00-4591-b2c1-878ac6010be5o%40googlegroups.com. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From chen... at gmail.com Mon Jun 8 01:04:20 2020 From: chen... at gmail.com (Chn) Date: Sun, 7 Jun 2020 18:04:20 -0700 (PDT) Subject: [CP2K-user] [CP2K:13465] Question about vibrational analysis In-Reply-To: References: Message-ID: <531c8722-6911-4184-a1f0-34c20e1118e7o@googlegroups.com> Dear Thomas, many thanks for your reply! regards, chn ? 2020?6?7???? UTC+8??6:45:53?tkuehne??? > > Dear Can, > > if not all vibrational modes are necessary, e.g. for the substrate, the > best > way to save computational time is to use the MODE_SELECTIVE option. > > Best, > Thomas > > Am 05.06.2020 um 09:35 schrieb Chn >: > > Dear experts in CP2K, > > I am a beginner of CP2K package and I am really thankful if my naive > question can be explained. > The model is PdCd (111) with small molecule adsorbed on it. When > performing a GEO_OPT calculation, I added the keyword "UKS" for > spin-polarized calculation in the section "DFT", due to the transition > metals that are Pd and Cd atoms in the system according to the tutorials > online. However it requires me about three times higher times for the > calculation. For the vibrational analysis of the adsorbed molecule, a very > tight threshold is needed for "EPS_SCF" to get accurate low frequencies, it > will take me too much time. I do not know weather the keyword "UKS" is > still necessary here. > Many thanks in advance! > > Regards, > chn > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/b1960a87-e117-4ac0-a3b0-94da7efea13ao%40googlegroups.com > > . > > > > > ============================== > Thomas D. K?hne > Dynamics of Condensed Matter > Chair of Theoretical Chemistry > University of Paderborn > Warburger Str. 100 > D-33098 Paderborn > Germany > td... at mail.upb.de > +49/(0)5251/60-5726 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunjia... at gmail.com Mon Jun 8 05:44:29 2020 From: sunjia... at gmail.com (Jiayu Sun SLE) Date: Sun, 7 Jun 2020 22:44:29 -0700 (PDT) Subject: [CP2K-user] Install cp2k in Ubuntu. Message-ID: Hi everyone, I am a fresher in cp2k, I have a question that, as the newest version of Ubuntu and cp2k launched, the installation of cp2k is quite easier than other methods. In the Ubuntu terminal, one row commends: " sudo get-apt install cp2k" can finish the installation. Am I right? I am not sure it is so much simple than other methods, feel like nor real or I miss some part. Please give me some hints. Thank you for your help. Sincerely SUN -------------- next part -------------- An HTML attachment was scrubbed... URL: From mayan... at gmail.com Mon Jun 8 14:50:05 2020 From: mayan... at gmail.com (Mayank Dodia) Date: Mon, 8 Jun 2020 07:50:05 -0700 (PDT) Subject: [CP2K-user] Bond sequences error In-Reply-To: References: <398f3bb5-93c8-458e-bb47-2cd1de56873c@googlegroups.com> Message-ID: <3b05cfe0-9714-4452-a140-0e12f6020536o@googlegroups.com> Hi Matt, Thanks for your response. The restart file had the same atom names and the restart file matched with the previous input files. Unfortunately I didn't noticed earlier before that I had an energy convergence problem for the QM/MM system caused by distortion of the geometry of an QM-treated water molecule, which caused a problem in the plain MM MD run as well. Best Regards, Mayank On Wednesday, June 3, 2020 at 8:21:18 PM UTC+2, Matt W wrote: > > Maybe check the names of atoms in the restart files. Perhaps H1 etc are > only being called H in the restart or similar? > > Matt > > On Wednesday, June 3, 2020 at 4:27:11 PM UTC+1, Mayank Dodia wrote: >> >> Hi, >> >> Sorry for reposting, but can someone help me understand what exactly the >> error is and how should I resolve it? >> >> On Monday, June 1, 2020 at 7:01:17 AM UTC+2, Mayank Dodia wrote: >>> >>> Hi, >>> >>> Has anyone experienced this sort of error? >>> >>> >>> ******************************************************************************* >>> * ___ >>> * >>> * / \ >>> * >>> * [ABORT] different sequence of bonds for same molecule kind molecule >>> type = * >>> * \___/ 1 molecule number= 634 NOT FOUND! Check the >>> connectivity of * >>> * | your system. >>> * >>> * O/| >>> * >>> * /| | >>> * >>> * / \ >>> topology_util.F:1117 * >>> >>> ******************************************************************************* >>> >>> >>> ===== Routine Calling Stack ===== >>> >>> 4 topology_molecules_check >>> 3 connectivity_control >>> 2 topology_control >>> 1 CP2K >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 >>> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 >>> : >>> system msg for write_line failure : Bad file descriptor >>> >>> I was running a QMMM file and this failure occurred after a restarted >>> calculation which ran without any issues before. I tried rerunning the >>> calculation by simplifying it to plain MM input with just solvent water >>> molecules, without success, and I am not really sure where the error is. >>> Can someone help me understand what exactly the error is and how should I >>> resolve it? >>> >>> Best Regards, >>> MayankDodia >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From hasanal... at gmail.com Mon Jun 8 17:14:57 2020 From: hasanal... at gmail.com (Hasan Al-Mahayni) Date: Mon, 8 Jun 2020 13:14:57 -0400 Subject: [CP2K-user] [CP2K:13451] Re: Displaying restart file In-Reply-To: <153ff752-aa0c-4acf-ab64-86f1ce3788bf@googlegroups.com> References: <7b835054-97fb-45d4-a843-da080e161e40@googlegroups.com> <153ff752-aa0c-4acf-ab64-86f1ce3788bf@googlegroups.com> Message-ID: Hi, I see, thank you. Does this mean that ASE will continue from where it left off always? Like if the job terminates in the middle of the script, will it continue from there? On Thu, Jun 4, 2020 at 1:44 AM Fabian Ducry wrote: > Are you running just an ENERGY_FORCE calculation with CP2K and perform the > optimization/MD in ASE? CP2K does not print a restart file for ENERGY_FORCE > calculations, because there is no change in the coordinates. ASE should > have all the information to restart the simulation. > > Fabian > > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/153ff752-aa0c-4acf-ab64-86f1ce3788bf%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhaoxia... at gmail.com Tue Jun 9 03:15:29 2020 From: zhaoxia... at gmail.com (Xiaokun Zhao) Date: Mon, 8 Jun 2020 20:15:29 -0700 (PDT) Subject: [CP2K-user] [CP2K:13453] Abnormal breakdown during the AIMD calculation. In-Reply-To: References: <2911f368-1290-4a5c-b69e-d05a90059c69@googlegroups.com> Message-ID: Dear Thomas? output file is attached. thanks! Best regards, Xiaokun ? 2020?6?7???? UTC+8??6:41:16?tkuehne??? > > Dear Xiaokun, > > can you also provide the output file? > > Cheers, > Thomas > > Am 04.06.2020 um 11:54 schrieb Xiaokun Zhao >: > > Dear CP2K users, > > Now I'm running the AIMD simulation at 300K under NVT ensemble. I have two > problems: > > 1) My calculation always breakdown after 200~300 aimd steps. I have > changed several HPC to do the calculation, but got the same result. So, I > don't think it's a hardware problem. I also check my input file for several > times and I am not sure if there are some mistakes in it. > > 2) Also, I found that my calculation would become slower after dozens of > aimd steps. I check the out file, it seems that the calculation needs more > minimize step during the scf iterative process. It is strage that once I > killed this calculation and make a restart. This scf iterative process > becomes very easy to converge, but as the calculation process it become > slower soon. I don't know why? > > I attached my input file cp2k.inp and cp2k-1.ener. > > Thanks a lot for your help in advance. > > Best regards, > Xiaokun > > > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/2911f368-1290-4a5c-b69e-d05a90059c69%40googlegroups.com > > . > > > > > > ============================== > Thomas D. K?hne > Dynamics of Condensed Matter > Chair of Theoretical Chemistry > University of Paderborn > Warburger Str. 100 > D-33098 Paderborn > Germany > td... at mail.upb.de > +49/(0)5251/60-5726 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: outfile Type: application/octet-stream Size: 305629 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: CP2K-1 (2).ener Type: application/octet-stream Size: 520201 bytes Desc: not available URL: From heps... at srmist.edu.in Tue Jun 9 07:01:09 2020 From: heps... at srmist.edu.in (Hepsibahpriyadarshini C) Date: Tue, 9 Jun 2020 00:01:09 -0700 (PDT) Subject: [CP2K-user] Band gap estimation error Message-ID: Hi, I encountered an error in the band gap when I used PBE functional. I could see an overlap between conduction band and valence band which shouldn't be as the material which I employ is a semiconductor. So I tried using the hybrid functional but I obtained a CPASSERT error. Does cp2k support hybrid functionals with K-point sampling. What about the usage of meta and DFT+U methods. Can somebody kindly provide insights on what has to be done. &XC &XC_FUNCTIONAL &XWPBE SCALE_X -0.25 SCALE_X0 1.0 OMEGA 0.11 &END &PBE SCALE_X 0.0 SCALE_C 1.0 &END PBE &END XC_FUNCTIONAL &HF &SCREENING EPS_SCHWARZ 1.0E-10 &END FRACTION 0.25 &INTERACTION_POTENTIAL POTENTIAL_TYPE SHORTRANGE OMEGA 0.11 &END &END &vdW_POTENTIAL DISPERSION_FUNCTIONAL PAIR_POTENTIAL &PAIR_POTENTIAL TYPE DFTD3 CALCULATE_C9_TERM .TRUE. PARAMETER_FILE_NAME /opt/apps/cp2k-5.1/data/dftd3.dat REFERENCE_FUNCTIONAL PBE R_CUTOFF 8. EPS_CN 0.01 &END PAIR_POTENTIAL &END vdW_POTENTIAL &END XC Regards C.Hepsibah -------------- next part -------------- An HTML attachment was scrubbed... URL: From fabia... at gmail.com Tue Jun 9 07:30:52 2020 From: fabia... at gmail.com (Fabian Ducry) Date: Tue, 9 Jun 2020 00:30:52 -0700 (PDT) Subject: [CP2K-user] [CP2K:13451] Re: Displaying restart file In-Reply-To: References: <7b835054-97fb-45d4-a843-da080e161e40@googlegroups.com> <153ff752-aa0c-4acf-ab64-86f1ce3788bf@googlegroups.com> Message-ID: <94fe3168-b9f7-4511-be44-1111198d4e83o@googlegroups.com> No, ASE does not automatically restart. The restarting is well documented on the ASE website, e.g for optimization see here: https://wiki.fysik.dtu.dk/ase/ase/optimize.html?highlight=restart Fabian -------------- next part -------------- An HTML attachment was scrubbed... URL: From fabia... at gmail.com Tue Jun 9 07:34:07 2020 From: fabia... at gmail.com (Fabian Ducry) Date: Tue, 9 Jun 2020 00:34:07 -0700 (PDT) Subject: [CP2K-user] Install cp2k in Ubuntu. In-Reply-To: References: Message-ID: Hi, This will install an old version of cp2k. Go to https://www.cp2k.org/download, click on UBUNTU and download the package from this page. Fabian On Monday, 8 June 2020 07:44:29 UTC+2, Jiayu Sun SLE wrote: > > Hi everyone, > > I am a fresher in cp2k, I have a question that, as the newest version of > Ubuntu and cp2k launched, the installation of cp2k is quite easier than > other methods. > > In the Ubuntu terminal, one row commends: " sudo get-apt install cp2k" can > finish the installation. > > Am I right? I am not sure it is so much simple than other methods, feel > like nor real or I miss some part. > > Please give me some hints. > > Thank you for your help. > > Sincerely > SUN > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pierre.a... at gmail.com Tue Jun 9 12:36:26 2020 From: pierre.a... at gmail.com (=?UTF-8?Q?Pierre-Andr=C3=A9_Cazade?=) Date: Tue, 9 Jun 2020 05:36:26 -0700 (PDT) Subject: [CP2K-user] Vibrational Analysis Restart Message-ID: Dear CP2K users, Is it possible to restart a vibrational analysis (phonons). I am performing a vibrational analysis on a very large crystal and the wall time limit provided by the supercomputer I am using doe not allow it to reach complition. Regards, Pierre -------------- next part -------------- An HTML attachment was scrubbed... URL: From pierre.a... at gmail.com Tue Jun 9 12:41:22 2020 From: pierre.a... at gmail.com (=?UTF-8?Q?Pierre-Andr=C3=A9_Cazade?=) Date: Tue, 9 Jun 2020 05:41:22 -0700 (PDT) Subject: [CP2K-user] Classical Forcefield Message-ID: Dear CP2K users, I would like to know which types of classical forcefields CP2K is capable of handling. I am well aware of the types of input formats CP2K can read (Amber, Charmm, Gromos) but I am more interested in the nature of the forcefield. Aside from Amber, Charmm and Gromos forcefields, can CP2K use AMOEBA? Can it use a multipolar model? What are the limits in terms of potential forms? etc Regards, Pierre -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunjia... at gmail.com Tue Jun 9 13:13:28 2020 From: sunjia... at gmail.com (Jiayu Sun) Date: Tue, 9 Jun 2020 22:13:28 +0900 Subject: [CP2K-user] [CP2K:13488] Re: Install cp2k in Ubuntu. In-Reply-To: References: Message-ID: Dear Fabian Thank you so much for your help Sincerely Sun [image: Mailtrack] Sender notified by Mailtrack 20/06/09 22:13:00 Fabian Ducry ?2020?6?9??? ??4:34??? > Hi, > > This will install an old version of cp2k. Go to > https://www.cp2k.org/download, click on UBUNTU and download the package > from this page. > > Fabian > > On Monday, 8 June 2020 07:44:29 UTC+2, Jiayu Sun SLE wrote: >> >> Hi everyone, >> >> I am a fresher in cp2k, I have a question that, as the newest version of >> Ubuntu and cp2k launched, the installation of cp2k is quite easier than >> other methods. >> >> In the Ubuntu terminal, one row commends: " sudo get-apt install cp2k" >> can finish the installation. >> >> Am I right? I am not sure it is so much simple than other methods, feel >> like nor real or I miss some part. >> >> Please give me some hints. >> >> Thank you for your help. >> >> Sincerely >> SUN >> > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/a8450747-9414-40ca-b90c-b486f1230b24o%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tku... at gmail.com Tue Jun 9 13:19:25 2020 From: tku... at gmail.com (=?utf-8?Q?Thomas_K=C3=BChne?=) Date: Tue, 9 Jun 2020 15:19:25 +0200 Subject: [CP2K-user] [CP2K:13490] Classical Forcefield In-Reply-To: References: Message-ID: Dear Pierre, to the best of my knowledge AMOEBA and multipolar FF?s aren?t implemented. However, in the subsections NONBONDED, BOND, BEND etc. within MM/FORCEFIELD there are quite a lot of potential forms that can be defined beyond the FFs you have mentioned. Greetings, Thomas > Am 09.06.2020 um 14:41 schrieb Pierre-Andr? Cazade : > > Dear CP2K users, > > I would like to know which types of classical forcefields CP2K is capable of handling. I am well aware of the types of input formats CP2K can read (Amber, Charmm, Gromos) but I am more interested in the nature of the forcefield. Aside from Amber, Charmm and Gromos forcefields, can CP2K use AMOEBA? Can it use a multipolar model? What are the limits in terms of potential forms? etc > > Regards, > Pierre > > -- > 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 cp... at googlegroups.com . > To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/b9f7720a-95df-4448-9bc2-4eb52ac0855co%40googlegroups.com . ============================== Thomas D. K?hne Dynamics of Condensed Matter Chair of Theoretical Chemistry University of Paderborn Warburger Str. 100 D-33098 Paderborn Germany tdku... at mail.upb.de +49/(0)5251/60-5726 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Tue Jun 9 13:25:43 2020 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Tue, 9 Jun 2020 15:25:43 +0200 Subject: [CP2K-user] [CP2K:13490] Classical Forcefield In-Reply-To: References: Message-ID: Hi besides simple pair potentials (with very general form of non-bonded terms), there are FF of the form EAM embedded atom model COS charge on spring (polarizable model) Multipole models (up to quadrupoles) plus some other custom made FF. 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: "Pierre-Andr? Cazade" Sent by: cp... at googlegroups.com Date: 06/09/2020 02:41PM Subject: [CP2K:13490] Classical Forcefield Dear CP2K users, I would like to know which types of classical forcefields CP2K is capable of handling. I am well aware of the types of input formats CP2K can read (Amber, Charmm, Gromos) but I am more interested in the nature of the forcefield. Aside from Amber, Charmm and Gromos forcefields, can CP2K use AMOEBA? Can it use a multipolar model? What are the limits in terms of potential forms? etc Regards, Pierre -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/b9f7720a-95df-4448-9bc2-4eb52ac0855co%40googlegroups.com. From pierre.a... at gmail.com Tue Jun 9 14:31:47 2020 From: pierre.a... at gmail.com (Pierre Cazade) Date: Tue, 9 Jun 2020 15:31:47 +0100 Subject: [CP2K-user] [CP2K:13492] Classical Forcefield In-Reply-To: References: Message-ID: <6e5dcde3-fdfe-e76f-269a-fa8a2bb585d5@gmail.com> Dear Juerg, Thank you for your answer. Another question, is it possible to have part of the ff provided by a file, let's say a charmm psf file, and the rest in CP2K input file? Regards, Pierre On 09/06/2020 14:25, hut... at chem.uzh.ch wrote: > Hi > > besides simple pair potentials (with very general form of non-bonded terms), > there are FF of the form > > EAM embedded atom model > COS charge on spring (polarizable model) > Multipole models (up to quadrupoles) > > plus some other custom made FF. > > 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: "Pierre-Andr? Cazade" > Sent by: cp... at googlegroups.com > Date: 06/09/2020 02:41PM > Subject: [CP2K:13490] Classical Forcefield > > Dear CP2K users, > > I would like to know which types of classical forcefields CP2K is capable of handling. I am well aware of the types of input formats CP2K can read (Amber, Charmm, Gromos) but I am more interested in the nature of the forcefield. Aside from Amber, Charmm and Gromos forcefields, can CP2K use AMOEBA? Can it use a multipolar model? What are the limits in terms of potential forms? etc > > Regards, > Pierre > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/b9f7720a-95df-4448-9bc2-4eb52ac0855co%40googlegroups.com. > > -- Dr Pierre Cazade, PhD AD3-023, Bernal Institute, University of Limerick, Plassey Park Road, Castletroy, co. Limerick, Ireland From tenebrosu... at gmail.com Tue Jun 9 15:16:47 2020 From: tenebrosu... at gmail.com (Anton S. Lytvynenko) Date: Tue, 9 Jun 2020 18:16:47 +0300 Subject: [CP2K-user] [CP2K:13488] Re: Install cp2k in Ubuntu. In-Reply-To: References: Message-ID: <2ad8c47a-9d3a-536c-1f6d-fba63ecac147@gmail.com> Dear Fabian, it seems to me that this way leads to the old packages as well. Do I completely miss something? Yours, Anton 09.06.20 10:34, Fabian Ducry ????: > Hi, > > This will install an old version of cp2k. Go to > https://www.cp2k.org/download, click on UBUNTU and download the > package from this page. > > Fabian > > On Monday, 8 June 2020 07:44:29 UTC+2, Jiayu Sun SLE wrote: > > Hi everyone, > > I am a fresher in cp2k, I have a question that, as the newest > version of Ubuntu and cp2k launched, the installation of cp2k is > quite easier than other methods. > > In the Ubuntu terminal, one row commends: " sudo get-apt install > cp2k" can finish the installation. > > Am I right? I am not sure it is so much simple than other methods, > feel like nor real or I miss some part. > > Please give me some hints. > > Thank you for your help. > > Sincerely > SUN > > -- > 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 cp... at googlegroups.com > . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/a8450747-9414-40ca-b90c-b486f1230b24o%40googlegroups.com > . -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunjia... at gmail.com Tue Jun 9 16:09:27 2020 From: sunjia... at gmail.com (Jiayu Sun SLE) Date: Tue, 9 Jun 2020 09:09:27 -0700 (PDT) Subject: [CP2K-user] Problems with cp2k - 6.1 installation on Ubuntu. Message-ID: To whom it may be concern Recently, I try to install cp2k-6.1 on Ubuntu 20. Following the steps in Iain Bethune's slides. [image: image.png] at the last step, error message shows, I attach here: [image: image.png] [image: image.png] [image: image.png] I cannot figure out what happened and how to handle this problem. I'd appreciate it if you can give me some help. Thank you so much. Sincerely SUN JIAYU -------------- next part -------------- An HTML attachment was scrubbed... URL: From fabia... at gmail.com Tue Jun 9 16:25:06 2020 From: fabia... at gmail.com (Fabian Ducry) Date: Tue, 9 Jun 2020 09:25:06 -0700 (PDT) Subject: [CP2K-user] [CP2K:13488] Re: Install cp2k in Ubuntu. In-Reply-To: <2ad8c47a-9d3a-536c-1f6d-fba63ecac147@gmail.com> References: <2ad8c47a-9d3a-536c-1f6d-fba63ecac147@gmail.com> Message-ID: <737c14ef-8c5d-43b3-8582-508fee1a69d8o@googlegroups.com> There you can download cp2k-6.1 which is newer than the 2.1 you get from "get-apt install cp2k". You can also install Debian packages, there a 7.1 package is available. Fabian On Tuesday, 9 June 2020 17:16:53 UTC+2, Anton S. Lytvynenko wrote: > > Dear Fabian, > > it seems to me that this way leads to the old packages as well. Do I > completely miss something? > > Yours, > > Anton > 09.06.20 10:34, Fabian Ducry ????: > > Hi, > > This will install an old version of cp2k. Go to > https://www.cp2k.org/download, click on UBUNTU and download the package > from this page. > > Fabian > > On Monday, 8 June 2020 07:44:29 UTC+2, Jiayu Sun SLE wrote: >> >> Hi everyone, >> >> I am a fresher in cp2k, I have a question that, as the newest version of >> Ubuntu and cp2k launched, the installation of cp2k is quite easier than >> other methods. >> >> In the Ubuntu terminal, one row commends: " sudo get-apt install cp2k" >> can finish the installation. >> >> Am I right? I am not sure it is so much simple than other methods, feel >> like nor real or I miss some part. >> >> Please give me some hints. >> >> Thank you for your help. >> >> Sincerely >> SUN >> > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/a8450747-9414-40ca-b90c-b486f1230b24o%40googlegroups.com > > . > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pierre.a... at gmail.com Tue Jun 9 16:49:18 2020 From: pierre.a... at gmail.com (=?UTF-8?Q?Pierre-Andr=C3=A9_Cazade?=) Date: Tue, 9 Jun 2020 09:49:18 -0700 (PDT) Subject: [CP2K-user] [CP2K:13492] Classical Forcefield In-Reply-To: <6e5dcde3-fdfe-e76f-269a-fa8a2bb585d5@gmail.com> References: <6e5dcde3-fdfe-e76f-269a-fa8a2bb585d5@gmail.com> Message-ID: Dear Juerg, As follow up questions: To my knowledge, CP2K only uses a core-shell approach to model polarisability. It does not use Thole method at all. Am I correct? if so, is there a systematic way to adapt parameters from a Thole model (CHARMM polarisable, AMOEBA) to a core-shell model? Are there any plans to implement this feature (Thole polarisation method) in CP2K? Thanks again for your help. Best regards, Pierre On Tuesday, June 9, 2020 at 3:31:54 PM UTC+1, Pierre-Andr? Cazade wrote: > > Dear Juerg, > > Thank you for your answer. Another question, is it possible to have part > of the ff provided by a file, let's say a charmm psf file, and the rest > in CP2K input file? > > Regards, > Pierre > > On 09/06/2020 14:25, hut... at chem.uzh.ch wrote: > > Hi > > > > besides simple pair potentials (with very general form of non-bonded > terms), > > there are FF of the form > > > > EAM embedded atom model > > COS charge on spring (polarizable model) > > Multipole models (up to quadrupoles) > > > > plus some other custom made FF. > > > > 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: "Pierre-Andr? Cazade" > > Sent by: cp... at googlegroups.com > > Date: 06/09/2020 02:41PM > > Subject: [CP2K:13490] Classical Forcefield > > > > Dear CP2K users, > > > > I would like to know which types of classical forcefields CP2K is > capable of handling. I am well aware of the types of input formats CP2K can > read (Amber, Charmm, Gromos) but I am more interested in the nature of the > forcefield. Aside from Amber, Charmm and Gromos forcefields, can CP2K use > AMOEBA? Can it use a multipolar model? What are the limits in terms of > potential forms? etc > > > > Regards, > > Pierre > > -- > > 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 cp... at googlegroups.com. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/b9f7720a-95df-4448-9bc2-4eb52ac0855co%40googlegroups.com. > > > > > > > -- > Dr Pierre Cazade, PhD > AD3-023, Bernal Institute, > University of Limerick, > Plassey Park Road, > Castletroy, co. Limerick, > Ireland > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Tue Jun 9 17:42:25 2020 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Tue, 9 Jun 2020 19:42:25 +0200 Subject: [CP2K-user] [CP2K:13498] Classical Forcefield In-Reply-To: References: , <6e5dcde3-fdfe-e76f-269a-fa8a2bb585d5@gmail.com> Message-ID: Hi we don't do any development of classical FF in my group. regards Juerg Hutter -------------------------------------------------------------- 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: "Pierre-Andr? Cazade" Sent by: cp... at googlegroups.com Date: 06/09/2020 06:49PM Subject: Re: [CP2K:13498] Classical Forcefield Dear Juerg, As follow up questions: To my knowledge, CP2K only uses a core-shell approach to model polarisability. It does not use Thole method at all. Am I correct? if so, is there a systematic way to adapt parameters from a Thole model (CHARMM polarisable, AMOEBA) to a core-shell model? Are there any plans to implement this feature (Thole polarisation method) in CP2K? Thanks again for your help. Best regards, Pierre On Tuesday, June 9, 2020 at 3:31:54 PM UTC+1, Pierre-Andr? Cazade wrote:Dear Juerg, Thank you for your answer. Another question, is it possible to have part of the ff provided by a file, let's say a charmm psf file, and the rest in CP2K input file? Regards, Pierre On 09/06/2020 14:25, hut... at chem.uzh.ch wrote: > Hi > > besides simple pair potentials (with very general form of non-bonded terms), > there are FF of the form > > EAM embedded atom model > COS charge on spring (polarizable model) > Multipole models (up to quadrupoles) > > plus some other custom made FF. > > 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: "Pierre-Andr? Cazade" > Sent by: cp... at googlegroups.com > Date: 06/09/2020 02:41PM > Subject: [CP2K:13490] Classical Forcefield > > Dear CP2K users, > > I would like to know which types of classical forcefields CP2K is capable of handling. I am well aware of the types of input formats CP2K can read (Amber, Charmm, Gromos) but I am more interested in the nature of the forcefield. Aside from Amber, Charmm and Gromos forcefields, can CP2K use AMOEBA? Can it use a multipolar model? What are the limits in terms of potential forms? etc > > Regards, > Pierre > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/b9f7720a-95df-4448-9bc2-4eb52ac0855co%40googlegroups.com. > > -- Dr Pierre Cazade, PhD AD3-023, Bernal Institute, University of Limerick, Plassey Park Road, Castletroy, co. Limerick, Ireland -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/a361025f-0991-43ac-af2a-3449bb4a2513o%40googlegroups.com. From jerry1... at hotmail.com Tue Jun 9 18:41:03 2020 From: jerry1... at hotmail.com (Tzu-Yao HSU) Date: Tue, 9 Jun 2020 11:41:03 -0700 (PDT) Subject: [CP2K-user] [CP2K:13460] energy jump in SCCS In-Reply-To: References: <16b1636efad847d0962ed6ba7fdb6361@psi.ch> <9ba5de66-d129-4f24-8c09-139d9f834286@googlegroups.com> Message-ID: <0cdd9100-84f6-43cd-a998-4ecdd68435fbo@googlegroups.com> Thank you very much Matthias! I made it work by lowering RHO_MIN. (Obtained negative polarisation energy instead of positive value) However, if I use a cut-off of 600 Ry, I would still get a positive polarisation energy. Tzu-Yao Matthias Krack? 2020?6?4???? UTC+2??10?39?13???? > > Hi Tzu-Yao > > > > You may try smaller values for RHO_MAX and RHO_MIN. A cut-off of 600 Ry > (maybe even 400 Ry) should large enough. > > > > HTH > > > > Matthias > > > > *From:* c... at googlegroups.com > *On Behalf Of *Tzu-Yao HSU > *Sent:* Donnerstag, 4. Juni 2020 16:44 > *To:* cp2k > > *Subject:* Re: [CP2K:13460] energy jump in SCCS > > > > Hi all, > > > > I got similar problem as Geng, but my calculation is pure DFT energy > evaluation. > > During the SCF run, the polarisation energy abruptly jumped up to a > positive value and the SCF convergence jumped down at certain convergence > level . > > Then the polarisation energy always stayed positive until the SCF run > converged. > > > > Here are my input file (.inp) and reduced output file (.out, grep 'Diag.' > and 'Polarisation energy' then paste) . > > My molecular structure (optimized.dat) was obtained by performing GEO_OPT > in vacuum. > > > > Further increasing the MGRID CUTOFF, EPS_SCF in SCCS section, simulation > box size, and decreasing CUTOFFs in XC section do not change the converged > energy. > > Since the converged polarisation energy is always positive, I still wonder > how may I improve my input file? > > > > I appreciate any response to this problem. > > Thank you very much > > Best regards > > Tzu-Yao > > > > > Matthias Krack? 2020?1?7???? UTC+1??7?40?51???? > > Hi Geng > > > > Such fluctuations are usually caused by numerical noise. A larger cutoff, > e.g. 800 instead of 400Ry, will most likely resolve that issue. > > > > HTH > > > > Matthias > > > > *From:* c... at googlegroups.com *On Behalf Of *Geng > Sun > *Sent:* Dienstag, 31. Dezember 2019 18:26 > *To:* cp2k > *Subject:* [CP2K:12697] energy jump in SCCS > > > > Dear CP2K users, > > > > I am trying to use the SCCS solvent model to optimize a H2O molecule in > solvent and calculate the solvation energy. > > I found that during the structure optimization, the total energy jumps up > almost 3 eV, but the structure of H2O still looks good. > > Finally, with the energy obtained in solvent ( -17.07615353442375 a.u.) > and energy in vacuum (-17.22203206260123), the solvation energy is positive. > > Therefore, there must be something wrong in the calculations, but I can > not figure it out. > > > > > > grep "Total energy:" cp2k.out gives: > > > > Total energy: - > 17.22994560779211 > Total energy: - > 17.23016218028583 > Total energy: - > 17.23052945533816 > Total energy: - > 17.23057483762070 > Total energy: - > 17.23059795728501 > Total energy: - > 17.23061684603447 > Total energy: - > 17.23062875959604 > Total energy: - > 17.23063230147527 > Total energy: - > 17.23063606787884 > Total energy: - > 17.23458599053544 > Total energy: - > 17.07789974445440 > Total energy: - > 17.23050622895307 > Total energy: - > 17.23059409756609 > Total energy: - > 17.23153569898144 > Total energy: - > 17.23062905094530 > Total energy: - > 17.23063896643257 > Total energy: - > 17.06258564479369 > Total energy: - > 17.23061553671926 > Total energy: - > 17.23064419320881 > Total energy: - > 17.23017384159302 > Total energy: - > 17.09997174618866 > Total energy: - > 17.23053249119082 > Total energy: - > 17.23061888501270 > Total energy: - > 17.23062632201262 > Total energy: - > 17.10641501376824 > Total energy: - > 17.23063629047595 > Total energy: - > 17.23099984646603 > Total energy: - > 17.11100171504137 > Total energy: - > 17.10215507558170 > Total energy: - > 17.13946950681089 > Total energy: - > 17.05320236101690 > Total energy: - > 17.23214150951693 > Total energy: - > 17.14172122406513 > Total energy: - > 17.05319840556444 > Total energy: - > 17.06170695684858 > Total energy: - > 17.11231720859150 > Total energy: - > 17.07455263629729 > Total energy: - > 17.07623660559768 > Total energy: - > 17.07963295606425 > Total energy: - > 17.07859069368490 > Total energy: - > 17.07694563368373 > Total energy: - > 17.07637515123947 > Total energy: - > 17.07632103460653 > Total energy: - > 17.07605114342309 > Total energy: - > 17.07615353442375 > > > > Here is the input file: > > &FORCE_EVAL > &DFT > UKS > BASIS_SET_FILE_NAME BASIS_MOLOPT_UCL > BASIS_SET_FILE_NAME BASIS_MOLOPT > POTENTIAL_FILE_NAME GTH_POTENTIALS > &MGRID > CUTOFF 400 > COMMENSURATE > &END MGRID > &QS > EXTRAPOLATION PS > EXTRAPOLATION_ORDER 3 > EPS_DEFAULT 1.0E-12 > MAP_CONSISTENT T > &END QS > &PRINT > &SCCS ON > &EACH > QS_SCF 1 > &END EACH > &END SCCS > &END PRINT > &SCCS > ALPHA [N*m^-1] 0.02 > GAMMA [mN/m] 0.0 > BETA [GPa] -0.08 > DELTA_RHO 2.0E-5 > DERIVATIVE_METHOD CD5 > DIELECTRIC_CONSTANT 6.02 > EPS_SCCS 1.0E-10 > EPS_SCF 0.03 > MAX_ITER 100 > METHOD Andreussi > MIXING 0.6 > &ANDREUSSI > RHO_MAX 0.003 > RHO_MIN 0.0003 > &END ANDREUSSI > &END SCCS > &SCF > EPS_SCF 1.0E-7 > MAX_SCF 31 > SCF_GUESS RESTART > &OT > ENERGY_GAP 0.002 > LINESEARCH 2PNT > PRECONDITIONER FULL_ALL > MINIMIZER DIIS > &END OT > &OUTER_SCF > EPS_SCF 1.0E-7 > MAX_SCF 20 > &END OUTER_SCF > &END SCF > &XC > &XC_FUNCTIONAL PBE > &END XC_FUNCTIONAL > &END XC > &END DFT > &SUBSYS > &KIND H > BASIS_SET TZVP-MOLOPT-GTH > POTENTIAL GTH-PBE-q1 > &END KIND > &KIND O > BASIS_SET TZVP-MOLOPT-GTH > POTENTIAL GTH-PBE-q6 > &END KIND > &COORD > O 7.424704500000000706e+00 9.621645000000000891e+00 > 1.106072519999999848e+01 > H 7.912573799999999657e+00 1.000790999999999897e+01 > 1.180680414000000056e+01 > H 6.473416799999999860e+00 9.760409999999998476e+00 > 1.119866495999999856e+01 > &END COORD > &CELL > PERIODIC XYZ > A 1.641000000000000014e+01 0.000000000000000000e+00 > 0.000000000000000000e+00 > B 0.000000000000000000e+00 1.650000000000000000e+01 > 0.000000000000000000e+00 > C 0.000000000000000000e+00 0.000000000000000000e+00 > 1.824599999999999866e+01 > &END CELL > &END SUBSYS > &PRINT > &FORCES ON > LOG_PRINT_KEY T > &END FORCES > &END PRINT > &END FORCE_EVAL > > > > I greatly appreciate any suggestions on fixing this. > > > > Thank you very much. > > > Best Regards, > > > > Geng > > > > -- > 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 c... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/be04892b-30f6-4654-b51a-5acc8228e885%40googlegroups.com > > . > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/9ba5de66-d129-4f24-8c09-139d9f834286%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunjia... at gmail.com Wed Jun 10 02:57:13 2020 From: sunjia... at gmail.com (Jiayu Sun SLE) Date: Tue, 9 Jun 2020 19:57:13 -0700 (PDT) Subject: [CP2K-user] Toolchain build for cp2k trunk: elpa-2015.11.001 compilation fails In-Reply-To: References: Message-ID: <98268551-9eb9-4d90-b0f1-e16e1d77a469o@googlegroups.com> Hi, Lai I have the same question, the official website provided a solution, the link is here: https://www.cp2k.org/faq:toolchain_non_zero_exit_code_detected Sincerely SUN ? 2016?7?14???? UTC+9??11:52:29?Feng Lai??? > > hello, > I used the script in toolchain folder to construct the arch file, and > everything is fine before the process reached the elpa compilation, The > procedure ended with a error > note(ERROR:(/usr/local/cp2k/tools/toochain/script/install_elpa.sh, line 68) > Non-zero exit code detected.) printed on the screen. When i peruse the log > file,i found that it looked like that something was wrong with the gcc > complier that the gcc cannot recognized the options: -V and -qversion. The > attached file is the config.log, and my order on command line is > ./install_cp2k_toochain.sh --with-openmpi=install --with-elpa=install My > corporate system is CentOS 7.The cp2k source code that i want to compiled > was downloaded from svn. I don't know whether or not it is suitable to use > the cp2k to do some simulation in the CentOS corporate system , but it is > too hard for me to find the right way the compile a efficient cp2k in this > system. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunjia... at gmail.com Wed Jun 10 03:05:14 2020 From: sunjia... at gmail.com (Jiayu Sun SLE) Date: Tue, 9 Jun 2020 20:05:14 -0700 (PDT) Subject: [CP2K-user] installation of cp2k on linux mint machine In-Reply-To: References: Message-ID: <50d548a5-8b1d-4f30-8941-51b6a8f48524o@googlegroups.com> Hi, I wonder have you handles this problems yet? I faced the same but in the open bash part. If so, could you give me some advice? Thank you so much. SUN ? 2018?8?29???? UTC+9??8:05:52?SS??? > > I was trying to install cp2k on my linux mint OS. I downloaded the cp2k > file and prerequisites files from cp2k website and followed the instruction > given in readme file after unzipping the cp2k files.When i tried to install > the toolchain using > > ./install_cp2k_toolchain.sh --install-all > it was showing an error message as follows > > Installing from scratch into /home/shyam/WORK/shyam/softwares/cp2k-5.1/tools/toolchain/install/scotch-6.0.0 > ERROR: (/home/shyam/WORK/shyam/softwares/cp2k-5.1/tools/toolchain/scripts/install_ptscotch.sh, line 43) Non-zero exit code detected. > > I have all tar.gz files. I tried to install this from individual scotch_6.0.0.tar.gz file and it was not working > > I am new to the software and it would be helpful if someone can give a step by step installation guide. > > Thank you > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tenebrosu... at gmail.com Wed Jun 10 09:00:25 2020 From: tenebrosu... at gmail.com (Anton S. Lytvynenko) Date: Wed, 10 Jun 2020 12:00:25 +0300 Subject: [CP2K-user] [CP2K:13497] Re: Install cp2k in Ubuntu. In-Reply-To: <737c14ef-8c5d-43b3-8582-508fee1a69d8o@googlegroups.com> References: <2ad8c47a-9d3a-536c-1f6d-fba63ecac147@gmail.com> <737c14ef-8c5d-43b3-8582-508fee1a69d8o@googlegroups.com> Message-ID: <96f25bba-bf5b-5e4c-87e9-1e2dc88618ed@gmail.com> Dear Fabian, indeed, it looks like Mint 19 offers CP2K 5.1 from repositories. Thank you for the suggestion. (I prefer building from scratch for the sake of performance, but hope this knowledge will help somebody anyway). Yours, Anton 09.06.20 19:25, Fabian Ducry ????: > There you can download cp2k-6.1 which is newer than the 2.1 you get > from "get-apt install cp2k". > You can also install Debian packages, there a 7.1 package is available. > > Fabian > > On Tuesday, 9 June 2020 17:16:53 UTC+2, Anton S. Lytvynenko wrote: > > Dear Fabian, > > it seems to me that this way leads to the old packages as well. Do > I completely miss something? > > Yours, > > Anton > > 09.06.20 10:34, Fabian Ducry ????: >> Hi, >> >> This will install an old version of cp2k. Go to >> https://www.cp2k.org/download, click on UBUNTU and download the >> package from this page. >> >> Fabian >> >> On Monday, 8 June 2020 07:44:29 UTC+2, Jiayu Sun SLE wrote: >> >> Hi everyone, >> >> I am a fresher in cp2k, I have a question that, as the newest >> version of Ubuntu and cp2k launched, the installation of cp2k >> is quite easier than other methods. >> >> In the Ubuntu terminal, one row commends: " sudo get-apt >> install cp2k" can finish the installation. >> >> Am I right? I am not sure it is so much simple than other >> methods, feel like nor real or I miss some part. >> >> Please give me some hints. >> >> Thank you for your help. >> >> Sincerely >> SUN >> >> -- >> 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 c... at googlegroups.com . >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/cp2k/a8450747-9414-40ca-b90c-b486f1230b24o%40googlegroups.com >> . > > -- > 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 cp... at googlegroups.com > . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/737c14ef-8c5d-43b3-8582-508fee1a69d8o%40googlegroups.com > . -------------- next part -------------- An HTML attachment was scrubbed... URL: From mba... at gmx.net Wed Jun 10 09:06:37 2020 From: mba... at gmx.net (Michael Banck) Date: Wed, 10 Jun 2020 11:06:37 +0200 Subject: [CP2K-user] [CP2K:13497] Re: Install cp2k in Ubuntu. In-Reply-To: <737c14ef-8c5d-43b3-8582-508fee1a69d8o@googlegroups.com> References: <2ad8c47a-9d3a-536c-1f6d-fba63ecac147@gmail.com> <737c14ef-8c5d-43b3-8582-508fee1a69d8o@googlegroups.com> Message-ID: <5ee0a29f.1c69fb81.4d8ae.7ed7@mx.google.com> Hi, On Tue, Jun 09, 2020 at 09:25:06AM -0700, Fabian Ducry wrote: > There you can download cp2k-6.1 which is newer than the 2.1 you get from > "get-apt install cp2k". If you "apt-get install cp2k", you get the cp2k version for you Ubuntu version; I am not aware of any recent Ubuntu version shipping cp2k-2.1, but maybe that was a typo. You can try to manually install other versions on your Ubuntu install, but those are compiled for newer Ubuntu versions, so might not work. There are no backports of current cp2k packages for older Ubuntu LTS or Debian stable versions right now, and at least I don't have the time to do that in some manual fashion. > You can also install Debian packages, there a 7.1 package is available. Yeah, that's a work-in-(long-)progress due to the libxc transition and only available for experimental. I need to get back to this. Michael From tku... at gmail.com Wed Jun 10 09:17:22 2020 From: tku... at gmail.com (=?utf-8?Q?Thomas_K=C3=BChne?=) Date: Wed, 10 Jun 2020 11:17:22 +0200 Subject: [CP2K-user] [CP2K:13498] Classical Forcefield In-Reply-To: References: <6e5dcde3-fdfe-e76f-269a-fa8a2bb585d5@gmail.com> Message-ID: Dear Pierre, I don?t know for sure, but I doubt this is possible since Thole-based polarization model typically entails a screened Coulomb potential to dampen the intra-molecular interactions between the shells ? Cheers, Thomas > Am 09.06.2020 um 18:49 schrieb Pierre-Andr? Cazade : > > Dear Juerg, > > As follow up questions: > > To my knowledge, CP2K only uses a core-shell approach to model polarisability. It does not use Thole method at all. Am I correct? > > if so, is there a systematic way to adapt parameters from a Thole model (CHARMM polarisable, AMOEBA) to a core-shell model? Are there any plans to implement this feature (Thole polarisation method) in CP2K? > > Thanks again for your help. > > Best regards, > Pierre > > On Tuesday, June 9, 2020 at 3:31:54 PM UTC+1, Pierre-Andr? Cazade wrote: > Dear Juerg, > > Thank you for your answer. Another question, is it possible to have part > of the ff provided by a file, let's say a charmm psf file, and the rest > in CP2K input file? > > Regards, > Pierre > > On 09/06/2020 14:25, hut... at chem.uzh.ch wrote: > > Hi > > > > besides simple pair potentials (with very general form of non-bonded terms), > > there are FF of the form > > > > EAM embedded atom model > > COS charge on spring (polarizable model) > > Multipole models (up to quadrupoles) > > > > plus some other custom made FF. > > > > 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: "Pierre-Andr? Cazade" > > Sent by: cp... at googlegroups.com > > Date: 06/09/2020 02:41PM > > Subject: [CP2K:13490] Classical Forcefield > > > > Dear CP2K users, > > > > I would like to know which types of classical forcefields CP2K is capable of handling. I am well aware of the types of input formats CP2K can read (Amber, Charmm, Gromos) but I am more interested in the nature of the forcefield. Aside from Amber, Charmm and Gromos forcefields, can CP2K use AMOEBA? Can it use a multipolar model? What are the limits in terms of potential forms? etc > > > > Regards, > > Pierre > > -- > > 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 cp... at googlegroups.com . > > To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/b9f7720a-95df-4448-9bc2-4eb52ac0855co%40googlegroups.com . > > > > > > -- > Dr Pierre Cazade, PhD > AD3-023, Bernal Institute, > University of Limerick, > Plassey Park Road, > Castletroy, co. Limerick, > Ireland > > > -- > 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 cp... at googlegroups.com . > To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/a361025f-0991-43ac-af2a-3449bb4a2513o%40googlegroups.com . -------------- next part -------------- An HTML attachment was scrubbed... URL: From pierre.a... at gmail.com Wed Jun 10 09:55:10 2020 From: pierre.a... at gmail.com (Pierre Cazade) Date: Wed, 10 Jun 2020 10:55:10 +0100 Subject: [CP2K-user] [CP2K:13504] Classical Forcefield In-Reply-To: References: <6e5dcde3-fdfe-e76f-269a-fa8a2bb585d5@gmail.com> Message-ID: Hi Thomas, Thank you for your answer. I agree there's no way to reproduce the Thole potential with how the core-shell model is, to my understanding, implemented in CP2K. My question is how one can extract q_core, q_shell, and k_cs from, let's say, CHARMM or AMOEBA Thole parameters. For example, for sodium and SWM4 in CHARMM, one can find: ATOM SOD? SODD???? 1.000? ALPHA -0.157 ATOM OH2? ODW????? 0.00000? TYPE DOH2??? ALPHA -0.97825258 THOLE 1.3 I assume the first value means q=q_core+q_shell. Then, there's the polarizability which I assume is in A**3. In CHARMM, k_cs=1000 kcal/mol/A**2 for all Drude oscillators. Finally, I think this relationship makes it possible to deduce k_cs and q_shell from one another: k_cs = (q_shell)**2/alpha (obviously one takes the absolute value of the alpha provided by CHARMM) The problem here is the homogeneity of the units. There's a missing conversion factor. So I wonder if anyone tried this before and what would it be? Finally there's the question of the sign of the q_shell. Is it given by the sign of the alpha parameter in CHARMM topology file? If so, it means all shells in CHARMM have a negative sign. Is it standard in the core-shell model for the charge of the shell to be negative? Similar questions arise when checking AMOEBA. Again for water: polarize??? 349????????? 0.8370???? 0.3900??? 350 polarize??? 350????????? 0.4960???? 0.3900??? 349 Here, the Thole factor (0.39) seems to be the same for all atom type save a couple of them. However, the polarizability is positive. Is it assumed that all shell charges are again negative or is the sign decided by other means? What is the meaning of the last column? Is it part of the exclusion list? I do realize this is an obscure forcefield discussion and that CP2K forum might not be the best place for this. My issue is that I need a polarizable model of water that can be used in CP2K and that is somewhat compatible with CHARMM36m for proteins. So, if anyone knows such a water model, I would be grateful if you could share it. Thanks, Pierre On 10/06/2020 10:17, Thomas K?hne wrote: > Dear Pierre, > > I don?t know for sure, but I doubt this is possible since Thole-based > polarization model > typically entails a screened Coulomb potential to dampen the > intra-molecular interactions > between the shells ? > > Cheers, > Thomas > >> Am 09.06.2020 um 18:49 schrieb Pierre-Andr? Cazade >> >: >> >> Dear Juerg, >> >> As follow up questions: >> >> To my knowledge, CP2K only uses a core-shell approach to model >> polarisability. It does not use Thole method at all. Am I correct? >> >> if so, is there a systematic way to adapt parameters from a Thole >> model (CHARMM polarisable, AMOEBA) to a core-shell model? Are there >> any plans to implement this feature (Thole polarisation method) in CP2K? >> >> Thanks again for your help. >> >> Best regards, >> Pierre >> >> On Tuesday, June 9, 2020 at 3:31:54 PM UTC+1, Pierre-Andr? Cazade wrote: >> >> Dear Juerg, >> >> Thank you for your answer. Another question, is it possible to >> have part >> of the ff provided by a file, let's say a charmm psf file, and >> the rest >> in CP2K input file? >> >> Regards, >> Pierre >> >> On 09/06/2020 14:25,hut... at chem.uzh.ch >> wrote: >> > Hi >> > >> > besides simple pair potentials (with very general form of >> non-bonded terms), >> > there are FF of the form >> > >> > EAM ?embedded atom model >> > COS ?charge on spring (polarizable model) >> > Multipole models (up to quadrupoles) >> > >> > plus some other custom made FF. >> > >> > 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... at chem.uzh.ch >> >> > Winterthurerstrasse 190 >> > CH-8057 Z?rich, Switzerland >> > --------------------------------------------------------------- >> > >> > -----cp... at googlegroups.com wrote: >> ----- >> > To: "cp2k" > >> > From: "Pierre-Andr? Cazade" >> > Sent by:... at googlegroups.com >> > Date: 06/09/2020 02:41PM >> > Subject: [CP2K:13490] Classical Forcefield >> > >> > Dear CP2K users, >> > >> > I would like to know which types of classical forcefields CP2K >> is capable of handling. I am well aware of the types of input >> formats CP2K can read (Amber, Charmm, Gromos) but I am more >> interested in the nature of the forcefield. Aside from Amber, >> Charmm and Gromos forcefields, can CP2K use AMOEBA? Can it use a >> multipolar model? What are the limits in terms of potential >> forms? etc >> > >> > Regards, >> > Pierre >> > ? ?-- >> > ? 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 toc... at googlegroups.com >> . >> > ? To view this discussion on the web >> visithttps://groups.google.com/d/msgid/cp2k/b9f7720a-95df-4448-9bc2-4eb52ac0855co%40googlegroups.com >> . >> > >> > >> >> -- >> Dr Pierre Cazade, PhD >> AD3-023, Bernal Institute, >> University of Limerick, >> Plassey Park Road, >> Castletroy, co. Limerick, >> Ireland >> >> >> -- >> 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 toc... at googlegroups.com >> . >> To view this discussion on the web >> visithttps://groups.google.com/d/msgid/cp2k/a361025f-0991-43ac-af2a-3449bb4a2513o%40googlegroups.com >> . > > -- > 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 cp... at googlegroups.com > . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/C5EA5FE1-1631-4F00-B9DD-20C1807D9589%40gmail.com > . -- Dr Pierre Cazade, PhD AD3-023, Bernal Institute, University of Limerick, Plassey Park Road, Castletroy, co. Limerick, Ireland -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdsimula... at gmail.com Wed Jun 10 10:53:57 2020 From: mdsimula... at gmail.com (MD Simulation) Date: Wed, 10 Jun 2020 03:53:57 -0700 (PDT) Subject: [CP2K-user] XC_DERIV options Message-ID: <0551f803-e861-4e24-9d65-ffc582705833o@googlegroups.com> Hello, Can someone give me a brief description of the XC_DERIV options? Thanks Stacey - COLLOCATE*Without description, yet.* - NN10_SMOOTH*Without description, yet.* - NN4_SMOOTH*Without description, yet.* - NN50_SMOOTH*Without description, yet.* - NN6_SMOOTH*Without description, yet.* - PW*Without description, yet.* - SPLINE2*Without description, yet.* - SPLINE2_SMOOTH*Without description, yet.* - SPLINE3*Without description, yet.* - SPLINE3_SMOOTH*Without description, yet.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From tfjer... at gmail.com Wed Jun 10 11:41:31 2020 From: tfjer... at gmail.com (Torstein Fjermestad) Date: Wed, 10 Jun 2020 04:41:31 -0700 (PDT) Subject: [CP2K-user] [CP2K:13372] Problem with geometry optimization using LS_SCF In-Reply-To: <5E53A3BB-CC62-47FF-9BBB-3E317BDD9298@gmail.com> References: <432b51c8-1d61-491e-a235-cb81b77bd3a7@googlegroups.com> <377E31B1-73C6-4260-9130-154B1845EF1E@gmail.com> <5E53A3BB-CC62-47FF-9BBB-3E317BDD9298@gmail.com> Message-ID: <10ba9db8-57bc-477f-af0c-a50f2cc3d7d5o@googlegroups.com> Dear Fabian and Thomas, Thanks a lot for your useful feedback. I thought I should give you an update to clarify a confusion I might have caused. When I said "normal" SCF, I meant orbital transformation (OT). Sorry for the sloppy terminology. I completely confused myself (and probably also you) when I reported the wall time for a single point / geometry step. When I look at the wall time per SCF iteration, the OT method is significantly faster than LS_SCF both for the CPU and GPU machine, see table below. I think the wall time per SCF iteration is a more relevant quantity to look at because for the OT method, the number of SCF iterations is reduced significantly when the start guess can be read from the previous geometry of a geometry optimization. Entry Total energy/ Ha machine nodes tasks-per-node tasks-per-socket cpus-per-task gpus-per-node threads wall time # SCF steps wall time/ SCF step Method purification method EPS_SCF dynamic threshold 1 -3499.007666 cpu - MPI 3 36 - - - - 309.3 8 38.7 LS_SCF sign 1.0E-07 FALSE 2 -3499.00768 cpu - MPI 3 36 - - - - 380.0 86 4.4 OT - 1.0E-06 - 3 -3499.00769 gpu -MPI/OMP 4 4 2 32 4 16 67.5 11 6.1 LS_SCF trs4 1.0E-06 TRUE 4 -3499.00768 gpu -MPI/OMP 4 4 2 32 4 16 361.7 86 4.2 OT - 1.0E-06 - Entry 1 and 2 are the same calculations as shown in Test 1 at the start of this thread. Best regards, Torstein mandag 25. mai 2020 21.59.49 UTC+2 skrev tkuehne f?lgende: > > Dear Torstein, > > beside the advice by Fabian to reduce the numerical noise within the > forces to improve > the convergence of the geometry optimization, set EXTRAPOLATION_ORDER to 3 > for > consistency. Since the sign-method is an alternative to diagonalization, > which is at variance > to OT that is a direct minimization method (inspite the fact that the > minimization steps > are also called SCF iterations within CP2K!), the largest difference is > due to the rather > simplistic mixing. You may try to use DIIS acceleration (LS_DIIS T > together with appropriate > values for INI_DIIS & NMIXING) or BROYDEN_MIXING inside RHO_MIXING. > > Cheers, > Thomas > > Am 25.05.2020 um 13:45 schrieb Torstein Fjermestad >: > > Dear Thomas, > > Thanks for your fast reply. > I did not restart the Hessian matrix in test 3. > The LS_SCF section with all default made explicit, you can see here: > The complete input file is attached. > Thanks > > Regards, > Torstein > > &LS_SCF > LS_DIIS F > INI_DIIS 2 > MAX_DIIS 4 > NMIXING 2 > EPS_DIIS 1.0000000000000001E-01 > MAX_SCF 20 > EPS_SCF 9.9999999999999995E-08 > MIXING_FRACTION 4.5000000000000001E-01 > EPS_FILTER 9.9999999999999995E-08 > EPS_LANCZOS 1.0000000000000000E-03 > MAX_ITER_LANCZOS 128 > MU -1.0000000000000001E-01 > FIXED_MU F > EXTRAPOLATION_ORDER 4 > S_PRECONDITIONER ATOMIC > PURIFICATION_METHOD SIGN_MATRIX > DYNAMIC_THRESHOLD F > NON_MONOTONIC T > MATRIX_CLUSTER_TYPE ATOMIC > SINGLE_PRECISION_MATRICES F > RESTART_WRITE F > RESTART_READ F > S_INVERSION SIGN_SQRT > SIGN_SQRT_ORDER 3 > REPORT_ALL_SPARSITIES T > PERFORM_MU_SCAN F > CHECK_S_INV F > &END LS_SCF > > > mandag 25. mai 2020 12.58.48 UTC+2 skrev tkuehne f?lgende: >> >> Dear Torstein, >> >> apparently you are not exploiting the WF guess in your LS_SCF run, as you >> have guessed. >> Without an input I can only speculate, but by default EXTRAPOLATION_ORDER >> is 4 within >> LS_SCF and 3 for all other methods. Regarding test 3, did you also >> restart the Hessian matrix? >> >> Cheers, >> Thomas >> >> Am 25.05.2020 um 12:34 schrieb Torstein Fjermestad : >> >> Dear all, >> >> First some background for my question: >> I got computing hours on a cluster with GPUs. I did some tests with >> single point calculations, and I found that linear scaling SCF ran about 5 >> times faster than "normal" SCF for my system on that cluster. The total >> energy between SCF and LS_SCF differed only by about 0.04 kJ mol-1; and I >> therefore found the results encouraging. >> >> I then went on to compare LS_SCF and "normal" SCF for geometry >> optimizations on a machine without GPUs. I did three tests: >> Test 1: Single point calculation >> Test 2: Geometry optimization starting from the geometry in Test 1 >> Test 3: Geometry optimization starting from the optimized geometry in >> Test 2 >> >> I used the following keywords in the LS_SCF section. >> >> &LS_SCF >> EPS_FILTER 1.0E-7 >> EPS_SCF 1.0E-7 >> &END >> >> At the beginning of the attached output files the complete input is >> echoed. >> >> I now describe the results of the tests. >> >> Test 1: Single point calculation. The total energy differs by 0.05 kJ >> mol-1 >> >> entry >> >> Total energy/ Ha >> >> wall time / s >> >> LS_SCF? >> >> 1 >> >> -3499.00767 >> >> 309 >> >> yes >> >> 2 >> >> -3499.00768 >> >> 380 >> >> no >> >> >> Test 2: Geometry optimization starting from the geometry in Test 1. >> SCF_GUESS ATOMIC is used >> >> entry >> >> Total energy, first geom / Ha >> >> max. grad of first step >> >> # geometry steps >> >> Total energy, optim geom / Ha >> >> wall time, s >> >> wall time / geom. step, s >> >> LS_SCF? >> >> 1 >> >> -3499.00767 >> >> 0.03493 >> >> 54 >> >> Did not converge within the requested wall time >> >> 7260 a >> >> 134 >> >> yes >> >> 2 >> >> -3499.00769 >> >> 0.03613 >> >> 123 >> >> -3499.11153 >> >> 4386 >> >> 36 >> >> no >> a Requested wall time in submit script >> >> In Test 2, the wall time per geometry step is much longer when LS_SCF is >> used than when "normal" SCF is used. This is in spite of Test 1 showing >> that LS_SCF is notably faster for a single point calculation. >> Am I doing something wrong here? >> Is the start guess of the wavefunction at each geometry step perhaps not >> adequate in the case of LS_SCF? >> How should I change the LS_SCF parameters in order to improve the >> calculation? >> >> Test 3: Re-optimization of the optimized structure in Test 2 (entry 2). SCF_GUESS >> ATOMIC is used >> >> >> entry >> >> Total energy, first geom / Ha >> >> max.grad of first step >> >> # geometry steps >> >> Total energy, optim geom / Ha >> >> wall time >> >> wall time / geom step >> >> LS_SCF? >> >> 1 >> >> -3499.11150 >> >> 0.00016 >> >> 1 >> >> -3499.11153 >> >> 396 >> >> 396 >> >> no >> >> 2 >> >> -3499.11147 >> >> 0.00183 >> >> 19 >> >> Did not converge within the requested wall time >> >> 7260a >> >> 382 >> >> yes >> a Requested wall time in submit script >> >> Not unexpectedly, in Test 3, the geometry optimization with "normal" SCF >> converges after 1 geometry step. >> However, the geometry optimization with LS_SCF did not converge within >> two hours and took only 19 geometry steps. >> I see that the max. gradient of the first geometry step is much higher in >> the case of LS_SCF than in the case of "normal" SCF. >> Are there some LS_SCF parameters I should adjust to check if the gradient >> has converged? >> >> I would really appreciate help in this matter, because in the current >> situation, I am not able to use LS_SCF for geometry optimizations. >> >> Thanks and regards, >> Torstein Fjermestad >> >> >> >> >> >> >> >> -- >> 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 c... at googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/cp2k/432b51c8-1d61-491e-a235-cb81b77bd3a7%40googlegroups.com >> >> . >> >> >> >> >> >> ============================== >> Thomas D. K?hne >> Dynamics of Condensed Matter >> Chair of Theoretical Chemistry >> University of Paderborn >> Warburger Str. 100 >> D-33098 Paderborn >> Germany >> td... at mail.upb.de >> +49/(0)5251/60-5726 >> >> > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/b88518c9-cfe4-4e9e-a465-c97ecb552942%40googlegroups.com > > . > > > > > > ============================== > Thomas D. K?hne > Dynamics of Condensed Matter > Chair of Theoretical Chemistry > University of Paderborn > Warburger Str. 100 > D-33098 Paderborn > Germany > td... at mail.upb.de > +49/(0)5251/60-5726 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tfjer... at gmail.com Wed Jun 10 13:56:53 2020 From: tfjer... at gmail.com (Torstein Fjermestad) Date: Wed, 10 Jun 2020 06:56:53 -0700 (PDT) Subject: [CP2K-user] Using TAMkin with CP2K - how is CP2K diagonalizing the Hessian matrix? Message-ID: <5724512a-d570-400e-b86b-1acc31b292ebo@googlegroups.com> Dear all, I would like to use TAMkin (http://molmod.github.io/tamkin/) to compute thermodynamic properties from the vibrational frequencies computed with CP2K. As I have understood it, the way TAMkin works is to read and diagonalize the Hessian matrix printed in the CP2K output. When I compare the frequencies obtained with TAMkin with those obtained with cp2k, the values are not the same (Compare column 2 and 3 in the table below). The first task is then to understand how CP2K computes the frequencies. To investigate this, I copied the Hessian matrix from the CP2K output (printed below the string "Hessian in cartesian coordinates") and pasted it into Excel and saved it as a csv file. This file I read into python and diagonalized the Hessian with numpy. The frequencies I get are different from those printed in the cp2k output file (compare column 3 and 4 in the table below). I have assumed that the units of the Hessian matrix in the cp2k output file are Ry*bohr-2*kamu-1 (kamu = 1000*amu). This assumption is based on trial and error; it was what got me closest to the cp2k frequencies. Table 1: The eight lowest frequencies. There are 48 in total. frequencies TAMkin / cm-1 cp2k / cm-1 Diag., cp2k Hessian / cm-1 1 31.1 27.3 32.6 2 38.3 40.8 40.1 3 47.7 51.0 50.2 4 74.7 74.0 78.2 5 82.0 80.0 85.8 6 111.0 109.9 116.3 7 223.7 224.1 234.3 8 245.6 246.3 257.3 What is wrong with my calculation? What steps should be done to go from the Hessian to the frequencies? The Hessian in csv format, the python script and the cp2k output file are attached. Thanks a lot for your help. Regards, Torstein Fjermestad -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hessian_v2.csv Type: text/csv Size: 21893 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: read_Hess_rev_h.py Type: text/x-python Size: 859 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cp2k-output.out Type: application/octet-stream Size: 427307 bytes Desc: not available URL: From sunjia... at gmail.com Thu Jun 11 03:06:39 2020 From: sunjia... at gmail.com (Jiayu Sun SLE) Date: Wed, 10 Jun 2020 20:06:39 -0700 (PDT) Subject: [CP2K-user] [CP2K:13497] Re: Install cp2k in Ubuntu. In-Reply-To: <5ee0a29f.1c69fb81.4d8ae.7ed7@mx.google.com> References: <2ad8c47a-9d3a-536c-1f6d-fba63ecac147@gmail.com> <737c14ef-8c5d-43b3-8582-508fee1a69d8o@googlegroups.com> <5ee0a29f.1c69fb81.4d8ae.7ed7@mx.google.com> Message-ID: <02894a5b-3596-430a-b49b-5feb010729d4o@googlegroups.com> Dear Michael Thank you for your reply for the installation. I have tried compiled the cp2k 7.1 version from toolchain script, the *sh file, and using the OpenBLAS 0.3.6, the error message are listed below: ==================== Installing OpenBLAS ==================== OpenBLAS-0.3.6.tar.gz is found Installing from scratch into /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/openblas-0.3.6 patching file kernel/x86_64/KERNEL.SKYLAKEX ERROR: (/home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/scripts/install_openblas.sh, line 72) Non-zero exit code detected. ERROR: (./scripts/install_mathlibs.sh, line 34) Non-zero exit code detected. How can I do this in this case? What the meaning of this sentence: "Non-zero exit code detected." When I compile other packages, this error occurs again, almost all the packages are facing the same questions. Thank you for your help or advice. Sincerely ? 2020?6?10???? UTC+9??6:06:44?Michael??? > > Hi, > > On Tue, Jun 09, 2020 at 09:25:06AM -0700, Fabian Ducry wrote: > > There you can download cp2k-6.1 which is newer than the 2.1 you get from > > "get-apt install cp2k". > > If you "apt-get install cp2k", you get the cp2k version for you Ubuntu > version; I am not aware of any recent Ubuntu version shipping cp2k-2.1, > but maybe that was a typo. > > You can try to manually install other versions on your Ubuntu install, > but those are compiled for newer Ubuntu versions, so might not work. > > There are no backports of current cp2k packages for older Ubuntu LTS or > Debian stable versions right now, and at least I don't have the time to > do that in some manual fashion. > > > You can also install Debian packages, there a 7.1 package is available. > > Yeah, that's a work-in-(long-)progress due to the libxc transition and > only available for experimental. I need to get back to this. > > > Michael > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunjia... at gmail.com Thu Jun 11 03:08:21 2020 From: sunjia... at gmail.com (Jiayu Sun SLE) Date: Wed, 10 Jun 2020 20:08:21 -0700 (PDT) Subject: [CP2K-user] "Non-zero exit code detected." when compile cp2k 7.1 Message-ID: Hi, everyone, I have tried compiled the cp2k 7.1 version from toolchain script, the *sh file, and using the OpenBLAS 0.3.6, the error message are listed below: ==================== Installing OpenBLAS ==================== OpenBLAS-0.3.6.tar.gz is found Installing from scratch into /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/openblas-0.3.6 patching file kernel/x86_64/KERNEL.SKYLAKEX ERROR: (/home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/scripts/install_openblas.sh, line 72) Non-zero exit code detected. ERROR: (./scripts/install_mathlibs.sh, line 34) Non-zero exit code detected. How can I do this in this case? What the meaning of this sentence: "Non-zero exit code detected." When I compile other packages, this error occurs again, almost all the packages are facing the same problem. Thank you for your help or advice. Sincerely -------------- next part -------------- An HTML attachment was scrubbed... URL: From tenebrosu... at gmail.com Thu Jun 11 10:26:29 2020 From: tenebrosu... at gmail.com (Anton S. Lytvynenko) Date: Thu, 11 Jun 2020 13:26:29 +0300 Subject: [CP2K-user] [CP2K:13511] "Non-zero exit code detected." when compile cp2k 7.1 In-Reply-To: References: Message-ID: 11.06.20 06:08, Jiayu Sun SLE ????: > > Installing from scratch into > /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/openblas-0.3.6 > patching file kernel/x86_64/KERNEL.SKYLAKEX > ERROR: > (/home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/scripts/install_openblas.sh, > line 72) Non-zero exit code detected. > ERROR: (./scripts/install_mathlibs.sh, line 34) Non-zero exit code > detected. > > > How can I do this in this case? > What the meaning of this sentence: "Non-zero exit code detected." When > I compile other packages, this error occurs again, almost all the > packages are facing the same problem. > Hi, When the program ends, it returns so called exit code -- an integer value indicating if it was successful. By convention, exit code 0 means successful execution, non-integer ones typically indicate some issues (they can have their own conventions depending on the system or software, but such conventions are more specific). The sentence you are citing means that the install_openblas.sh script failed for some reason. I guess your system misses some packages necessary to build the code, and you should figure out which ones and install them. Please check the logs on the openblas build (see "[CP2K:10684] installation of cp2k on linux mint machine" topic for similar situation and discussion how to find them). Yours, Anton -------------- next part -------------- An HTML attachment was scrubbed... URL: From tenebrosu... at gmail.com Thu Jun 11 11:13:35 2020 From: tenebrosu... at gmail.com (Anton S. Lytvynenko) Date: Thu, 11 Jun 2020 14:13:35 +0300 Subject: [CP2K-user] [CP2K:13511] "Non-zero exit code detected." when compile cp2k 7.1 In-Reply-To: References: Message-ID: By the way, did you run sudo ./install_requirements.sh first? 11.06.20 06:08, Jiayu Sun SLE ????: > Hi, everyone, > I have tried compiled the?cp2k 7.1 version from toolchain script, the > *sh file, and using the OpenBLAS 0.3.6, the error message are listed > below: > > ==================== Installing OpenBLAS ==================== > OpenBLAS-0.3.6.tar.gz is found > Installing from scratch into > /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/openblas-0.3.6 > patching file kernel/x86_64/KERNEL.SKYLAKEX > ERROR: > (/home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/scripts/install_openblas.sh, > line 72) Non-zero exit code detected. > ERROR: (./scripts/install_mathlibs.sh, line 34) Non-zero exit code > detected. > > > How can I do this in this case? > What the meaning of this sentence: "Non-zero exit code detected." When > I compile other packages, this error occurs again, almost all the > packages are facing the same problem. > > Thank you for your help or advice. > > Sincerely > > -- > 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 cp... at googlegroups.com > . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/f5027fe3-52b4-4b7a-b58a-288bad9d3954o%40googlegroups.com > . -------------- next part -------------- An HTML attachment was scrubbed... URL: From pierre.a... at gmail.com Thu Jun 11 14:29:07 2020 From: pierre.a... at gmail.com (=?UTF-8?Q?Pierre-Andr=C3=A9_Cazade?=) Date: Thu, 11 Jun 2020 07:29:07 -0700 (PDT) Subject: [CP2K-user] Multipoles and core-shell model Message-ID: <309c2e81-3d78-4fff-99ef-31cccf535ec8o@googlegroups.com> Dear CP2K users, I am checking the DIPOLE and QUADRUPOLE subsections in FORCE_EVAL%SUBSYS%MULTIPOLES. I am puzzled by the absence of specification of a local framework. To my experience, the latter is necessary as multipoles are not defined in a univoque way when the previous terms are not null and are therefore framework dependant. How does CP2K account for this? Does CP2K define automatically the framework based on connectivity? Is the multipolar interactions subjected to the exclusion list (no nonbonded interactions between 1-2 and 1-3 atoms)? Finally, when using a core-shell model to model polarisation, is there a way to exclude bonded atoms (1-2 and 1-3) from the interactions aside from the SHELL_CUTOFF in FORCE_EVAL%MM%FORCEFIELD%SHELL? Regards, Pierre -------------- next part -------------- An HTML attachment was scrubbed... URL: From chen... at gmail.com Fri Jun 12 01:50:59 2020 From: chen... at gmail.com (Chn) Date: Thu, 11 Jun 2020 18:50:59 -0700 (PDT) Subject: [CP2K-user] Problems in calculating adsorption energy Message-ID: <069b72e5-49d5-4894-9ad3-9b052ee4af06o@googlegroups.com> Dear CP2K experts, I am calculating the adsorption energy of HCOOH on Pd (111) surface (2x2-slab with 4 layers). However, I obtained a very huge adsorption energy of ~-5.7 eV compared to the literature (around 0.4 eV). I tried to do the BSSE calculation according to the other posts in group but it didn't work.. I have no idea about how to fix it, any suggestion will be greatly appreciated..Many thanks in advance..! Attachments are the input files. Regards, chn -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: inputs.7z Type: application/x-7z-compressed Size: 4351 bytes Desc: not available URL: From sunjia... at gmail.com Fri Jun 12 13:01:19 2020 From: sunjia... at gmail.com (Jiayu Sun SLE) Date: Fri, 12 Jun 2020 06:01:19 -0700 (PDT) Subject: [CP2K-user] "Non-zero exit code detected." when compile cp2k 7.1 In-Reply-To: References: Message-ID: Hi Anton Thank you for you kindly help. I haven't run the install_requirements.sh first. After running it, the screen printed: Selecting previously unselected package libopts25:amd64. (Reading database ... 186821 files and directories currently installed.) Preparing to unpack .../00-libopts25_1%3a5.18.16-3_amd64.deb ... Unpacking libopts25:amd64 (1:5.18.16-3) ... Selecting previously unselected package libopts25-dev:amd64. Preparing to unpack .../01-libopts25-dev_1%3a5.18.16-3_amd64.deb ... Unpacking libopts25-dev:amd64 (1:5.18.16-3) ... Selecting previously unselected package autogen. Preparing to unpack .../02-autogen_1%3a5.18.16-3_amd64.deb ... Unpacking autogen (1:5.18.16-3) ... Replaced by files in installed package libopts25-dev:amd64 (1:5.18.16-3) ... Selecting previously unselected package liberror-perl. Preparing to unpack .../03-liberror-perl_0.17029-1_all.deb ... Unpacking liberror-perl (0.17029-1) ... Selecting previously unselected package git-man. Preparing to unpack .../04-git-man_1%3a2.25.1-1ubuntu3_all.deb ... Unpacking git-man (1:2.25.1-1ubuntu3) ... Selecting previously unselected package git. Preparing to unpack .../05-git_1%3a2.25.1-1ubuntu3_amd64.deb ... Unpacking git (1:2.25.1-1ubuntu3) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../06-libblas3_3.9.0-1build1_amd64.deb ... Unpacking libblas3:amd64 (3.9.0-1build1) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../07-liblapack3_3.9.0-1build1_amd64.deb ... Unpacking liblapack3:amd64 (3.9.0-1build1) ... Selecting previously unselected package make. Preparing to unpack .../08-make_4.2.1-1.2_amd64.deb ... Unpacking make (4.2.1-1.2) ... Selecting previously unselected package python-pkg-resources. Preparing to unpack .../09-python-pkg-resources_44.0.0-2_all.deb ... Unpacking python-pkg-resources (44.0.0-2) ... Selecting previously unselected package python-numpy. Preparing to unpack .../10-python-numpy_1%3a1.16.5-2ubuntu7_amd64.deb ... Unpacking python-numpy (1:1.16.5-2ubuntu7) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../11-zlib1g-dev_1%3a1.2.11.dfsg-2ubuntu1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu1) ... Setting up python-pkg-resources (44.0.0-2) ... Setting up libopts25:amd64 (1:5.18.16-3) ... Setting up liberror-perl (0.17029-1) ... Setting up libblas3:amd64 (3.9.0-1build1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up make (4.2.1-1.2) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu1) ... Setting up git-man (1:2.25.1-1ubuntu3) ... Setting up liblapack3:amd64 (3.9.0-1build1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up python-numpy (1:1.16.5-2ubuntu7) ... Setting up libopts25-dev:amd64 (1:5.18.16-3) ... Setting up autogen (1:5.18.16-3) ... Setting up git (1:2.25.1-1ubuntu3) ... Processing triggers for libc-bin (2.31-0ubuntu9) ... Processing triggers for man-db (2.9.1-1) ... Processing triggers for install-info (6.7.0.dfsg.2-5) ... I cannot figure out what I should do next, what's the meaning of these codes? Does this message show the missing package I should install but not yet? Thank you so much. SUN ? 2020?6?11???? UTC+9??12:08:21?Jiayu Sun SLE??? > > Hi, everyone, > I have tried compiled the cp2k 7.1 version from toolchain script, the *sh > file, and using the OpenBLAS 0.3.6, the error message are listed below: > > ==================== Installing OpenBLAS ==================== > OpenBLAS-0.3.6.tar.gz is found > Installing from scratch into > /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/openblas-0.3.6 > patching file kernel/x86_64/KERNEL.SKYLAKEX > ERROR: > (/home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/scripts/install_openblas.sh, > line 72) Non-zero exit code detected. > ERROR: (./scripts/install_mathlibs.sh, line 34) Non-zero exit code > detected. > > > How can I do this in this case? > What the meaning of this sentence: "Non-zero exit code detected." When I > compile other packages, this error occurs again, almost all the packages > are facing the same problem. > > Thank you for your help or advice. > > Sincerely > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tenebrosu... at gmail.com Fri Jun 12 14:44:34 2020 From: tenebrosu... at gmail.com (Anton S. Lytvynenko) Date: Fri, 12 Jun 2020 17:44:34 +0300 Subject: [CP2K-user] [CP2K:13516] Re: "Non-zero exit code detected." when compile cp2k 7.1 In-Reply-To: References: Message-ID: <7e949a63-4798-f5ac-c2f1-5bdadaa796fe@gmail.com> Hi, 12.06.20 16:01, Jiayu Sun SLE ????: > I cannot figure out what I should do next, what's the meaning of these > codes? These codes report a successful installation of the necessary packages. Besides some specific staff shipped together with CP2K, the program relies on a number of additional common software necessary to build the binaries -- namely, compilers, libraries, building systems etc. This software comes from your distribution, but some of them are not installed by default -- so, they are accessible from the repository, but must be installed explicitly. That script (install_requirements.sh) just forces your system to install missing packages (via APT manager, i.e. by a conventional way employed in Ubuntu/Mint/Debian). After that, you can return to install_cp2k_toolchain.sh script -- now it should proceed without errors. Anton From sunjia... at gmail.com Fri Jun 12 18:44:15 2020 From: sunjia... at gmail.com (Jiayu Sun SLE) Date: Fri, 12 Jun 2020 11:44:15 -0700 (PDT) Subject: [CP2K-user] "Non-zero exit code detected." when compile cp2k 7.1 In-Reply-To: References: Message-ID: Hi Anton Thank you for your kindly help and patience. Now, I installed some packages and rerun the sh script and almost all the packages are installed, then the code skips, but only two packages shows error message, I print here: ==================== Installing ScaLAPACK ==================== scalapack-2.0.2.tgz is found Installing from scratch into /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/scalapack-2.0.2 ERROR: (./scripts/install_scalapack.sh, line 47) Non-zero exit code detected. ==================== Installing ELPA ==================== elpa-2019.05.001.tar.gz is found Installing from scratch into /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/elpa-2019.05.001 ERROR: (./scripts/install_elpa.sh, line 84) Non-zero exit code detected. Step ptscotch took 0.00 seconds. Step parmetis took 0.00 seconds. Step metis took 0.00 seconds. Step superlu took 0.00 seconds. Step pexsi took 0.00 seconds. Step quip took 0.00 seconds. Step plumed took 0.00 seconds I tried to install Scalapack by myself, before that, the packages of blas, lapcak, cblas are all installed successfully, but the installation of Scalapack failed eventually. It's a tough way, now only two packages left, can you give me some advice? Thank you so much!! ? 2020?6?11???? UTC+9??12:08:21?Jiayu Sun SLE??? > > Hi, everyone, > I have tried compiled the cp2k 7.1 version from toolchain script, the *sh > file, and using the OpenBLAS 0.3.6, the error message are listed below: > > ==================== Installing OpenBLAS ==================== > OpenBLAS-0.3.6.tar.gz is found > Installing from scratch into > /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/openblas-0.3.6 > patching file kernel/x86_64/KERNEL.SKYLAKEX > ERROR: > (/home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/scripts/install_openblas.sh, > line 72) Non-zero exit code detected. > ERROR: (./scripts/install_mathlibs.sh, line 34) Non-zero exit code > detected. > > > How can I do this in this case? > What the meaning of this sentence: "Non-zero exit code detected." When I > compile other packages, this error occurs again, almost all the packages > are facing the same problem. > > Thank you for your help or advice. > > Sincerely > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tenebrosu... at gmail.com Sat Jun 13 19:32:23 2020 From: tenebrosu... at gmail.com (=?UTF-8?B?0JDQvdGC0L7QvSDQmy4=?=) Date: Sat, 13 Jun 2020 22:32:23 +0300 Subject: [CP2K-user] [CP2K:13518] Re: "Non-zero exit code detected." when compile cp2k 7.1 In-Reply-To: References: Message-ID: Hi, first of all, please decide if you really need ScaLAPACK -- or, more generally, if you really need MPI parallelization at all (AFAIK both ScaLAPACK and ELPA depend on MPI). If you plan to run CP2K on a single regular desktop, then you can safely avoid MPI employing only OpenMP parallelization -- I wonder if you could gain any performance profit via MPI over OpenMP. If so, just disable MPI by running ./install_cp2k_toolchain.sh --mpi-mode=no Otherwise, if you believe that you indeed want MPI parallelization, e.g. you intend to run the code on a cluster node or on a few desktops connected by network, then you should enter build/scalapack-2.0.2 subfolder and inspect all files with .log extension. Details of any errors should be reported there. Hope this helps. Am Fr., 12. Juni 2020 um 21:44 Uhr schrieb Jiayu Sun SLE < sunjia... at gmail.com>: > Hi Anton > Thank you for your kindly help and patience. > > Now, I installed some packages and rerun the sh script and almost all the > packages are installed, then the code skips, but only two packages shows > error message, I print here: > > ==================== Installing ScaLAPACK ==================== > scalapack-2.0.2.tgz is found > Installing from scratch into > /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/scalapack-2.0.2 > ERROR: (./scripts/install_scalapack.sh, line 47) Non-zero exit code > detected. > ==================== Installing ELPA ==================== > elpa-2019.05.001.tar.gz is found > Installing from scratch into > /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/elpa-2019.05.001 > ERROR: (./scripts/install_elpa.sh, line 84) Non-zero exit code detected. > Step ptscotch took 0.00 seconds. > Step parmetis took 0.00 seconds. > Step metis took 0.00 seconds. > Step superlu took 0.00 seconds. > Step pexsi took 0.00 seconds. > Step quip took 0.00 seconds. > Step plumed took 0.00 seconds > > I tried to install Scalapack by myself, before that, the packages of > blas, lapcak, cblas are all installed successfully, but the installation > of Scalapack failed eventually. > It's a tough way, now only two packages left, can you give me some advice? > > Thank you so much!! > > > ? 2020?6?11???? UTC+9??12:08:21?Jiayu Sun SLE??? >> >> Hi, everyone, >> I have tried compiled the cp2k 7.1 version from toolchain script, the >> *sh file, and using the OpenBLAS 0.3.6, the error message are listed below: >> >> ==================== Installing OpenBLAS ==================== >> OpenBLAS-0.3.6.tar.gz is found >> Installing from scratch into >> /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/openblas-0.3.6 >> patching file kernel/x86_64/KERNEL.SKYLAKEX >> ERROR: >> (/home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/scripts/install_openblas.sh, >> line 72) Non-zero exit code detected. >> ERROR: (./scripts/install_mathlibs.sh, line 34) Non-zero exit code >> detected. >> >> >> How can I do this in this case? >> What the meaning of this sentence: "Non-zero exit code detected." When I >> compile other packages, this error occurs again, almost all the packages >> are facing the same problem. >> >> Thank you for your help or advice. >> >> Sincerely >> > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/c9de5a21-ee28-471e-a60a-f540210742f6o%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdsimula... at gmail.com Sun Jun 14 12:37:51 2020 From: mdsimula... at gmail.com (MD Simulation) Date: Sun, 14 Jun 2020 05:37:51 -0700 (PDT) Subject: [CP2K-user] How to calculate XPS Message-ID: <48d9de5f-5c07-442e-b51a-793b887f8530o@googlegroups.com> Hello, Can someone explain how to calculate XPS? I tried to follow this: https://www.cp2k.org/_media/exercises:2019_conexs_newcastle:conexs_xps_md.pdf But I'm still confused on what I need to actually do to calculate XPS. Thanks, Steve -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunjia... at gmail.com Sun Jun 14 23:38:05 2020 From: sunjia... at gmail.com (Jiayu Sun) Date: Mon, 15 Jun 2020 08:38:05 +0900 Subject: [CP2K-user] [CP2K:13518] Re: "Non-zero exit code detected." when compile cp2k 7.1 In-Reply-To: References: Message-ID: Hi, Thank you for your reply. I understand the situation. For now, I mainly use it on my PC, so maybe the two packages are no needed. Thank you again. Sincerely [image: Mailtrack] Sender notified by Mailtrack 20/06/15 08:30:23 ????? ?. ?2020?6?14??? ??4:32??? > Hi, > > first of all, please decide if you really need ScaLAPACK -- or, more > generally, if you really need MPI parallelization at all (AFAIK both > ScaLAPACK and ELPA depend on MPI). If you plan to run CP2K on a single > regular desktop, then you can safely avoid MPI employing only OpenMP > parallelization -- I wonder if you could gain any performance profit via > MPI over OpenMP. > > If so, just disable MPI by running ./install_cp2k_toolchain.sh > --mpi-mode=no > > Otherwise, if you believe that you indeed want MPI parallelization, e.g. > you intend to run the code on a cluster node or on a few desktops connected > by network, then you should enter build/scalapack-2.0.2 subfolder and > inspect all files with .log extension. Details of any errors should be > reported there. > > Hope this helps. > > > Am Fr., 12. Juni 2020 um 21:44 Uhr schrieb Jiayu Sun SLE < > sunjia... at gmail.com>: > >> Hi Anton >> Thank you for your kindly help and patience. >> >> Now, I installed some packages and rerun the sh script and almost all the >> packages are installed, then the code skips, but only two packages shows >> error message, I print here: >> >> ==================== Installing ScaLAPACK ==================== >> scalapack-2.0.2.tgz is found >> Installing from scratch into >> /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/scalapack-2.0.2 >> ERROR: (./scripts/install_scalapack.sh, line 47) Non-zero exit code >> detected. >> ==================== Installing ELPA ==================== >> elpa-2019.05.001.tar.gz is found >> Installing from scratch into >> /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/elpa-2019.05.001 >> ERROR: (./scripts/install_elpa.sh, line 84) Non-zero exit code detected. >> Step ptscotch took 0.00 seconds. >> Step parmetis took 0.00 seconds. >> Step metis took 0.00 seconds. >> Step superlu took 0.00 seconds. >> Step pexsi took 0.00 seconds. >> Step quip took 0.00 seconds. >> Step plumed took 0.00 seconds >> >> I tried to install Scalapack by myself, before that, the packages of >> blas, lapcak, cblas are all installed successfully, but the installation >> of Scalapack failed eventually. >> It's a tough way, now only two packages left, can you give me some advice? >> >> Thank you so much!! >> >> >> ? 2020?6?11???? UTC+9??12:08:21?Jiayu Sun SLE??? >>> >>> Hi, everyone, >>> I have tried compiled the cp2k 7.1 version from toolchain script, the >>> *sh file, and using the OpenBLAS 0.3.6, the error message are listed below: >>> >>> ==================== Installing OpenBLAS ==================== >>> OpenBLAS-0.3.6.tar.gz is found >>> Installing from scratch into >>> /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/openblas-0.3.6 >>> patching file kernel/x86_64/KERNEL.SKYLAKEX >>> ERROR: >>> (/home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/scripts/install_openblas.sh, >>> line 72) Non-zero exit code detected. >>> ERROR: (./scripts/install_mathlibs.sh, line 34) Non-zero exit code >>> detected. >>> >>> >>> How can I do this in this case? >>> What the meaning of this sentence: "Non-zero exit code detected." When I >>> compile other packages, this error occurs again, almost all the packages >>> are facing the same problem. >>> >>> Thank you for your help or advice. >>> >>> Sincerely >>> >> -- >> 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 cp... at googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/cp2k/c9de5a21-ee28-471e-a60a-f540210742f6o%40googlegroups.com >> >> . >> > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/CABN9yY8pbGYo%2B_foe53DUYCbUTs5C-6YpWNJbg6QZ9FKnZfc2w%40mail.gmail.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From z5476... at gmail.com Mon Jun 15 01:59:08 2020 From: z5476... at gmail.com (Tong Zhu) Date: Sun, 14 Jun 2020 18:59:08 -0700 (PDT) Subject: [CP2K-user] Automatically neutralize a charged system in the SP calculation Message-ID: <4d166a27-704e-4d6c-b03b-592fb7db81a6o@googlegroups.com> Dear all? We want to perform single-point calculation for a charged periodic system. However, the system is too small that we don't want to add explicit neutralized charges. Can CP2K apply a homogeneous neutralizing background charge with opposite sign in the cell automatically? Thank you very much for your help! Best, Tong -------------- next part -------------- An HTML attachment was scrubbed... URL: From zq97... at gmail.com Mon Jun 15 03:16:04 2020 From: zq97... at gmail.com (qi zhang) Date: Sun, 14 Jun 2020 20:16:04 -0700 (PDT) Subject: [CP2K-user] [CP2K:12268] Binding energy with charged unit cell In-Reply-To: References: , > <8bce9cc8-5988-4a57-b8f4-6ad34f4fa316@googlegroups.com> Message-ID: <10ee95d3-0265-417e-a760-cfc51b09a99bo@googlegroups.com> Dear jgh: I'm new to CP2K. My system is also a charged system, and periodic. I want to compute the single point energy of this system. So is there any way I can see the neutralizing background charge that you mentioned above. THANKS qzhang ? 2019?9?25???? UTC+8??6:19:39?jgh??? > > Forgot: If the system is charged, you get a neutralizing background > charge for periodic systems. This leads to slow convergence of > binding energies. > > Juerg Hutter > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: h... at chem.uzh.ch > > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----c... at googlegroups.com wrote: ----- > To: c... at googlegroups.com > From: h... at chem.uzh.ch > Sent by: c... at googlegroups.com > Date: 09/25/2019 12:18PM > Subject: Re: [CP2K:12268] Binding energy with charged unit cell > > Hi > > your problem is equivalent to the problem of calculating > charged defect energies in solids. There is a huge literature > on how to solve the problems related to periodic boundary > conditions. See for example the papers by Alfredo Pasquarello. > > regards > > Juerg Hutter > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: h... at chem.uzh.ch > > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----c... at googlegroups.com wrote: ----- > To: "cp2k" > > From: "LK" > Sent by: c... at googlegroups.com > Date: 09/23/2019 10:32PM > Subject: [CP2K:12258] Binding energy with charged unit cell > > Hello All, > > I'm trying to calculate the binding energy of an ion inside a condensed > phase unit cell. > > The energy difference equals the energy of the full (neutral) liquid > system minus the energy of two oppositely charged systems: vacuum-phase > molecule (in this case, negatively charged) and liquid/hole combo > (positively charged). > > Simply setting the CHARGE setting in my input file leads to spurious > results, especially large dependence on vacuum-phase ion's energy on the > unit cell size. > > I've been playing around with turning the liquid unit cell into a cluster, > and trying to calculate the energy without periodicity, i.e. using WAVELET > poisson with ANALYTIC solver. But I'm not sure whether this plays nice with > the CHARGE keyword. > > Maybe a better way would be to stay within periodic boundary conditions, > but turn on MULTIPOLE poisson method...again, not sure how this plays with > having a charged unit cell. > > I can't find in the documentation what exactly setting a nonzero CHARGE > does... does it do nothing, or does it automatically turn on a background > jellium? > > Any suggestions would be greatly appreciated. > > Thanks, > > L.K. > > > > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/8bce9cc8-5988-4a57-b8f4-6ad34f4fa316%40googlegroups.com. > > > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/OFAD59B041.B4ACA85F-ONC1258480.0038672C-C1258480.003890FD%40lotus.uzh.ch. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Mon Jun 15 08:38:19 2020 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Mon, 15 Jun 2020 10:38:19 +0200 Subject: [CP2K-user] [CP2K:13522] Automatically neutralize a charged system in the SP calculation In-Reply-To: <4d166a27-704e-4d6c-b03b-592fb7db81a6o@googlegroups.com> References: <4d166a27-704e-4d6c-b03b-592fb7db81a6o@googlegroups.com> Message-ID: Hi charged periodic systems always have a compensating uniform background charge in CP2K. This is by default, nothing to be specified in the input. regards Juerg Hutter -------------------------------------------------------------- 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: "Tong Zhu" Sent by: cp... at googlegroups.com Date: 06/15/2020 03:59AM Subject: [CP2K:13522] Automatically neutralize a charged system in the SP calculation Dear all? We want to perform single-point calculation for a charged periodic system. However, the system is too small that we don't want to add explicit neutralized charges. Can CP2K apply a homogeneous neutralizing background charge with opposite sign in the cell automatically? Thank you very much for your help! Best, Tong -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/4d166a27-704e-4d6c-b03b-592fb7db81a6o%40googlegroups.com. From dev.... at gmail.com Mon Jun 15 23:14:37 2020 From: dev.... at gmail.com (Dev Rana) Date: Mon, 15 Jun 2020 16:14:37 -0700 (PDT) Subject: [CP2K-user] Visualizing Vibrational Frequency Modes Message-ID: <792379d3-2ac4-42a9-92e9-607502fe4bcfo@googlegroups.com> Hello Friends, What is the recommended method of visualizing the vibrational frequency modes that are output from the &VIBRATIONAL_ANALYSIS run type? Thanks! Dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From pierre.a... at gmail.com Wed Jun 17 10:41:17 2020 From: pierre.a... at gmail.com (=?UTF-8?Q?Pierre-Andr=C3=A9_Cazade?=) Date: Wed, 17 Jun 2020 03:41:17 -0700 (PDT) Subject: [CP2K-user] G3X3 and VIRTUAL_SITES Message-ID: <0a1b04bc-ad4c-4cd0-babc-7f694e836288o@googlegroups.com> Dear CP2K users, I am trying to use G3X3 constraints on my water molecules during a CELL_OPT motion. Needless to say, that it does not work. The "manual" is not very clear about the indexes that need to be provided. Should I use the index of the atoms in the coordinate file, for example 15761 15762 15763, or the indexes within the water molecule itself: 1 2 3. Does such constraint apply to all my water molecules provided they have the same molname "SWM4" or do I need an entry for each water molecule? What about VIRTUAL_SITES? Finally, the "CONTRAINT_INFO ON" section does not print a single information in the output to help me out. I attached my input file for clarity. Regards, Pierre -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lyso4.inp Type: chemical/x-gamess-input Size: 395593 bytes Desc: not available URL: From azade.y... at gmail.com Wed Jun 17 11:19:51 2020 From: azade.y... at gmail.com (Azade Yazdan Yar) Date: Wed, 17 Jun 2020 13:19:51 +0200 Subject: [CP2K-user] [CP2K:13526] G3X3 and VIRTUAL_SITES In-Reply-To: <0a1b04bc-ad4c-4cd0-babc-7f694e836288o@googlegroups.com> References: <0a1b04bc-ad4c-4cd0-babc-7f694e836288o@googlegroups.com> Message-ID: Hi Pierre, I know some of the answers to your first question. What you use in the ATOMS should be the index of atoms within that molecule. Constraints will be applied to all molecules with the same MOLNAME or MOLECULE number. >From your input file, I cannot see how the SWM4 molecules are defined in the coordinates section. You have to define the MOLNAME in that part as below (what I have as H2O, or MOLECULE 1). Note that if you use MOLECULE, it is the '*molecule kind number' *and not molecule number. Hope this helps, Azade &G3X3 MOLECULE 1 ATOMS 1..3 DISTANCES a b c &END G3X3 O 5.1692824047308950E+00 5.3185376653354242E+00 2.1483827179189252E+01 H2O 1 On Wed, Jun 17, 2020 at 12:41 PM Pierre-Andr? Cazade < pierre.a... at gmail.com> wrote: > Dear CP2K users, > > I am trying to use G3X3 constraints on my water molecules during a > CELL_OPT motion. Needless to say, that it does not work. The "manual" is > not very clear about the indexes that need to be provided. Should I use the > index of the atoms in the coordinate file, for example 15761 15762 15763, > or the indexes within the water molecule itself: 1 2 3. Does such > constraint apply to all my water molecules provided they have the same > molname "SWM4" or do I need an entry for each water molecule? > > What about VIRTUAL_SITES? > > Finally, the "CONTRAINT_INFO ON" section does not print a single > information in the output to help me out. > > I attached my input file for clarity. > > Regards, > Pierre > > > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/0a1b04bc-ad4c-4cd0-babc-7f694e836288o%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pierre.a... at gmail.com Wed Jun 17 11:53:49 2020 From: pierre.a... at gmail.com (=?UTF-8?Q?Pierre-Andr=C3=A9_Cazade?=) Date: Wed, 17 Jun 2020 04:53:49 -0700 (PDT) Subject: [CP2K-user] [CP2K:13526] G3X3 and VIRTUAL_SITES In-Reply-To: References: <0a1b04bc-ad4c-4cd0-babc-7f694e836288o@googlegroups.com> Message-ID: Hi Azade, Thanks for your answer. The molname is defined in the PSF file, in the topology section. The molname seems to be identified correctly as it is present in the output file (attached) in the description of the topology. Regards, Pierre On Wednesday, June 17, 2020 at 12:20:32 PM UTC+1, Azade Yazdan Yar wrote: > > Hi Pierre, > I know some of the answers to your first question. > What you use in the ATOMS should be the index of atoms within that > molecule. Constraints will be applied to all molecules with the same > MOLNAME or MOLECULE number. > From your input file, I cannot see how the SWM4 molecules are defined in > the coordinates section. You have to define the MOLNAME in that part as > below (what I have as H2O, or MOLECULE 1). Note that if you use MOLECULE, > it is the '*molecule kind number' *and not molecule number. > > Hope this helps, > Azade > > &G3X3 > MOLECULE 1 > ATOMS 1..3 > DISTANCES a b c > &END G3X3 > > O 5.1692824047308950E+00 5.3185376653354242E+00 > 2.1483827179189252E+01 H2O 1 > > On Wed, Jun 17, 2020 at 12:41 PM Pierre-Andr? Cazade < > pie... at gmail.com > wrote: > >> Dear CP2K users, >> >> I am trying to use G3X3 constraints on my water molecules during a >> CELL_OPT motion. Needless to say, that it does not work. The "manual" is >> not very clear about the indexes that need to be provided. Should I use the >> index of the atoms in the coordinate file, for example 15761 15762 15763, >> or the indexes within the water molecule itself: 1 2 3. Does such >> constraint apply to all my water molecules provided they have the same >> molname "SWM4" or do I need an entry for each water molecule? >> >> What about VIRTUAL_SITES? >> >> Finally, the "CONTRAINT_INFO ON" section does not print a single >> information in the output to help me out. >> >> I attached my input file for clarity. >> >> Regards, >> Pierre >> >> >> -- >> 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 c... at googlegroups.com . >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/cp2k/0a1b04bc-ad4c-4cd0-babc-7f694e836288o%40googlegroups.com >> >> . >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lyso4.out Type: application/octet-stream Size: 2859920 bytes Desc: not available URL: From alinm... at gmail.com Wed Jun 17 12:02:03 2020 From: alinm... at gmail.com (Alin Marin Elena) Date: Wed, 17 Jun 2020 13:02:03 +0100 Subject: [CP2K-user] [CP2K:13528] G3X3 and VIRTUAL_SITES In-Reply-To: References: <0a1b04bc-ad4c-4cd0-babc-7f694e836288o@googlegroups.com> Message-ID: Hi Pierre, there are some example in tests/Fist/regtest-1-3/h2o-32-g3x3-mult.inp Regards, Alin Without Questions there are no Answers! ______________________________________________________________________ Dr. Alin Marin ELENA http://alin.elena.space/ ______________________________________________________________________ On Wed, 17 Jun 2020 at 12:54, Pierre-Andr? Cazade wrote: > > Hi Azade, > > Thanks for your answer. The molname is defined in the PSF file, in the topology section. The molname seems to be identified correctly as it is present in the output file (attached) in the description of the topology. > > Regards, > Pierre > > On Wednesday, June 17, 2020 at 12:20:32 PM UTC+1, Azade Yazdan Yar wrote: >> >> Hi Pierre, >> I know some of the answers to your first question. >> What you use in the ATOMS should be the index of atoms within that molecule. Constraints will be applied to all molecules with the same MOLNAME or MOLECULE number. >> From your input file, I cannot see how the SWM4 molecules are defined in the coordinates section. You have to define the MOLNAME in that part as below (what I have as H2O, or MOLECULE 1). Note that if you use MOLECULE, it is the 'molecule kind number' and not molecule number. >> >> Hope this helps, >> Azade >> >> &G3X3 >> MOLECULE 1 >> ATOMS 1..3 >> DISTANCES a b c >> &END G3X3 >> >> O 5.1692824047308950E+00 5.3185376653354242E+00 2.1483827179189252E+01 H2O 1 >> >> On Wed, Jun 17, 2020 at 12:41 PM Pierre-Andr? Cazade wrote: >>> >>> Dear CP2K users, >>> >>> I am trying to use G3X3 constraints on my water molecules during a CELL_OPT motion. Needless to say, that it does not work. The "manual" is not very clear about the indexes that need to be provided. Should I use the index of the atoms in the coordinate file, for example 15761 15762 15763, or the indexes within the water molecule itself: 1 2 3. Does such constraint apply to all my water molecules provided they have the same molname "SWM4" or do I need an entry for each water molecule? >>> >>> What about VIRTUAL_SITES? >>> >>> Finally, the "CONTRAINT_INFO ON" section does not print a single information in the output to help me out. >>> >>> I attached my input file for clarity. >>> >>> Regards, >>> Pierre >>> >>> >>> -- >>> 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 c... at googlegroups.com. >>> To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/0a1b04bc-ad4c-4cd0-babc-7f694e836288o%40googlegroups.com. > > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/eb929574-947c-45dd-8f2c-dd767482b7f1o%40googlegroups.com. From pierre.a... at gmail.com Wed Jun 17 12:13:00 2020 From: pierre.a... at gmail.com (=?UTF-8?Q?Pierre-Andr=C3=A9_Cazade?=) Date: Wed, 17 Jun 2020 05:13:00 -0700 (PDT) Subject: [CP2K-user] [CP2K:13528] G3X3 and VIRTUAL_SITES In-Reply-To: References: <0a1b04bc-ad4c-4cd0-babc-7f694e836288o@googlegroups.com> Message-ID: <4938882e-e085-43c3-bb2b-f2706eb77cfdo@googlegroups.com> Hi Alin, Thanks for the example. I checked some of the regtest but not the one you mentioned. This quite helpful. Yet, if you check my input file, this exactly what I am doing, so I am puzzled as for why it seems the constraints (at least g3x3) are not enforced. This leads to distorted water molecules (I checked the restart file) and then to the bad contacts causing cp2k to crash. Regards, Pierre On Wednesday, June 17, 2020 at 1:02:19 PM UTC+1, Alin Marin Elena wrote: > > Hi Pierre, > > there are some example in tests/Fist/regtest-1-3/h2o-32-g3x3-mult.inp > > > Regards, > Alin > > Without Questions there are no Answers! > ______________________________________________________________________ > Dr. Alin Marin ELENA > http://alin.elena.space/ > ______________________________________________________________________ > > On Wed, 17 Jun 2020 at 12:54, Pierre-Andr? Cazade > > wrote: > > > > Hi Azade, > > > > Thanks for your answer. The molname is defined in the PSF file, in the > topology section. The molname seems to be identified correctly as it is > present in the output file (attached) in the description of the topology. > > > > Regards, > > Pierre > > > > On Wednesday, June 17, 2020 at 12:20:32 PM UTC+1, Azade Yazdan Yar > wrote: > >> > >> Hi Pierre, > >> I know some of the answers to your first question. > >> What you use in the ATOMS should be the index of atoms within that > molecule. Constraints will be applied to all molecules with the same > MOLNAME or MOLECULE number. > >> From your input file, I cannot see how the SWM4 molecules are defined > in the coordinates section. You have to define the MOLNAME in that part as > below (what I have as H2O, or MOLECULE 1). Note that if you use MOLECULE, > it is the 'molecule kind number' and not molecule number. > >> > >> Hope this helps, > >> Azade > >> > >> &G3X3 > >> MOLECULE 1 > >> ATOMS 1..3 > >> DISTANCES a b c > >> &END G3X3 > >> > >> O 5.1692824047308950E+00 5.3185376653354242E+00 > 2.1483827179189252E+01 H2O 1 > >> > >> On Wed, Jun 17, 2020 at 12:41 PM Pierre-Andr? Cazade < > pie... at gmail.com> wrote: > >>> > >>> Dear CP2K users, > >>> > >>> I am trying to use G3X3 constraints on my water molecules during a > CELL_OPT motion. Needless to say, that it does not work. The "manual" is > not very clear about the indexes that need to be provided. Should I use the > index of the atoms in the coordinate file, for example 15761 15762 15763, > or the indexes within the water molecule itself: 1 2 3. Does such > constraint apply to all my water molecules provided they have the same > molname "SWM4" or do I need an entry for each water molecule? > >>> > >>> What about VIRTUAL_SITES? > >>> > >>> Finally, the "CONTRAINT_INFO ON" section does not print a single > information in the output to help me out. > >>> > >>> I attached my input file for clarity. > >>> > >>> Regards, > >>> Pierre > >>> > >>> > >>> -- > >>> 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 c... at googlegroups.com. > >>> To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/0a1b04bc-ad4c-4cd0-babc-7f694e836288o%40googlegroups.com. > > > > > -- > > 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 c... at googlegroups.com . > > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/eb929574-947c-45dd-8f2c-dd767482b7f1o%40googlegroups.com. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pierre.a... at gmail.com Wed Jun 17 15:08:28 2020 From: pierre.a... at gmail.com (Pierre Cazade) Date: Wed, 17 Jun 2020 16:08:28 +0100 Subject: [CP2K-user] [CP2K:13532] G3X3 and VIRTUAL_SITES In-Reply-To: <26730b5e-18ae-4efe-9baf-ae01fec7519do@googlegroups.com> References: <0a1b04bc-ad4c-4cd0-babc-7f694e836288o@googlegroups.com> <4938882e-e085-43c3-bb2b-f2706eb77cfdo@googlegroups.com> <26730b5e-18ae-4efe-9baf-ae01fec7519do@googlegroups.com> Message-ID: Hi Matt, I have just realized going through the source code that shake is only used with MD. Thanks, Pierre On 17/06/2020 15:44, Matt W wrote: > Constraints only work with MD not geo or cell opt. > > On Wednesday, June 17, 2020 at 1:13:01 PM UTC+1, Pierre-Andr? Cazade > wrote: > > Hi Alin, > > Thanks for the example. I checked some of the regtest but not the > one you mentioned. This quite helpful. Yet, if you check my input > file, this exactly what I am doing, so I am puzzled as for why it > seems the constraints (at least g3x3) are not enforced. This leads > to distorted water molecules (I checked the restart file) and then > to the bad contacts causing cp2k to crash. > > Regards, > Pierre > > On Wednesday, June 17, 2020 at 1:02:19 PM UTC+1, Alin Marin Elena > wrote: > > Hi Pierre, > > there are some example in > tests/Fist/regtest-1-3/h2o-32-g3x3-mult.inp > > > Regards, > Alin > > Without Questions there are no Answers! > ______________________________________________________________________ > > Dr. Alin Marin ELENA > http://alin.elena.space/ > ______________________________________________________________________ > > > On Wed, 17 Jun 2020 at 12:54, Pierre-Andr? Cazade > wrote: > > > > Hi Azade, > > > > Thanks for your answer. The molname is defined in the PSF > file, in the topology section. The molname seems to be > identified correctly as it is present in the output file > (attached) in the description of the topology. > > > > Regards, > > Pierre > > > > On Wednesday, June 17, 2020 at 12:20:32 PM UTC+1, Azade > Yazdan Yar wrote: > >> > >> Hi Pierre, > >> I know some of the answers to your first question. > >> What you use in the ATOMS should be the index of atoms > within that molecule. Constraints will be applied to all > molecules with the same MOLNAME or MOLECULE number. > >> From your input file, I cannot see how the SWM4 molecules > are defined in the coordinates section. You have to define the > MOLNAME in that part as below (what I have as H2O, or MOLECULE > 1). Note that if you use MOLECULE, it is the 'molecule kind > number' and not molecule number. > >> > >> Hope this helps, > >> Azade > >> > >> &G3X3 > >> ? ? ? ?MOLECULE ?1 > >> ? ? ? ?ATOMS ?1..3 > >> ? ? ? ?DISTANCES ? ? a b c > >> ?&END G3X3 > >> > >> O ? ?5.1692824047308950E+00 ?5.3185376653354242E+00 ? > ?2.1483827179189252E+01 H2O 1 > >> > >> On Wed, Jun 17, 2020 at 12:41 PM Pierre-Andr? Cazade > wrote: > >>> > >>> Dear CP2K users, > >>> > >>> I am trying to use G3X3 constraints on my water molecules > during a CELL_OPT motion. Needless to say, that it does not > work. The "manual" is not very clear about the indexes that > need to be provided. Should I use the index of the atoms in > the coordinate file, for example 15761 15762 15763, or the > indexes within the water molecule itself: 1 2 3. Does such > constraint apply to all my water molecules provided they have > the same molname "SWM4" or do I need an entry for each water > molecule? > >>> > >>> What about VIRTUAL_SITES? > >>> > >>> Finally, the "CONTRAINT_INFO ON" section does not print a > single information in the output to help me out. > >>> > >>> I attached my input file for clarity. > >>> > >>> Regards, > >>> Pierre > >>> > >>> > >>> -- > >>> 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 c... at googlegroups.com. > >>> To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/0a1b04bc-ad4c-4cd0-babc-7f694e836288o%40googlegroups.com > . > > > > > -- > > 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 c... at googlegroups.com. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/eb929574-947c-45dd-8f2c-dd767482b7f1o%40googlegroups.com > . > > > -- > 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 cp... at googlegroups.com > . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/26730b5e-18ae-4efe-9baf-ae01fec7519do%40googlegroups.com > . -- Dr Pierre Cazade, PhD AD3-023, Bernal Institute, University of Limerick, Plassey Park Road, Castletroy, co. Limerick, Ireland -------------- next part -------------- An HTML attachment was scrubbed... URL: From fabia... at gmail.com Wed Jun 17 14:34:40 2020 From: fabia... at gmail.com (Fabian Ducry) Date: Wed, 17 Jun 2020 07:34:40 -0700 (PDT) Subject: [CP2K-user] Band gap estimation error In-Reply-To: References: Message-ID: <77ab5ed1-5ace-4727-b628-eb2a03a23aa7o@googlegroups.com> CP2K does not support the use of hybrid or meta-GGA functionals and DFT+U with k-point sampling. So you cannot calculate the band structure with these methods. What do you want to calculate? If you just need the band gap you can use a super cell (make sure that all relevant k-points are folded into the gamma point) and compute the density-of-states. Best, Fabian -------------- next part -------------- An HTML attachment was scrubbed... URL: From mattwa... at gmail.com Wed Jun 17 14:44:01 2020 From: mattwa... at gmail.com (Matt W) Date: Wed, 17 Jun 2020 07:44:01 -0700 (PDT) Subject: [CP2K-user] [CP2K:13528] G3X3 and VIRTUAL_SITES In-Reply-To: <4938882e-e085-43c3-bb2b-f2706eb77cfdo@googlegroups.com> References: <0a1b04bc-ad4c-4cd0-babc-7f694e836288o@googlegroups.com> <4938882e-e085-43c3-bb2b-f2706eb77cfdo@googlegroups.com> Message-ID: <26730b5e-18ae-4efe-9baf-ae01fec7519do@googlegroups.com> Constraints only work with MD not geo or cell opt. On Wednesday, June 17, 2020 at 1:13:01 PM UTC+1, Pierre-Andr? Cazade wrote: > > Hi Alin, > > Thanks for the example. I checked some of the regtest but not the one you > mentioned. This quite helpful. Yet, if you check my input file, this > exactly what I am doing, so I am puzzled as for why it seems the > constraints (at least g3x3) are not enforced. This leads to distorted water > molecules (I checked the restart file) and then to the bad contacts causing > cp2k to crash. > > Regards, > Pierre > > On Wednesday, June 17, 2020 at 1:02:19 PM UTC+1, Alin Marin Elena wrote: >> >> Hi Pierre, >> >> there are some example in tests/Fist/regtest-1-3/h2o-32-g3x3-mult.inp >> >> >> Regards, >> Alin >> >> Without Questions there are no Answers! >> ______________________________________________________________________ >> Dr. Alin Marin ELENA >> http://alin.elena.space/ >> ______________________________________________________________________ >> >> On Wed, 17 Jun 2020 at 12:54, Pierre-Andr? Cazade >> wrote: >> > >> > Hi Azade, >> > >> > Thanks for your answer. The molname is defined in the PSF file, in the >> topology section. The molname seems to be identified correctly as it is >> present in the output file (attached) in the description of the topology. >> > >> > Regards, >> > Pierre >> > >> > On Wednesday, June 17, 2020 at 12:20:32 PM UTC+1, Azade Yazdan Yar >> wrote: >> >> >> >> Hi Pierre, >> >> I know some of the answers to your first question. >> >> What you use in the ATOMS should be the index of atoms within that >> molecule. Constraints will be applied to all molecules with the same >> MOLNAME or MOLECULE number. >> >> From your input file, I cannot see how the SWM4 molecules are defined >> in the coordinates section. You have to define the MOLNAME in that part as >> below (what I have as H2O, or MOLECULE 1). Note that if you use MOLECULE, >> it is the 'molecule kind number' and not molecule number. >> >> >> >> Hope this helps, >> >> Azade >> >> >> >> &G3X3 >> >> MOLECULE 1 >> >> ATOMS 1..3 >> >> DISTANCES a b c >> >> &END G3X3 >> >> >> >> O 5.1692824047308950E+00 5.3185376653354242E+00 >> 2.1483827179189252E+01 H2O 1 >> >> >> >> On Wed, Jun 17, 2020 at 12:41 PM Pierre-Andr? Cazade < >> pie... at gmail.com> wrote: >> >>> >> >>> Dear CP2K users, >> >>> >> >>> I am trying to use G3X3 constraints on my water molecules during a >> CELL_OPT motion. Needless to say, that it does not work. The "manual" is >> not very clear about the indexes that need to be provided. Should I use the >> index of the atoms in the coordinate file, for example 15761 15762 15763, >> or the indexes within the water molecule itself: 1 2 3. Does such >> constraint apply to all my water molecules provided they have the same >> molname "SWM4" or do I need an entry for each water molecule? >> >>> >> >>> What about VIRTUAL_SITES? >> >>> >> >>> Finally, the "CONTRAINT_INFO ON" section does not print a single >> information in the output to help me out. >> >>> >> >>> I attached my input file for clarity. >> >>> >> >>> Regards, >> >>> Pierre >> >>> >> >>> >> >>> -- >> >>> 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 c... at googlegroups.com. >> >>> To view this discussion on the web visit >> https://groups.google.com/d/msgid/cp2k/0a1b04bc-ad4c-4cd0-babc-7f694e836288o%40googlegroups.com. >> >> > >> > -- >> > 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 c... at googlegroups.com. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/cp2k/eb929574-947c-45dd-8f2c-dd767482b7f1o%40googlegroups.com. >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fabia... at gmail.com Thu Jun 18 14:43:49 2020 From: fabia... at gmail.com (Fabian Ducry) Date: Thu, 18 Jun 2020 07:43:49 -0700 (PDT) Subject: [CP2K-user] excluding selected interactions from DFT-D3 Message-ID: <85d53f08-cb06-440d-9c88-4677223d5827o@googlegroups.com> Dear all, I would like to study 2D materials on top of a metal (Au) substrate. To correctly describe the interlayer distance between the layers of the 2D materials I use the D3(BJ) correction. This, however, causes the metal to contract leading to a poor description of the metal surface. Is there a way to disable the D3 correction between the Au atoms while keeping the interaction of the metal with the 2D materials? I am aware of the XC%VDW_POTENTIAL%PAIR_POTENTIAL%D3_EXCLUDE_KIND keyword to exclude Au from the correction but I just want to exclude the Au-Au terms, not the e.g Au-S interactions. Best, Fabian -------------- next part -------------- An HTML attachment was scrubbed... URL: From mada... at gmail.com Fri Jun 19 07:20:26 2020 From: mada... at gmail.com (yulei wang) Date: Fri, 19 Jun 2020 00:20:26 -0700 (PDT) Subject: [CP2K-user] Geometry Optimization for Copper Message-ID: Hello all, I am fairly new to cp2k so I believe this problem is easily resolvable. I am doing structural optimization of periodic copper surface under the action of electric field, and I fixed 3 atomic layers below ( input file is cu.inp and date.coord). I get the wrong results as the position of atom 7 is too high compared to other atoms in the same layer (the result is in cu-pos-1.xyz). It is undoubtedly unreasonable, and then I tried to do the geometry optimization without the action of electric field, and the result is just the same. Any ideas? Thank you for your help or advice. Best Regards, Yulei Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: cu.out Type: application/octet-stream Size: 952384 bytes Desc: not available URL: From mattwa... at gmail.com Fri Jun 19 10:23:42 2020 From: mattwa... at gmail.com (Matt W) Date: Fri, 19 Jun 2020 03:23:42 -0700 (PDT) Subject: [CP2K-user] Geometry Optimization for Copper In-Reply-To: References: Message-ID: <6b3a82d9-2e59-4c8d-ad47-fa2b83464ad3o@googlegroups.com> Your scf convergence criteria is not good enough, you should have EPS_SCF much smaller, maybe 10-6 to ensure energies are converged to at least micro hartree level. I am not at all sure that the electric field and poisson solver work with k-points. I also don't have experience with the implicit psolver to comment on that setup. I'd remove that and check you can optimize a slab with periodic boundaries first then tackle the more complicated problem afterwards. Matt On Friday, June 19, 2020 at 8:20:26 AM UTC+1, yulei wang wrote: > > Hello all, > > I am fairly new to cp2k so I believe this problem is easily resolvable. I > am doing structural optimization of periodic copper surface under the > action of electric field, and I fixed 3 atomic layers below ( input file > is cu.inp and date.coord). I get the wrong results as the position of atom > 7 is too high compared to other atoms in the same layer (the result is in > cu-pos-1.xyz). It is undoubtedly unreasonable, and then I tried to do > the geometry optimization without the action of electric field, and the > result is just the same. Any ideas? > > Thank you for your help or advice. > > Best Regards, > Yulei Wang > -------------- next part -------------- An HTML attachment was scrubbed... URL: From janel... at gmail.com Fri Jun 19 15:38:01 2020 From: janel... at gmail.com (Jan Elsner) Date: Fri, 19 Jun 2020 08:38:01 -0700 (PDT) Subject: [CP2K-user] SCF convergence using PBE+50%HFX on +ve dimer Message-ID: Dear all, I'm running a single point calculation on a positively charged rubrene (C42H 28) dimer (spin polarized calculation) using PBE+50%HFX, restarting from a converged PBE wavefunction. Unfortunately the SCF does not converge after 350 steps. The "convergence" value jumps to huge values at SCF step 2 ("convergence" at SCF step1 = *3.3*, "convergence" at SCF step2 = *12281*) and at longer times (around SCF step 150 onwards), it shows oscillatory behaviour. The behaviour is the same if I use RESTART ATOMIC. I note: - The SCF also doesn't converge for the neutral dimer - The SCF *does converges *for both the neutral and cationic *single rubrene molecule* - For the dimer, I have tried a number of settings: different mixing schemes (BROYDEN, DIRECT_P_MIXING), diagonalization and OT method, larger CUTOFF, smaller EPS_SCHWARZ - I also can't converge the SCF using PBE0, where I observe similar behaviour I attach the relevant files. Any help would be much appreciated. Best, Jan *EDIT:* I thought I should also add, when I try to use Fermi-Dirac smearing, I get the following errors: "WARNING in qs_mo_occupation.F:118 :: Fermi-Dirac smearing includes the first MO" and "WARNING in qs_mo_occupation.F:122 :: Fermi-Dirac smearing includes the last MO => Add more MOs for proper smearing. " This occurs even when I use a tiny Electronic Temperature (0.1 K) and 100 added MOs for each spin channel (files attached). -------------- next part -------------- An HTML attachment was scrubbed... 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Name: dimer-pbe-50hfx-smearing.out Type: application/octet-stream Size: 13868 bytes Desc: not available URL: From mada... at gmail.com Sat Jun 20 03:31:55 2020 From: mada... at gmail.com (yulei wang) Date: Fri, 19 Jun 2020 20:31:55 -0700 (PDT) Subject: [CP2K-user] Geometry Optimization for Copper In-Reply-To: <6b3a82d9-2e59-4c8d-ad47-fa2b83464ad3o@googlegroups.com> References: <6b3a82d9-2e59-4c8d-ad47-fa2b83464ad3o@googlegroups.com> Message-ID: <3611a8fc-9c16-46ec-8884-e8f30d7b0429o@googlegroups.com> Hi Matt Thank you for your help. I had tried to set EPS_SCF as 1.0E-06, but the result is similar to before. And I have a question about POISSON_SOLVER PERIODIC. If I just want to repeat the periodicity in both X and Y directions, it will report an error as "Illegal combination of periodicity and Poisson solver periodic3d". How can I setting parameters to achieve my goal. Thanks Yulei Wang ? 2020?6?19???? UTC+8??6:23:43?Matt W??? > > Your scf convergence criteria is not good enough, you should have EPS_SCF > much smaller, maybe 10-6 to ensure energies are converged to at least micro > hartree level. > > I am not at all sure that the electric field and poisson solver work with > k-points. I also don't have experience with the implicit psolver to comment > on that setup. I'd remove that and check you can optimize a slab with > periodic boundaries first then tackle the more complicated problem > afterwards. > > Matt > > On Friday, June 19, 2020 at 8:20:26 AM UTC+1, yulei wang wrote: >> >> Hello all, >> >> I am fairly new to cp2k so I believe this problem is easily >> resolvable. I am doing structural optimization of periodic copper surface >> under the action of electric field, and I fixed 3 atomic layers below ( >> input file is cu.inp and date.coord). I get the wrong results as the >> position of atom 7 is too high compared to other atoms in the same layer >> (the result is in cu-pos-1.xyz). It is undoubtedly unreasonable, and >> then I tried to do the geometry optimization without the action of >> electric field, and the result is just the same. Any ideas? >> >> Thank you for your help or advice. >> >> Best Regards, >> Yulei Wang >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eluni... at gmail.com Sat Jun 20 05:48:13 2020 From: eluni... at gmail.com (Lucas Lodeiro) Date: Sat, 20 Jun 2020 01:48:13 -0400 Subject: [CP2K-user] GPW vs GAPW methods Message-ID: Hello all, I am a little confused about GPW and GAPW method. I understand both use gaussian basis sets to compute de wavefunctions and the density is computed by PW and APW method. But, when is necessary to use GAPW or GPW? For all-electron calculations is mandatory to use GAPW? Can I use both method independent of occupied basis set? If somebody has a little manual about both methods, I appreciate it. Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Sat Jun 20 10:47:00 2020 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Sat, 20 Jun 2020 12:47:00 +0200 Subject: [CP2K-user] [CP2K:13538] GPW vs GAPW methods In-Reply-To: References: Message-ID: Hi all electron calculations need the GAPW method. This is also true for mixed all-electron/pseudopotential calculations. Pseudopotential calculations can be done either with GPW or GAPW. The advantage of GAPW is the reduced cutoff and increased stability of forces. The disadvantage is, that not all features and properties are available. GAPW is also less efficient, although this can vary. regards Juerg Hutter -------------------------------------------------------------- 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: cp... at googlegroups.com From: "Lucas Lodeiro" Sent by: cp... at googlegroups.com Date: 06/20/2020 07:46AM Subject: [CP2K:13538] GPW vs GAPW methods Hello all, I am a little confused about GPW and GAPW method. I understand both use gaussian basis sets to compute de wavefunctions and the density is computed by PW and APW method. But, when is necessary to use GAPW or GPW? For all-electron calculations is mandatory to use GAPW? Can I use both method independent of occupied basis set? If somebody has a little manual about both methods, I appreciate it. Regards -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/CAOFT4P%2Bmfwhno0MqzwHRDTS6FtOfRF-uN0Dgviz%3D2T6bDH9iaw%40mail.gmail.com. From hut... at chem.uzh.ch Sat Jun 20 10:40:51 2020 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Sat, 20 Jun 2020 12:40:51 +0200 Subject: [CP2K-user] [CP2K:13534] excluding selected interactions from DFT-D3 In-Reply-To: <85d53f08-cb06-440d-9c88-4677223d5827o@googlegroups.com> References: <85d53f08-cb06-440d-9c88-4677223d5827o@googlegroups.com> Message-ID: Hi I don't see a way to achieve this with currently available options. The way to go would be to introduce an option D3_EXCLUDE_KIND_PAIR (repeatable) and add corresponding tests with CYCLE commands in the loops. The 3-center terms would need special care. regards Juerg Hutter -------------------------------------------------------------- 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: "Fabian Ducry" Sent by: cp... at googlegroups.com Date: 06/18/2020 04:44PM Subject: [CP2K:13534] excluding selected interactions from DFT-D3 Dear all, I would like to study 2D materials on top of a metal (Au) substrate. To correctly describe the interlayer distance between the layers of the 2D materials I use the D3(BJ) correction. This, however, causes the metal to contract leading to a poor description of the metal surface. Is there a way to disable the D3 correction between the Au atoms while keeping the interaction of the metal with the 2D materials? I am aware of the XC%VDW_POTENTIAL%PAIR_POTENTIAL%D3_EXCLUDE_KIND keyword to exclude Au from the correction but I just want to exclude the Au-Au terms, not the e.g Au-S interactions. Best, Fabian -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/85d53f08-cb06-440d-9c88-4677223d5827o%40googlegroups.com. From mattwa... at gmail.com Sat Jun 20 14:01:55 2020 From: mattwa... at gmail.com (Matt W) Date: Sat, 20 Jun 2020 07:01:55 -0700 (PDT) Subject: [CP2K-user] Geometry Optimization for Copper In-Reply-To: <3611a8fc-9c16-46ec-8884-e8f30d7b0429o@googlegroups.com> References: <6b3a82d9-2e59-4c8d-ad47-fa2b83464ad3o@googlegroups.com> <3611a8fc-9c16-46ec-8884-e8f30d7b0429o@googlegroups.com> Message-ID: <1756bdbf-a249-4f06-bc83-6864f5a19a71o@googlegroups.com> Add periodic XYZ in the cell section as well as the psolver section. On Saturday, June 20, 2020 at 4:31:55 AM UTC+1, yulei wang wrote: > > Hi Matt > > Thank you for your help. I had tried to set EPS_SCF as 1.0E-06, but the > result is similar to before. > > And I have a question about POISSON_SOLVER PERIODIC. If I just want to > repeat the periodicity in both X and Y directions, it will report an error > as "Illegal combination of periodicity and Poisson solver periodic3d". How > can I setting parameters to achieve my goal. > > Thanks > Yulei Wang > > ? 2020?6?19???? UTC+8??6:23:43?Matt W??? >> >> Your scf convergence criteria is not good enough, you should have EPS_SCF >> much smaller, maybe 10-6 to ensure energies are converged to at least micro >> hartree level. >> >> I am not at all sure that the electric field and poisson solver work with >> k-points. I also don't have experience with the implicit psolver to comment >> on that setup. I'd remove that and check you can optimize a slab with >> periodic boundaries first then tackle the more complicated problem >> afterwards. >> >> Matt >> >> On Friday, June 19, 2020 at 8:20:26 AM UTC+1, yulei wang wrote: >>> >>> Hello all, >>> >>> I am fairly new to cp2k so I believe this problem is easily >>> resolvable. I am doing structural optimization of periodic copper surface >>> under the action of electric field, and I fixed 3 atomic layers below ( >>> input file is cu.inp and date.coord). I get the wrong results as the >>> position of atom 7 is too high compared to other atoms in the same layer >>> (the result is in cu-pos-1.xyz). It is undoubtedly unreasonable, and >>> then I tried to do the geometry optimization without the action of >>> electric field, and the result is just the same. Any ideas? >>> >>> Thank you for your help or advice. >>> >>> Best Regards, >>> Yulei Wang >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From eluni... at gmail.com Sat Jun 20 23:50:01 2020 From: eluni... at gmail.com (Lucas Lodeiro) Date: Sat, 20 Jun 2020 19:50:01 -0400 Subject: [CP2K-user] [CP2K:13540] GPW vs GAPW methods In-Reply-To: References: Message-ID: Thanks Hutter :D El s?b., 20 jun. 2020 a las 6:47, escribi?: > Hi > > all electron calculations need the GAPW method. This is also > true for mixed all-electron/pseudopotential calculations. > > Pseudopotential calculations can be done either with GPW or > GAPW. The advantage of GAPW is the reduced cutoff and increased > stability of forces. The disadvantage is, that not all > features and properties are available. GAPW is also less > efficient, although this can vary. > > regards > > Juerg Hutter > -------------------------------------------------------------- > 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: cp... at googlegroups.com > From: "Lucas Lodeiro" > Sent by: cp... at googlegroups.com > Date: 06/20/2020 07:46AM > Subject: [CP2K:13538] GPW vs GAPW methods > > Hello all, > > I am a little confused about GPW and GAPW method. I understand both use > gaussian basis sets to compute de wavefunctions and the density is computed > by PW and APW method. > But, when is necessary to use GAPW or GPW? > For all-electron calculations is mandatory to use GAPW? > > Can I use both method independent of occupied basis set? > If somebody has a little manual about both methods, I appreciate it. > > Regards > > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/CAOFT4P%2Bmfwhno0MqzwHRDTS6FtOfRF-uN0Dgviz%3D2T6bDH9iaw%40mail.gmail.com > . > > > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/OF34EFF0F6.DDDBA32E-ONC125858D.003B3C16-C125858D.003B3C18%40lotus.uzh.ch > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eluni... at gmail.com Sun Jun 21 05:14:48 2020 From: eluni... at gmail.com (Lucas Lodeiro) Date: Sun, 21 Jun 2020 01:14:48 -0400 Subject: [CP2K-user] Single Molecule Molecular Dynamics Message-ID: Hi all, I want to perform single molecule molecular dynamics. First I do a convergence test for cutoff, cell size and poisson solver. I read in old mails, that MT is better than WAVELET for MD, due to the first is translational invariant. After that I start a MD from the optimized molecular geometry at the same level of theory. I want to obtain statistical information for a given temperature (300K for example), I think an NVT is not well behaved for a single molecule, then I ran NVE MD. As the geometry is at the minimum, I start with 2*T (where T is the target temperature) thinking in virial theorem (at equilibrium equal potential and kinetic energy). But the system is not converging (the average temperature) at the desired temperature. It shows a weird temperature oscillation (different as expected due to bond oscillation), it present in some moment higher temperature than the initial and a potential energy lower than the initial... Also, the molecular rotation exhibits variations along the MD and translation in the box. For that I start a new MD with the same INPUT and geometry, adding ANGVEL_ZERO. The MD starts without rotation but in 300 fs it starts to rotate. I attach the files for both MD. I read about the geometrical constraints, it would be useful for diatomic molecules, but for H2O or complexer molecules is not a solution. Has somebody faced these problems? some advice? regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From eluni... at gmail.com Sun Jun 21 05:41:23 2020 From: eluni... at gmail.com (Lucas Lodeiro) Date: Sun, 21 Jun 2020 01:41:23 -0400 Subject: [CP2K-user] Single Molecule Molecular Dynamics In-Reply-To: References: Message-ID: El dom., 21 jun. 2020 a las 1:14, Lucas Lodeiro () escribi?: > Hi all, > I want to perform single molecule molecular dynamics. > First I do a convergence test for cutoff, cell size and poisson solver. I > read in old mails, that MT is better than WAVELET for MD, due to the first > is translational invariant. > After that I start a MD from the optimized molecular geometry at the same > level of theory. I want to obtain statistical information for a given > temperature (300K for example), I think an NVT is not well behaved for a > single molecule, then I ran NVE MD. As the geometry is at the minimum, I > start with 2*T (where T is the target temperature) thinking in virial > theorem (at equilibrium equal potential and kinetic energy). > But the system is not converging (the average temperature) at the desired > temperature. It shows a weird temperature oscillation (different as > expected due to bond oscillation), it present in some moment higher > temperature than the initial and a potential energy lower than the > initial... Also, the molecular rotation exhibits variations along the MD > and translation in the box. For that I start a new MD with the same INPUT > and geometry, adding ANGVEL_ZERO. The MD starts without rotation but in 300 > fs it starts to rotate. > I attach the files for both MD. > > I read about the geometrical constraints, it would be useful for diatomic > molecules, but for H2O or complexer molecules is not a solution. > > Has somebody faced these problems? some advice? > > regards > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: FILE.tar.gz Type: application/gzip Size: 1275218 bytes Desc: not available URL: From z5476... at gmail.com Sun Jun 21 08:07:50 2020 From: z5476... at gmail.com (Tong Zhu) Date: Sun, 21 Jun 2020 16:07:50 +0800 Subject: [CP2K-user] [CP2K:13523] Automatically neutralize a charged system in the SP calculation In-Reply-To: References: <4d166a27-704e-4d6c-b03b-592fb7db81a6o@googlegroups.com> Message-ID: Dear Prof. Hutter, Thank you very much! Best, Tong ?2020?6?15??? ??4:38??? > Hi > > charged periodic systems always have a compensating uniform > background charge in CP2K. This is by default, nothing to be > specified in the input. > > regards > > Juerg Hutter > -------------------------------------------------------------- > 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: "Tong Zhu" > Sent by: cp... at googlegroups.com > Date: 06/15/2020 03:59AM > Subject: [CP2K:13522] Automatically neutralize a charged system in the SP > calculation > > Dear all? > > We want to perform single-point calculation for a charged periodic system. > However, the system is too small that we don't want to add explicit > neutralized charges. Can CP2K apply a homogeneous neutralizing background > charge with opposite sign in the cell automatically? > > Thank you very much for your help! > > Best, > Tong > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/4d166a27-704e-4d6c-b03b-592fb7db81a6o%40googlegroups.com > . > > > -- > You received this message because you are subscribed to a topic in the > Google Groups "cp2k" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/cp2k/jEdCfUarq7s/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/OFF33EFEA8.D544B883-ONC1258588.002F7463-C1258588.002F7464%40lotus.uzh.ch > . > -- ?Tong Zhu ------------------------------------------------------------------ State Key Laboratory of Precision Spectroscopy & Department of Physics, East China Normal University, Shanghai 200062, China ------------------------------------------------------------------ ------------------------------------------------------------------ ?? ????????? ??????????? ??????????3663??????? ???200062 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From tku... at gmail.com Mon Jun 22 09:54:46 2020 From: tku... at gmail.com (=?utf-8?Q?Thomas_K=C3=BChne?=) Date: Mon, 22 Jun 2020 11:54:46 +0200 Subject: [CP2K-user] [CP2K:13543] Single Molecule Molecular Dynamics In-Reply-To: References: Message-ID: <404EE40E-BC28-4A32-8B53-6513F7D47F8C@gmail.com> Dear Lucas, have you conducted the geometry optimization with exactly the same settings, i.e. basis set, PW cutoff, EPS_SCF, etc.? Since your system has so few DOFs, fluctuations will be large and conservation by cancellation inherently poor. Hence, with such a tiny system I would rather stick with NVT instead of NVE + viral theorem and not use ANGVEL_ZERO ? Greetings, Thomas > Am 21.06.2020 um 07:14 schrieb Lucas Lodeiro : > > Hi all, > I want to perform single molecule molecular dynamics. > First I do a convergence test for cutoff, cell size and poisson solver. I read in old mails, that MT is better than WAVELET for MD, due to the first is translational invariant. > After that I start a MD from the optimized molecular geometry at the same level of theory. I want to obtain statistical information for a given temperature (300K for example), I think an NVT is not well behaved for a single molecule, then I ran NVE MD. As the geometry is at the minimum, I start with 2*T (where T is the target temperature) thinking in virial theorem (at equilibrium equal potential and kinetic energy). > But the system is not converging (the average temperature) at the desired temperature. It shows a weird temperature oscillation (different as expected due to bond oscillation), it present in some moment higher temperature than the initial and a potential energy lower than the initial... Also, the molecular rotation exhibits variations along the MD and translation in the box. For that I start a new MD with the same INPUT and geometry, adding ANGVEL_ZERO. The MD starts without rotation but in 300 fs it starts to rotate. > I attach the files for both MD. > > I read about the geometrical constraints, it would be useful for diatomic molecules, but for H2O or complexer molecules is not a solution. > > Has somebody faced these problems? some advice? > > regards > > > > -- > 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 cp... at googlegroups.com . > To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/CAOFT4P%2BMnqg3JM5dGm-%3DQzSD912dx1A1qo8shYaMgdNLgFzTqA%40mail.gmail.com . -------------- next part -------------- An HTML attachment was scrubbed... URL: From 22b... at gmail.com Mon Jun 22 15:56:50 2020 From: 22b... at gmail.com (Brian Day) Date: Mon, 22 Jun 2020 08:56:50 -0700 (PDT) Subject: [CP2K-user] Band Structure Sets with cp2k_bs2csv.py Message-ID: <0d862f0e-0582-459c-807b-a8d062d1ba0eo@googlegroups.com> Could anybody explain to me the difference between all of the different 'material.bs-setN.csv' files generated by the cp2k_bs2csv.py code? My understanding is that there is typically one per K-point set, but I'm a bit confused as to how I should be plotting the csv files. Should I only be plotting set 1? Or should I be plotting all the sets in a concatenated fashion, or taking the range between the k-points of that set, etc.? Any clarification would be hugely appreciated - Thanks! -Brian -------------- next part -------------- An HTML attachment was scrubbed... URL: From dev.... at gmail.com Mon Jun 22 17:20:40 2020 From: dev.... at gmail.com (Dev Rana) Date: Mon, 22 Jun 2020 10:20:40 -0700 (PDT) Subject: [CP2K-user] Calculation of Gibbs Free Energy and Equilibrium Constant from AIMD Message-ID: Hello Friends, In my AIMD system of interacting metal and carbon atoms, I have reached an equilibrium state in which I can see a repetitive association and disassociation of complexes of M and C. I'd like to understand the Gibbs Free Energy and K of the interaction/reaction as a function of Temperature. What would be the best way of doing this from an MD simulation? Best Regards, Dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From 22b... at gmail.com Mon Jun 22 18:52:41 2020 From: 22b... at gmail.com (Brian Day) Date: Mon, 22 Jun 2020 11:52:41 -0700 (PDT) Subject: [CP2K-user] Band Structure Sets with cp2k_bs2csv.py In-Reply-To: <0d862f0e-0582-459c-807b-a8d062d1ba0eo@googlegroups.com> References: <0d862f0e-0582-459c-807b-a8d062d1ba0eo@googlegroups.com> Message-ID: <205289e9-ad3c-4a2c-a416-aac5c415fc7ao@googlegroups.com> Answering my own question: Each 'material.bs-setN.csv' file is the set of energies for all points between the corresponding set of k points, so in order to plot the full band structure between all k-point sets, each file needs to be loaded. One could make the argument for returning a single CSV file rather than multiple, but in the case of disjointed paths, distinct files is preferred. Hopefully this answers any questions future users might have. -Brian -------------- next part -------------- An HTML attachment was scrubbed... URL: From hasanal... at gmail.com Mon Jun 22 21:05:40 2020 From: hasanal... at gmail.com (Hasan Al-Mahayni) Date: Mon, 22 Jun 2020 14:05:40 -0700 (PDT) Subject: [CP2K-user] First NEB run Message-ID: Hello, I am trying to test NEB for the first time. I have two slabs (inital.xyz and final.xyz) and I have included the input file as well (Cp2kNEB). When I run the job, it creates 239 input and output files called "slabNEB-r-239.inp/out". The job quickly runs out of memory. What is the problem? Thank you, Hasan. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- !&EXT_RESTART !RESTART_FILE_NAME slanNEB-1.restart !&END &GLOBAL PRINT_LEVEL Medium PROJECT slabNEB RUN_TYPE BAND # Nudged elastic band calculation &END GLOBAL &MOTION &BAND NUMBER_OF_REPLICA 5 # Number of "replica" geometries along the path K_SPRING 0.05 &OPTIMIZE_BAND OPT_TYPE DIIS &DIIS MAX_STEPS 1000 &END &END &CONVERGENCE_CONTROL MAX_FORCE 0.0045 RMS_FORCE 0.003 MAX_DR 0.002 RMS_DR 0.001 &END BAND_TYPE CI-NEB # Climbing-image NEB &CI_NEB NSTEPS_IT 3 # First take 5 normal steps, then start CI &END &REPLICA COORD_FILE_NAME slab1.xyz &END &REPLICA COORD_FILE_NAME slab2.xyz &END &PROGRAM_RUN_INFO INITIAL_CONFIGURATION_INFO &END &CONVERGENCE_INFO &EACH BAND 1 REPLICA_EVAL 1 &END &END &END BAND &CONSTRAINT &FIXED_ATOMS COMPONENTS_TO_FIX XYZ LIST 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 &END &END CONSTRAINT &END MOTION &FORCE_EVAL METHOD Quickstep &DFT UKS .TRUE. !Requests a spin-polarized calculation using alpha and beta orbitals, i.e. no spin restriction is applied CHARGE 0 !Total charge BASIS_SET_FILE_NAME BASIS_MOLOPT POTENTIAL_FILE_NAME GTH_POTENTIALS WFN_RESTART_FILE_NAME slabNEB-RESTART.kp &MGRID NGRIDS 5 RELATIVE_CUTOFF 50 &END MGRID &QS EPS_DEFAULT 1.0E-12 METHOD GPW EXTRAPOLATION USE_GUESS &END QS &SCF EPS_SCF 1.0E-7 SCF_GUESS RESTART !Use the RESTART file as an initial guess (and ATOMIC if not present). MAX_SCF 30 ADDED_MOS 200 CHOLESKY OFF &OUTER_SCF F EPS_SCF 1.0E-5 MAX_SCF 30 &END OUTER_SCF &SMEAR T METHOD FERMI_DIRAC ELECTRONIC_TEMPERATURE 3.0000000000000000E+02 &END SMEAR &MIXING T METHOD BROYDEN_MIXING ALPHA 4.0000000000000002E-01 BETA 1.5000000000000000E+00 NMIXING 5 NBUFFER 8 &END MIXING &END SCF &XC FUNCTIONAL_ROUTINE NEW DENSITY_CUTOFF 1.0e-12 GRADIENT_CUTOFF 1.0e-12 TAU_CUTOFF 1.0e-12 &XC_FUNCTIONAL &END XC_FUNCTIONAL &XC_GRID USE_FINER_GRID .TRUE. &END XC_GRID &END XC &POISSON POISSON_SOLVER PERIODIC PERIODIC XYZ &END POISSON &KPOINTS SCHEME MONKHORST-PACK 3 3 1 FULL_GRID .TRUE. &END KPOINTS &END DFT &SUBSYS &CELL ABC 10.22390 10.22390 30.17390 ALPHA_BETA_GAMMA 90.000000 90.000000 120.000000 PERIODIC XYZ &END CELL &KIND Cu BASIS_SET DZVP-MOLOPT-SR-GTH-q11 POTENTIAL GTH-PBE-q11 &END KIND &KIND O BASIS_SET DZVP-MOLOPT-SR-GTH-q6 POTENTIAL GTH-PBE-q6 &END KIND &KIND C BASIS_SET DZVP-MOLOPT-SR-GTH-q4 POTENTIAL GTH-PBE-q4 &END KIND &TOPOLOGY COORD_FILE_FORMAT XYZ COORD_FILE_NAME slab1.xyz CONN_FILE_FORMAT off &END TOPOLOGY &END SUBSYS &END FORCE_EVAL -------------- next part -------------- A non-text attachment was scrubbed... Name: slab1.xyz Type: chemical/x-xyz Size: 5687 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slab2.xyz Type: chemical/x-xyz Size: 5685 bytes Desc: not available URL: From dev.... at gmail.com Tue Jun 23 14:47:26 2020 From: dev.... at gmail.com (Dev Rana) Date: Tue, 23 Jun 2020 07:47:26 -0700 (PDT) Subject: [CP2K-user] Vibrational Analysis Thermochemistry Message-ID: Hello, I'm trying to obtain thermochemistry information (Electronic Energy, Enthalpy correction Hcorr, Gibbs correction Gcorr, zero point energy correction ZPEcorr, etc.) in order to calculate Gibbs Free Energy dG and Equilibrium Constant K of my reaction as well as some other thermochemical properties. When i run thermochemistry of a single atom, I don't receive any information. Specifically, I'm running it for C and Al individually. Could someone help? I've also rerun the same input at 0K, 1000K, and 298K. I use the same file just switching the element from C to Al. All of the simulations end up with no data. I've attached my input and output. Best Regards, Dev -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: C Type: text/x-csrc Size: 1967 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: C.out Type: application/octet-stream Size: 19639 bytes Desc: not available URL: From eluni... at gmail.com Wed Jun 24 07:11:09 2020 From: eluni... at gmail.com (Lucas Lodeiro) Date: Wed, 24 Jun 2020 03:11:09 -0400 Subject: [CP2K-user] [CP2K:13546] Single Molecule Molecular Dynamics In-Reply-To: <404EE40E-BC28-4A32-8B53-6513F7D47F8C@gmail.com> References: <404EE40E-BC28-4A32-8B53-6513F7D47F8C@gmail.com> Message-ID: Thanks Thomas for the advice about the MD. Yes the geometry optimization was with the same settings, using the default convergence criteria. I attach the input and output. There is a little energy difference (1 E-5) between the geo_opt run (optimized configuration) and the zero step in the MD, due to the centering positions keyword, I understand that is due to non-continuous fourier grid. But the potential energy minima along the MD is 1 E-4 lower than the geo_opt geometry minima... and I cannot understand why. Regards El lun., 22 jun. 2020 a las 5:54, Thomas K?hne () escribi?: > Dear Lucas, > > have you conducted the geometry optimization with exactly the same > settings, > i.e. basis set, PW cutoff, EPS_SCF, etc.? Since your system has so few > DOFs, > fluctuations will be large and conservation by cancellation inherently > poor. > Hence, with such a tiny system I would rather stick with NVT instead of > NVE + > viral theorem and not use ANGVEL_ZERO ? > > Greetings, > Thomas > > Am 21.06.2020 um 07:14 schrieb Lucas Lodeiro : > > Hi all, > I want to perform single molecule molecular dynamics. > First I do a convergence test for cutoff, cell size and poisson solver. I > read in old mails, that MT is better than WAVELET for MD, due to the first > is translational invariant. > After that I start a MD from the optimized molecular geometry at the same > level of theory. I want to obtain statistical information for a given > temperature (300K for example), I think an NVT is not well behaved for a > single molecule, then I ran NVE MD. As the geometry is at the minimum, I > start with 2*T (where T is the target temperature) thinking in virial > theorem (at equilibrium equal potential and kinetic energy). > But the system is not converging (the average temperature) at the desired > temperature. It shows a weird temperature oscillation (different as > expected due to bond oscillation), it present in some moment higher > temperature than the initial and a potential energy lower than the > initial... Also, the molecular rotation exhibits variations along the MD > and translation in the box. For that I start a new MD with the same INPUT > and geometry, adding ANGVEL_ZERO. The MD starts without rotation but in 300 > fs it starts to rotate. > I attach the files for both MD. > > I read about the geometrical constraints, it would be useful for diatomic > molecules, but for H2O or complexer molecules is not a solution. > > Has somebody faced these problems? some advice? > > regards > > > > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/CAOFT4P%2BMnqg3JM5dGm-%3DQzSD912dx1A1qo8shYaMgdNLgFzTqA%40mail.gmail.com > > . > > > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/404EE40E-BC28-4A32-8B53-6513F7D47F8C%40gmail.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mshakiba.... at gmail.com Wed Jun 24 12:21:46 2020 From: mshakiba.... at gmail.com (Mohammad Shakiba) Date: Wed, 24 Jun 2020 05:21:46 -0700 (PDT) Subject: [CP2K-user] TDDFPT excitation analysis problem Message-ID: Hello everyone, I ran TDDFPT calculations for (CdSe)33 QDs. The problem is that the excited state energy for two considered excited states are the same in excitation analysis and also their excitation coefficient amplitudes are the same. Is it correct or an error? Thanks in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: From k.doblh... at lic.leidenuniv.nl Wed Jun 24 13:23:48 2020 From: k.doblh... at lic.leidenuniv.nl (Katharina Doblhoff-Dier) Date: Wed, 24 Jun 2020 06:23:48 -0700 (PDT) Subject: [CP2K-user] IC-QMMM with single charge in front of a metal plane: open boundary corrections Message-ID: <5774878e-630c-4699-a67e-5040897c1b2do@googlegroups.com> Dear CP2K community, I am confused about the IC-QMMM method as implemented in CP2K. I am not 100% sure whether my question is related to my misunderstanding of the method (as implemented) or on how to use it. Originally, my confusion came from my not-understanding of the parameter V_0 (i.e., EXT_POTENTIAL in the CP2K implementation): In periodic boundary conditions, this parameter does not seem to make much sense to me: Depending on the average potential in the quantum region, defining V_0 will make the charge Q on the metal adapt in such a way that the average potential in the cell is zero (I know that the latter is logic, but in view of this, the physical meaning of V_0 becmes unclear to me): [image: tmp1.png] Alternatively, if a charge is put into the QM part (e.g. an H2+) and V0 is adjusted such that the total charge Q on the metal is exaclty -1, a spurious field will result over the cell (due to Ewald summation) and again, V_0 does not have an obvious physical meaning. [image: tmp2.png] Considering that the periodic boundary conditions lead to lots of spurious stuff, I then tried to go to MT boundary corrections or the IMPLICIT poisson solver as implemented in CP2K. This gave me the following results (note that I shifted the green and the blue curve by 0.4V for better comparison) red: IMPLICIT poissn solver with Neumann BC at z=0 and z=60 and homogeneous Dirichlet BC at z=30 green: MT (Martyna-Tuckerman) poisson solver (shifted by 0.4V) blue: normal Ewald summation (shifted by 0.4V) [image: tmp3.png] The corresponding V_0 (optimized such that Q=-1) were 1.11V for IMPLICIT boundary conditions, 1.24V for MT boundary conditions and -0.37V for periodic boundary conditions. While for periodic boundary conditions (blue line) this can be seen to correspond to the potential in the metal part, this is not the case for MT boundary conditions (green), where the potential in the metal varies from about -0.4 to -0.5 (remember that I shifted the curves by 0.4 volt) and for IMPLICIT boundary conditions. Overall, to me, it looks as if the IC-QMMM method was ignoring the boundary conditions and optimizing the charges for the periodic boundary conditions and then keeping them fixed no matter what I set as POISSON_SOLVER. In the MT boundary condition case (geen) we can thus see the influence of the charges shieding the (spurious) field in periodic boundary conditions (hence the slope in the metal part, which has the same slope as the average field in the periodic solver). Finally, I decided that, in principle, it should be possible to find an energy minimum when Q_image=-Q_QM (as also shown in the original paper by Siepmann and Sprik). With none of the boundary conditions could I find this minimum correctly. However, here comes my non-understanding of Eq. 4 in the paper by Golze, Iannuzzi, ..., and Hutter (https://pubs-acs-org.ezproxy.leidenuniv.nl:2443/doi/10.1021/ct400698y) into play: Here, the energy is written as: [image: tmp4.png] I would have thought this to be a grand canonical energy (grand canonical only in the charges on the metal) expression, where the last term accounts for the -N_i*mu_i term. Again, this does not seem physical to me if I think of a capacitor (or a charge+image charge in a box that is periodic in x and y, as I would then expect a correction for the charges in the QM region too (unless the vacuum potential on the QM side is zero and open boundary conditions are used, but likely this is wrong and this may be where my entire confusion starts. So summarizing, this boils down to a few questions: 1.) can the IC-QMMM method be combined with poisson solvers other than periodic? If so, how? I simply set the poisson solver in the MM and the DFT part. 2.) What do I need to do in order to find an energy minimum for Q_image=-Q_QM? 3.) What is the meaning of V_0 and why is it substracted in the energy expression. Any physical insight is appreciated! Thank you and best regards, Katharina -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: tmp1.png Type: image/png Size: 61511 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: tmp2.png Type: image/png Size: 29616 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: tmp3.png Type: image/png Size: 12821 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: tmp4.png Type: image/png Size: 2942 bytes Desc: not available URL: From doroth... at googlemail.com Wed Jun 24 14:04:39 2020 From: doroth... at googlemail.com (Dorothea Golze) Date: Wed, 24 Jun 2020 17:04:39 +0300 Subject: [CP2K-user] [CP2K:13546] IC-QMMM with single charge in front of a metal plane: open boundary corrections In-Reply-To: <5774878e-630c-4699-a67e-5040897c1b2do@googlegroups.com> References: <5774878e-630c-4699-a67e-5040897c1b2do@googlegroups.com> Message-ID: Hi Katharina, I am not sure if I understand your question correctly and what your computational setup is. The basic electrostatic consideration is that the potential should be constant within a conductor. If no external potential is applied, the electrostatic potential is zero within a metal, i.e., V_0=0. That is the default. It can be also set to another value in principle, e.g., maybe to approximate the application of a potential to an electrode. But it seems that's not what you want to do here. Note that the IC-QM/MM does not introduce actual charges, only image charges. You can run with the normal periodic solver when you have a (neutral) molecule on top of the metal (MM). If you have a charged system in the QM part, then you need a solver like MT, like in a standard QM calculation. Best regards, Dorothea Am Mi., 24. Juni 2020 um 16:23 Uhr schrieb Katharina Doblhoff-Dier < k.doblh... at lic.leidenuniv.nl>: > Dear CP2K community, > > I am confused about the IC-QMMM method as implemented in CP2K. I am not > 100% sure whether my question is related to my misunderstanding of the > method (as implemented) or on how to use it. > Originally, my confusion came from my not-understanding of the parameter > V_0 (i.e., EXT_POTENTIAL in the CP2K implementation): In periodic boundary > conditions, this parameter does not seem to make much sense to me: > Depending on the average potential in the quantum region, defining V_0 will > make the charge Q on the metal adapt in such a way that the average > potential in the cell is zero (I know that the latter is logic, but in view > of this, the physical meaning of V_0 becmes unclear to me): > > [image: tmp1.png] > > Alternatively, if a charge is put into the QM part (e.g. an H2+) and V0 is > adjusted such that the total charge Q on the metal is exaclty -1, a > spurious field will result over the cell (due to Ewald summation) and > again, V_0 does not have an obvious physical meaning. > > [image: tmp2.png] > > Considering that the periodic boundary conditions lead to lots of spurious > stuff, I then tried to go to MT boundary corrections or the IMPLICIT > poisson solver as implemented in CP2K. This gave me the following results > (note that I shifted the green and the blue curve by 0.4V for better > comparison) > > red: IMPLICIT poissn solver with Neumann BC at z=0 and z=60 and > homogeneous Dirichlet BC at z=30 > green: MT (Martyna-Tuckerman) poisson solver (shifted by 0.4V) > blue: normal Ewald summation (shifted by 0.4V) > > [image: tmp3.png] > > > The corresponding V_0 (optimized such that Q=-1) were 1.11V for IMPLICIT > boundary conditions, 1.24V for MT boundary conditions and -0.37V for > periodic boundary conditions. While for periodic boundary conditions (blue > line) this can be seen to correspond to the potential in the metal part, > this is not the case for MT boundary conditions (green), where the > potential in the metal varies from about -0.4 to -0.5 (remember that I > shifted the curves by 0.4 volt) and for IMPLICIT boundary conditions. > Overall, to me, it looks as if the IC-QMMM method was ignoring the boundary > conditions and optimizing the charges for the periodic boundary conditions > and then keeping them fixed no matter what I set as POISSON_SOLVER. In the > MT boundary condition case (geen) we can thus see the influence of the > charges shieding the (spurious) field in periodic boundary conditions > (hence the slope in the metal part, which has the same slope as the average > field in the periodic solver). > > > Finally, I decided that, in principle, it should be possible to find an > energy minimum when Q_image=-Q_QM (as also shown in the original paper by > Siepmann and Sprik). With none of the boundary conditions could I find this > minimum correctly. However, here comes my non-understanding of Eq. 4 in the > paper by Golze, Iannuzzi, ..., and Hutter ( > https://pubs-acs-org.ezproxy.leidenuniv.nl:2443/doi/10.1021/ct400698y) > into play: Here, the energy is written as: > > > [image: tmp4.png] > > I would have thought this to be a grand canonical energy (grand canonical > only in the charges on the metal) expression, where the last term accounts > for the -N_i*mu_i term. Again, this does not seem physical to me if I think > of a capacitor (or a charge+image charge in a box that is periodic in x and > y, as I would then expect a correction for the charges in the QM region too > (unless the vacuum potential on the QM side is zero and open boundary > conditions are used, but likely this is wrong and this may be where my > entire confusion starts. > > > So summarizing, this boils down to a few questions: > > 1.) can the IC-QMMM method be combined with poisson solvers other than > periodic? If so, how? I simply set the poisson solver in the MM and the DFT > part. > > 2.) What do I need to do in order to find an energy minimum for > Q_image=-Q_QM? > > 3.) What is the meaning of V_0 and why is it substracted in the energy > expression. > > > Any physical insight is appreciated! > Thank you and best regards, > Katharina > > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/5774878e-630c-4699-a67e-5040897c1b2do%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: tmp1.png Type: image/png Size: 61511 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: tmp2.png Type: image/png Size: 29616 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: tmp3.png Type: image/png Size: 12821 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: tmp4.png Type: image/png Size: 2942 bytes Desc: not available URL: From k.doblh... at lic.leidenuniv.nl Wed Jun 24 14:36:18 2020 From: k.doblh... at lic.leidenuniv.nl (Katharina Doblhoff-Dier) Date: Wed, 24 Jun 2020 07:36:18 -0700 (PDT) Subject: [CP2K-user] [CP2K:13546] IC-QMMM with single charge in front of a metal plane: open boundary corrections In-Reply-To: References: <5774878e-630c-4699-a67e-5040897c1b2do@googlegroups.com> Message-ID: Dear Dorothea, Thank you for your answer. I am not sure if I understand your question correctly > On the longer run, we are interested in describing an electrolyte above a metal surface and using a charge imbalance to create a potential drop at the interface very much as one would do in a pure DFT calculation, but then withouth the need to describe the metal quantum mechanically. I know that this is not the original idea behind the image charge method as implemented in cp2k, but I thought it may offer a work around. So to understand how things work, I simply considered an H2+ molecule above a surface. This is similar to the model system used by Siepmann and Sprik in their 1995 publication, just that they used an MM point charge above a metal. In principle, it should be possible to determine V_0 from the condition that the energy should be minimized, and the resulting counter charge should exactly cancel the charge in front of the metal. and what your computational setup is. > I paste here an example of the input that I used with MT boundary conditions. The resulting plot for the Hartree-potential (obtained using &V_HARTREE_CUBE and then averaging over x and y to get a plot over z) is shown in the third image in my original post (green line). As you can see, I simply adapted the input file from the GUA example on the web, by replacing the GUA in the xyz file by H2, setting the DFT charge to 1 and changing the poisson solver in the DFT and MM part. The potential EXT_POTENTIAL was determined by running 2 calculations with changing EXT_POTENTIAL_1 and EXT_POTENTIAL_2, and then determining EXT_POTENTIAL_3 by requiring that the resulting charge should be -1 and assuming a linear relationship (which for this system is perfectly followed, giving me a total charge on the metal of -1) -----------------Begin sample input file using the MT poisson solver------------------ &FORCE_EVAL METHOD QMMM &DFT CHARGE 1 LSD BASIS_SET_FILE_NAME BASIS_MOLOPT POTENTIAL_FILE_NAME GTH_POTENTIALS &POISSON &EWALD EWALD_TYPE ewald ALPHA .44 GMAX 21 &END EWALD POISSON_SOLVER MT PERIODIC XY &END POISSON &MGRID COMMENSURATE CUTOFF 300 NGRIDS 5 &END MGRID &QS METHOD GPW EXTRAPOLATION ASPC EXTRAPOLATION_ORDER 3 &END QS &SCF MAX_SCF 300 SCF_GUESS ATOMIC # SCF_GUESS RESTART EPS_SCF 1.0E-6 &OT PRECONDITIONER FULL_SINGLE_INVERSE MINIMIZER DIIS &END &END SCF &XC &XC_FUNCTIONAL PBE &END XC_FUNCTIONAL &VDW_POTENTIAL DISPERSION_FUNCTIONAL PAIR_POTENTIAL &PAIR_POTENTIAL TYPE DFTD3 CALCULATE_C9_TERM .TRUE. REFERENCE_C9_TERM PARAMETER_FILE_NAME dftd3.dat REFERENCE_FUNCTIONAL PBE R_CUTOFF [angstrom] 16.0 &END PAIR_POTENTIAL &END VDW_POTENTIAL &END XC &PRINT &V_HARTREE_CUBE &END &END &END DFT &MM &FORCEFIELD &CHARGE ATOM Au CHARGE 0 &END CHARGE &CHARGE ATOM H CHARGE 0 &END CHARGE &SPLINE EPS_SPLINE 1.E-5 #EMAX_SPLINE 2.0 &END &NONBONDED &EAM atoms Au Au PARM_FILE_NAME Au.pot &END EAM &LENNARD-JONES atoms Au H EPSILON 0.0 SIGMA 3.166 RCUT 15 &END LENNARD-JONES &LENNARD-JONES atoms H H EPSILON 0.0 SIGMA 3.166 RCUT 15 &END LENNARD-JONES &END &END FORCEFIELD &POISSON &EWALD EWALD_TYPE ewald ALPHA .44 GMAX 21 &END EWALD POISSON_SOLVER MT PERIODIC XY &END POISSON &END MM &QMMM CENTER NEVER &CELL ABC [angstrom] 34.6055 29.9693 60.0 PERIODIC XY &END CELL &QM_KIND H MM_INDEX 577..578 &END QM_KIND &IMAGE_CHARGE EXT_POTENTIAL 1.24534 MM_ATOM_LIST 1..576 WIDTH 3.5 &END IMAGE_CHARGE &PRINT &IMAGE_CHARGE_INFO &END &END &END QMMM &SUBSYS &CELL ABC [angstrom] 34.6055 29.9693 60.0 PERIODIC XY &END CELL &TOPOLOGY COORD_FILE_NAME Au_gua_image_dampFunc-opt.xyz COORDINATE xyz &END &KIND H BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q1 &END KIND &END SUBSYS &END FORCE_EVAL &GLOBAL PROJECT Au_gua_image_dampFunc RUN_TYPE energy &END GLOBAL -----------------End sample input file using the MT poisson solver------------------ >If you have a charged system in the QM part, then you need a solver like MT, like in a standard QM calculation. Yes, I would have thought, that this is what I am doing, but the resulting plot for the hartree potential looks strange (shielding charges in the metal, leading to a potential gradient in the metal instead of a constant) and I cannot seem to find an energy minimum, when the potential is chosen such, that the image charge is exatly shielded, which was one of the test systems in the Siepmann Sprik paper (https://aip.scitation.org/doi/abstract/10.1063/1.469429). I guess the latter is my main issue, as we will depend heavily on the energies. (Hence I need to understand what they contain) Thank you for your help, Katharina -------------- next part -------------- An HTML attachment was scrubbed... URL: From hasanal... at gmail.com Thu Jun 25 21:01:24 2020 From: hasanal... at gmail.com (Hasan Al-Mahayni) Date: Thu, 25 Jun 2020 14:01:24 -0700 (PDT) Subject: [CP2K-user] GEO_OPT on single atom catalysts graphene structure Message-ID: <96f6b3f5-2b6d-41ed-b0bb-8861a666d77eo@googlegroups.com> Hi all, I am trying to run geo_opt (with ASE python code) on a graphene structure with Copper in the middle and two nitrogens. I use maximum force of 0.01 as convergence criteria to start off. I included all the files below. My SCF does not converge and my energies seem to be going crazy... What is wrong with my input file? These are the results: Step Time Energy fmax *Force-consistent energies used in optimization. LBFGS: 0 16:50:20 9139.239727* 1687.8341 LBFGS: 1 16:52:29 13502.225247* 1231.9027 LBFGS: 2 16:54:31 11300.743617* 987.9389 LBFGS: 3 16:56:52 20088.494364* 1986.4853 Thanks, Hasan. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: SAC_CU_2N.xyz Type: chemical/x-xyz Size: 1113 bytes Desc: not available URL: -------------- next part -------------- !!! Generated by ASE !!! &MOTION &GEO_OPT MAX_ITER 400 OPTIMIZER LBFGS &END GEO_OPT &PRINT &TRAJECTORY FORMAT XYZ &END TRAJECTORY &END PRINT &END MOTION &FORCE_EVAL METHOD Quickstep STRESS_TENSOR ANALYTICAL &PRINT &STRESS_TENSOR ON &END STRESS_TENSOR &END PRINT &DFT UKS .TRUE. WFN_RESTART_FILE_NAME cp2k-RESTART.wfn BASIS_SET_FILE_NAME BASIS_MOLOPT POTENTIAL_FILE_NAME GTH_POTENTIALS &MGRID NGRIDS 5 RELATIVE_CUTOFF 50 CUTOFF [eV] 4.081709419799999978e+03 &END MGRID &QS EPS_DEFAULT 1.0E-12 METHOD GPW EXTRAPOLATION USE_GUESS &END QS &SCF EPS_SCF 1.0E-7 SCF_GUESS RESTART CHOLESKY OFF MAX_SCF 50 &OUTER_SCF F EPS_SCF 1.0E-7 MAX_SCF 50 &END OUTER_SCF &END SCF &XC FUNCTIONAL_ROUTINE NEW DENSITY_CUTOFF 1.0e-12 GRADIENT_CUTOFF 1.0e-12 TAU_CUTOFF 1.0e-12 &XC_FUNCTIONAL &PBE &END PBE &END XC_FUNCTIONAL &END XC &LS_SCF MAX_SCF 50 &END LS_SCF &END DFT &SUBSYS &COORD Cu 9.342449999999999477e+00 1.006705000000000005e+01 1.006830000000000069e+01 C 6.222349999999999604e+00 5.943249999999999922e+00 1.093880000000000052e+01 C 5.164149999999999352e+00 8.254450000000000287e+00 1.144790000000000063e+01 C 7.281850000000000378e+00 5.216950000000000642e+00 1.001850000000000129e+01 C 8.650050000000000239e+00 5.934549999999999770e+00 1.019710000000000072e+01 C 6.107049999999999201e+00 7.434250000000000469e+00 1.051360000000000028e+01 C 7.474649999999999572e+00 8.067650000000000432e+00 1.062250000000000050e+01 C 5.113649999999999807e+00 9.741550000000000153e+00 1.095180000000000042e+01 C 6.554949999999999832e+00 1.035585000000000022e+01 1.084020000000000117e+01 C 5.244049999999999656e+00 1.203545000000000087e+01 9.269700000000000273e+00 C 9.806350000000000122e+00 5.305950000000000166e+00 9.391500000000000625e+00 C 1.111154999999999937e+01 6.111850000000000449e+00 9.726000000000000867e+00 C 8.495950000000000557e+00 7.382050000000000445e+00 9.773200000000000998e+00 C 9.776149999999999451e+00 8.132350000000000634e+00 1.007360000000000078e+01 C 7.433650000000000091e+00 9.473950000000000315e+00 1.007770000000000010e+01 C 6.423549999999999649e+00 1.181044999999999945e+01 1.023590000000000089e+01 C 7.713949999999999640e+00 1.233305000000000007e+01 9.447499999999999787e+00 C 5.059949999999999726e+00 1.357264999999999944e+01 9.096899999999999764e+00 C 6.337449999999999584e+00 1.424385000000000012e+01 8.552100000000001145e+00 C 1.232075000000000031e+01 5.475550000000000139e+00 9.036200000000000898e+00 C 1.361814999999999998e+01 6.255650000000000155e+00 9.372500000000000497e+00 C 1.097384999999999877e+01 7.634249999999999758e+00 9.329299999999999926e+00 C 1.230945000000000000e+01 8.405150000000000787e+00 9.721000000000000085e+00 N 1.116874999999999929e+01 1.063374999999999915e+01 1.004739999999999966e+01 N 8.920249999999999346e+00 1.195594999999999963e+01 1.007990000000000030e+01 C 1.011284999999999989e+01 1.262904999999999944e+01 9.641099999999999781e+00 C 7.552349999999999675e+00 1.388475000000000037e+01 9.434400000000000119e+00 C 8.842249999999999943e+00 1.459735000000000049e+01 8.940100000000001046e+00 C 1.336854999999999905e+01 7.454349999999999810e+00 1.033440000000000047e+01 C 1.472165000000000035e+01 8.197549999999999670e+00 1.045570000000000022e+01 C 1.215315000000000012e+01 9.731550000000000367e+00 1.062220000000000120e+01 C 1.356214999999999904e+01 1.041495000000000104e+01 1.052430000000000021e+01 C 1.117954999999999899e+01 1.200324999999999953e+01 1.048869999999999969e+01 C 1.251875000000000071e+01 1.262405000000000044e+01 1.020730000000000004e+01 C 9.992049999999998988e+00 1.411945000000000050e+01 9.874100000000000321e+00 C 1.136575000000000024e+01 1.478304999999999936e+01 9.573199999999999932e+00 C 1.460984999999999978e+01 9.524750000000000938e+00 1.122789999999999999e+01 C 1.355614999999999881e+01 1.187475000000000058e+01 1.105809999999999960e+01 C 1.494004999999999939e+01 1.251624999999999943e+01 1.080349999999999966e+01 C 1.245054999999999978e+01 1.412995000000000090e+01 1.052350000000000030e+01 C 1.384154999999999980e+01 1.474385000000000012e+01 1.026500000000000057e+01 C 1.489215000000000089e+01 1.402684999999999960e+01 1.116350000000000087e+01 &END COORD &CELL PERIODIC NONE A 2.000000000000000000e+01 0.000000000000000000e+00 0.000000000000000000e+00 B 0.000000000000000000e+00 2.000000000000000000e+01 0.000000000000000000e+00 C 0.000000000000000000e+00 0.000000000000000000e+00 2.000000000000000000e+01 &END CELL &KIND C BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE &END KIND &KIND N BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE &END KIND &KIND Cu BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE &END KIND &END SUBSYS &END FORCE_EVAL &GLOBAL PROJECT cp2k PRINT_LEVEL LOW &END GLOBAL -------------- next part -------------- Step Time Energy fmax LBFGS: 0 16:50:20 9139.239727* 1687.8341 LBFGS: 1 16:52:29 13502.225247* 1231.9027 LBFGS: 2 16:54:31 11300.743617* 987.9389 LBFGS: 3 16:56:52 20088.494364* 1986.4853 From k.doblh... at lic.leidenuniv.nl Fri Jun 26 13:32:48 2020 From: k.doblh... at lic.leidenuniv.nl (Katharina Doblhoff-Dier) Date: Fri, 26 Jun 2020 06:32:48 -0700 (PDT) Subject: [CP2K-user] [CP2K:13546] IC-QMMM with single charge in front of a metal plane: open boundary corrections In-Reply-To: References: <5774878e-630c-4699-a67e-5040897c1b2do@googlegroups.com> Message-ID: <168440d5-5b57-4075-900e-876a99f8e437o@googlegroups.com> Dear Dorothea, To break a complex problem down: Should I consider it a bug, that I get non-constant potentials in the plot of the hartree energies, when using MT or implicit BCs and that potential in the metal does not match EXT_POTENTIAL? (see plot below - also posted in the original question) Or is there a good reason for this behavior? red: IMPLICIT poissn solver with Neumann BC at z=0 and z=60 and >> homogeneous Dirichlet BC at z=30 >> green: MT (Martyna-Tuckerman) poisson solver (shifted by 0.4V) >> blue: normal Ewald summation (shifted by 0.4V) >> >> [image: tmp3.png] >> >> >> >> Thank you for your help! Best regards, Katharina -------------- next part -------------- An HTML attachment was scrubbed... URL: From doroth... at googlemail.com Fri Jun 26 14:00:46 2020 From: doroth... at googlemail.com (Dorothea Golze) Date: Fri, 26 Jun 2020 17:00:46 +0300 Subject: [CP2K-user] [CP2K:13550] IC-QMMM with single charge in front of a metal plane: open boundary corrections In-Reply-To: <168440d5-5b57-4075-900e-876a99f8e437o@googlegroups.com> References: <5774878e-630c-4699-a67e-5040897c1b2do@googlegroups.com> <168440d5-5b57-4075-900e-876a99f8e437o@googlegroups.com> Message-ID: Dear Katharina, in short, it is very likely no bug; I think the basic problem is that you try to run a periodic DFT calculation for a charged system. The constant potential condition is a hard constraint for the average. I tested with the standard periodic solver (for periodic systems) and the MT solver (for a cluster-type of approach). I don't have it in the paper, but in my thesis, I have an example, where I placed an ion above a slab (Figure 3.7 page 31, https://www.zora.uzh.ch/id/eprint/116638/) For the MT solver, I have the suspicion you are not applying this solver correctly, which can lead to technical artifacts. You need lots of vacuum around your system since you also specified a periodic cell, this seems not to be the case. I suggest to test the MT solver for a single molecule (DFT only) first to get a feeling how much vacuum you need, i.e., to converge out the cell size and how this solver behaves. Best regards, Dorothea Am Fr., 26. Juni 2020 um 16:32 Uhr schrieb Katharina Doblhoff-Dier < k.doblh... at lic.leidenuniv.nl>: > Dear Dorothea, > To break a complex problem down: Should I consider it a bug, that I get > non-constant potentials in the plot of the hartree energies, when using MT > or implicit BCs and that potential in the metal does not match > EXT_POTENTIAL? (see plot below - also posted in the original question) Or > is there a good reason for this behavior? > > red: IMPLICIT poissn solver with Neumann BC at z=0 and z=60 and >>> homogeneous Dirichlet BC at z=30 >>> green: MT (Martyna-Tuckerman) poisson solver (shifted by 0.4V) >>> blue: normal Ewald summation (shifted by 0.4V) >>> >>> [image: tmp3.png] >>> >>> >>> >>> Thank you for your help! > Best regards, > Katharina > > -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/168440d5-5b57-4075-900e-876a99f8e437o%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From doroth... at googlemail.com Fri Jun 26 17:55:59 2020 From: doroth... at googlemail.com (Dorothea Golze) Date: Fri, 26 Jun 2020 20:55:59 +0300 Subject: [CP2K-user] [CP2K:13550] IC-QMMM with single charge in front of a metal plane: open boundary corrections In-Reply-To: References: <5774878e-630c-4699-a67e-5040897c1b2do@googlegroups.com> <168440d5-5b57-4075-900e-876a99f8e437o@googlegroups.com> Message-ID: Dear Katharina, I just ran a quick test for the EXT_POTENTIAL keyword. System: small organic molecule on top of gold (charge-neutral periodic system using standard periodic solver). The keyword still seems to work as intended: when preparing a plane-averaged plot in z-direction, the potential is not zero in the region of the metal, but the value defined by EXT_POTENTIAL. I can send you my example input files; feel free to contact me directly ( doroth... at aalto.fi). Best regards, Dorothea Am Fr., 26. Juni 2020 um 17:00 Uhr schrieb Dorothea Golze < doroth... at googlemail.com>: > Dear Katharina, > > in short, it is very likely no bug; I think the basic problem is that you > try to run a periodic DFT calculation for a charged system. > The constant potential condition is a hard constraint for the average. I > tested with the standard periodic solver (for periodic systems) and the MT > solver (for a cluster-type of approach). > I don't have it in the paper, but in my thesis, I have an example, where I > placed an ion above a slab (Figure 3.7 page 31, > https://www.zora.uzh.ch/id/eprint/116638/) > For the MT solver, I have the suspicion you are not applying this solver > correctly, which can lead to technical artifacts. You need lots of vacuum > around your system since you also specified a periodic cell, this seems not > to be the case. I suggest to test the MT solver for a single molecule (DFT > only) first to get a feeling how much vacuum you need, i.e., to converge > out the cell size and how this solver behaves. > > Best regards, > Dorothea > > > Am Fr., 26. Juni 2020 um 16:32 Uhr schrieb Katharina Doblhoff-Dier < > k.doblh... at lic.leidenuniv.nl>: > >> Dear Dorothea, >> To break a complex problem down: Should I consider it a bug, that I get >> non-constant potentials in the plot of the hartree energies, when using MT >> or implicit BCs and that potential in the metal does not match >> EXT_POTENTIAL? (see plot below - also posted in the original question) Or >> is there a good reason for this behavior? >> >> red: IMPLICIT poissn solver with Neumann BC at z=0 and z=60 and >>>> homogeneous Dirichlet BC at z=30 >>>> green: MT (Martyna-Tuckerman) poisson solver (shifted by 0.4V) >>>> blue: normal Ewald summation (shifted by 0.4V) >>>> >>>> [image: tmp3.png] >>>> >>>> >>>> >>>> Thank you for your help! >> Best regards, >> Katharina >> >> -- >> 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 cp... at googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/cp2k/168440d5-5b57-4075-900e-876a99f8e437o%40googlegroups.com >> >> . >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nedo... at gmail.com Fri Jun 26 20:29:45 2020 From: nedo... at gmail.com (Alex) Date: Fri, 26 Jun 2020 13:29:45 -0700 (PDT) Subject: [CP2K-user] ssmp and CPU loads Message-ID: Hi all, We've just built the latest version according to https://www.cp2k.org/howto:compile?s[]=ssmp The main use case is single-node multi-CPU (36 cores /72 threads available), so SSMP appeared like the correct option, i.e., none of the run commands involving mpirun. Our understanding is that the executable will use all available threads. We have confirmed it using a small system (~50 atoms) -- the system load shows one instance of cp2k with something like 2400% load, which is similar to for example how Gromacs runs using OpenMP. So, all is great. However, when running a large system containing ~1000 atoms, there is a single cp2k instance with 100% load and ~1TB RAM usage. SCF updates are sluggish, but it's a large system, so we can't tell if it's due to size or the fact that the CPU load is improperly low. Here is my question: is this correct behavior? Is there a way or need to force a particular number of threads to run on? Are we building the correct version for our needs? Another, more minor question: does multithreading help CP2K performance? The same machine is used for coupled cluster calculations and the users insist that HT hurts their performance, so it's currently off. Many thanks, Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: From sp05... at gmail.com Sat Jun 27 03:44:23 2020 From: sp05... at gmail.com (Sun Peng) Date: Fri, 26 Jun 2020 20:44:23 -0700 (PDT) Subject: [CP2K-user] Final step of compiling of CP2K-7.1.0 Message-ID: <1831bbaf-051c-4303-a21f-41cb480d089bo@googlegroups.com> Hi, everyone. I encountered a problem when I was going to compile the CP2K-7.1.0 after I compile all the software using the toolchains method and copy the local.popt to arch file.As shown in following picture, it said "No DBCSR submodule available, please run 'git submodule update --init --recursive'". However, when I run 'git submodule update --init --recursive', nothing changed. If anyone has encountered this problem, please help me. Thanks a lot! [image: error.png] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: error.png Type: image/png Size: 15401 bytes Desc: not available URL: From dev.... at gmail.com Thu Jun 25 22:58:19 2020 From: dev.... at gmail.com (Dev Rana) Date: Thu, 25 Jun 2020 15:58:19 -0700 (PDT) Subject: [CP2K-user] General Question About Thermochemistry Message-ID: Hello, I have a general question about thermochemistry data which is obtained post vibrational frequency analysis. Are there specific ways of calculating Gibbs free energy G(T) and equilibrium constant K(T) from the vibrational frequency data? The system I'm trying to investigate is aluminum carbide species formation at high temperatures. I.e. molten (liquid) aluminum and carbon. What might be the best way of doing this sort of calculations based on the data output from vibrational frequency analysis? Any software recommendations which can take electronic energy/vibrational/rot/trans energy and output the various H/S/G as a function of temperature? Best Regards, Dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From khomen... at gmail.com Sun Jun 28 08:45:09 2020 From: khomen... at gmail.com (Maxim Khomenko) Date: Sun, 28 Jun 2020 01:45:09 -0700 (PDT) Subject: [CP2K-user] Final step of compiling of CP2K-7.1.0 In-Reply-To: <1831bbaf-051c-4303-a21f-41cb480d089bo@googlegroups.com> References: <1831bbaf-051c-4303-a21f-41cb480d089bo@googlegroups.com> Message-ID: <32cbc434-f4d5-4786-a59c-7ab454138f7bo@googlegroups.com> Hello! I usually extract the dbcsr-2.0.0.tar.gz archive into directory $CP2K_DIR/ext/dbcsr/ and it works for me. ???????, 27 ???? 2020 ?., 6:44:23 UTC+3 ???????????? Sun Peng ???????: > > Hi, everyone. I encountered a problem when I was going to compile > the CP2K-7.1.0 after I compile all the software using the toolchains method > and copy the local.popt to arch file.As shown in following picture, it > said "No DBCSR submodule available, please run 'git submodule update --init > --recursive'". However, when I run 'git submodule update --init > --recursive', nothing changed. If anyone has encountered this problem, > please help me. > Thanks a lot! > > [image: error.png] > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From polla... at gmail.com Sun Jun 28 21:14:42 2020 From: polla... at gmail.com (Travis) Date: Sun, 28 Jun 2020 14:14:42 -0700 (PDT) Subject: [CP2K-user] [CP2K:12102] Re: Cell Optimization for Copper. In-Reply-To: References: <4b71e89c-34f6-437f-9471-dbef4bf50993@googlegroups.com> <98af7aa1-2d51-4485-9b89-c3def2b59272@googlegroups.com> Message-ID: Hi, Download the 'Computed' or 'Conventional Standard' CIF from Materials Project and use an editor like Avogadro to load it and then save as XYZ or convert the file by hand since it's only a few atoms. CP2K can read CIF format directly too though I sometimes have issues with it. -T From polla... at gmail.com Sun Jun 28 21:16:36 2020 From: polla... at gmail.com (Travis) Date: Sun, 28 Jun 2020 14:16:36 -0700 (PDT) Subject: [CP2K-user] [CP2K:12102] Re: Cell Optimization for Copper. In-Reply-To: References: <4b71e89c-34f6-437f-9471-dbef4bf50993@googlegroups.com> <98af7aa1-2d51-4485-9b89-c3def2b59272@googlegroups.com> Message-ID: Hi, In this specific instance I used Atomic Simulation Environment to convert the CIF to XYZ. -T From mejdit... at gmail.com Mon Jun 29 13:01:46 2020 From: mejdit... at gmail.com (mejdeddine mokhtar) Date: Mon, 29 Jun 2020 06:01:46 -0700 (PDT) Subject: [CP2K-user] Compute the charge transfer for Na - Cl using CDFT Message-ID: Dear cp2k users, I try to use the CDFT implementation within cp2k to calculate the charge transfer in Na - Cl by constraining a positive charge on Na and a negative charge on Cl. To this end, I struggled to make the script below and I hope you can help me to achieve that. Could you please all check if I did something wrong in defining the charge and the constraint atoms? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cdft_nacl.inp Type: chemical/x-gamess-input Size: 4713 bytes Desc: not available URL: From mattwa... at gmail.com Mon Jun 29 13:24:59 2020 From: mattwa... at gmail.com (Matt W) Date: Mon, 29 Jun 2020 06:24:59 -0700 (PDT) Subject: [CP2K-user] TDDFPT excitation analysis problem In-Reply-To: References: Message-ID: <3dc75578-aa70-4214-a472-984dad539996o@googlegroups.com> Impossible to say from the information you give us. If the system has symmetry then two states could well have the same energies. On Wednesday, June 24, 2020 at 1:21:46 PM UTC+1, Mohammad Shakiba wrote: > > Hello everyone, > > I ran TDDFPT calculations for (CdSe)33 QDs. The problem is that the > excited state energy for two considered excited states are the same in > excitation analysis and also their excitation coefficient amplitudes are > the same. Is it correct or an error? > > Thanks in advance. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Mon Jun 29 09:50:21 2020 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Mon, 29 Jun 2020 11:50:21 +0200 Subject: [CP2K-user] [CP2K:13553] ssmp and CPU loads In-Reply-To: References: Message-ID: Hi you get the most flexibility and best performance when using the PSMP version of the code. The optimal combination of MPI ranks and OpenMP threads will depend on your hardware and input. My first guess is usually N MPI ranks and 1 OpenMP thread. Your memory problem might be related to overhead (within CP2K) from the SSMP code. regards Juerg Hutter -------------------------------------------------------------- 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: "Alex" Sent by: cp... at googlegroups.com Date: 06/26/2020 10:29PM Subject: [CP2K:13553] ssmp and CPU loads Hi all, We've just built the latest version according to https://www.cp2k.org/howto:compile?s[]=ssmp The main use case is single-node multi-CPU (36 cores /72 threads available), so SSMP appeared like the correct option, i.e., none of the run commands involving mpirun. Our understanding is that the executable will use all available threads. We have confirmed it using a small system (~50 atoms) -- the system load shows one instance of cp2k with something like 2400% load, which is similar to for example how Gromacs runs using OpenMP. So, all is great. However, when running a large system containing ~1000 atoms, there is a single cp2k instance with 100% load and ~1TB RAM usage. SCF updates are sluggish, but it's a large system, so we can't tell if it's due to size or the fact that the CPU load is improperly low. Here is my question: is this correct behavior? Is there a way or need to force a particular number of threads to run on? Are we building the correct version for our needs? Another, more minor question: does multithreading help CP2K performance? The same machine is used for coupled cluster calculations and the users insist that HT hurts their performance, so it's currently off. Many thanks, Alex -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/dad49414-499b-4804-afc0-fc4855d0772bo%40googlegroups.com. From eluni... at gmail.com Sun Jun 28 18:10:50 2020 From: eluni... at gmail.com (Lucas Lodeiro) Date: Sun, 28 Jun 2020 14:10:50 -0400 Subject: [CP2K-user] Hirshfeld charges, neutral system with no zero total Hirshfeld charge Message-ID: Hi all, I want to obtain Hirshfeld charges for a neutral bulk liquid system (372 atoms), but when I compute the Hirshfeld charges, the total system charge is different to zero. To obtain the charges I set: &PRINT &HIRSHFELD FILENAME SELF_CONSISTENT .TRUE. SHAPE_FUNCTION DENSITY &END HIRSHFELD &END PRINT I explore the four combinations between nonSCf / SCF and density / gaussian shape functions. The SCF does not change the behavior of total charges (just correct the atomic charges as the reference paper explains). The density shape function corrects the total charge from -1.1 to -0.167, but it still remains different from zero. I compute the total charge of an isolated molecule (the charge is different of zero too, but little) and multiply this value for the number of molecules in the bulk liquid system, and I get -0.084, this is a half the bulk total charge. I understand there is numerical "noise" and approximations (just 3 decimals), but I am not pretty sure if this is "normal" or I am missing something. I think if I use more accurate SCF convergence for Hirshfeld charges it could be corrected, but I do not find any parameter that chose it. Is what I am getting correct? Regards - Lucas Lodeiro -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Mon Jun 29 09:52:08 2020 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Mon, 29 Jun 2020 11:52:08 +0200 Subject: [CP2K-user] [CP2K:13555] Hirshfeld charges, neutral system with no zero total Hirshfeld charge In-Reply-To: References: Message-ID: Hi there is not enough information to investigate your problem and to suggest a solution. In all my tests I get combined Hirshfeld charges < 0.0005. regards Juerg Hutter -------------------------------------------------------------- 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: cp... at googlegroups.com From: "Lucas Lodeiro" Sent by: cp... at googlegroups.com Date: 06/28/2020 08:08PM Subject: [CP2K:13555] Hirshfeld charges, neutral system with no zero total Hirshfeld charge Hi all, I want to obtain Hirshfeld charges for a neutral bulk liquid system (372 atoms), but when I compute the Hirshfeld charges, the total system charge is different to zero. To obtain the charges I set: &PRINT &HIRSHFELD FILENAME SELF_CONSISTENT .TRUE. SHAPE_FUNCTION DENSITY &END HIRSHFELD &END PRINT I explore the four combinations between nonSCf / SCF and density / gaussian shape functions. The SCF does not change the behavior of total charges (just correct the atomic charges as the reference paper explains). The density shape function corrects the total charge from -1.1 to -0.167, but it still remains different from zero. I compute the total charge of an isolated molecule (the charge is different of zero too, but little) and multiply this value for the number of molecules in the bulk liquid system, and I get -0.084, this is a half the bulk total charge. I understand there is numerical "noise" and approximations (just 3 decimals), but I am not pretty sure if this is "normal" or I am missing something. I think if I use more accurate SCF convergence for Hirshfeld charges it could be corrected, but I do not find any parameter that chose it. Is what I am getting correct? Regards - Lucas Lodeiro -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/CAOFT4P%2BsvSemLPx_gL%3DL70TxoCQsS6npVdnbeqwpmHS8xkhzag%40mail.gmail.com. From mejdit... at gmail.com Mon Jun 29 08:42:34 2020 From: mejdit... at gmail.com (mejdeddine mokhtar) Date: Mon, 29 Jun 2020 01:42:34 -0700 (PDT) Subject: [CP2K-user] CDFT In-Reply-To: References: Message-ID: <53f0bd0b-88ba-4bb4-8b96-693be144f998o@googlegroups.com> Hello Andres, I'm trying to run your script in my laptop (Ubuntu 18.04) but I don't know how to run the script. Could you please tell me a bit how do I run a simple CDFT calculation in a small machine ? Which command I have to run after built up the input file ? The tutorial is not really easy to understand. Le mardi 19 mars 2019 12:26:00 UTC+1, Andres Ortega a ?crit : > > Dear CP2K users, > > I have been trying to conduct a CDFT calculation in CP2K 5.1. > > I have been trying different configurations and I always get this error > related to the inverse of the Jacobian. > > Matrix to be inverted of zero size > > > I have tried different options and I was wondering if you could give me > some advice to go through these calculations. > > > Please find here the input and output > > > > best, > > > > Andres Ortega > > EPFL LSMO > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mejdit... at gmail.com Mon Jun 29 09:20:43 2020 From: mejdit... at gmail.com (mejdeddine mokhtar) Date: Mon, 29 Jun 2020 02:20:43 -0700 (PDT) Subject: [CP2K-user] CDFT Tutorial Zn- Zn+ Message-ID: I try to run the script for the Zn - Zn+ in the tutorial but I did not get the full output files as mentioned in the tutorial. Please notice that I use cp2k 5.1 installed locally. I was wondering what command line needed to run this script (I've tried ./energy.bash )? I'd also plot the curve showing how the energy varies according to the interatomic distance. I wonder if the script was running for just a particular distance? or for different distances? -------------- next part -------------- An HTML attachment was scrubbed... URL: From goweix... at gmail.com Tue Jun 30 04:37:32 2020 From: goweix... at gmail.com (Xin Wei) Date: Mon, 29 Jun 2020 21:37:32 -0700 (PDT) Subject: [CP2K-user] Geo-opt for gas molecule ( Message-ID: <89b4d9ea-e7a7-48e1-9899-13e6c6ea8c67o@googlegroups.com> Hello everyone, I am doing geometry optimization using cp2k for isopropanol alcohol (gas phase). However, I don't know how to fix the error below: Can anyone help me with it? (I centered my molecule using &CENTER_COORDINATES) *** WARNING in pw/ps_wavelet_methods.F:236 :: Density non-zero on the edges of the unit cell: wrong results in WAVELET solver Will the cell size affect the geometry optimization results for single-molecule in the gas phase? and do I have to use a cubic cell? &CELL PERIODIC NONE ABC 14.83 14.83 14.83 ALPHA_BETA_GAMMA 60.0 60.0 60.0 &END CELL Here is my input file: (my output file and xyz file are attached) &GLOBAL PROJECT IPA RUN_TYPE GEO_OPT PRINT_LEVEL LOW &END GLOBAL &FORCE_EVAL METHOD Quickstep &DFT BASIS_SET_FILE_NAME /ihome/crc/build/cp2k/cp2k-6.1-intel-mkl/data/BASIS_MOLOPT &POISSON PERIODIC NONE PSOLVER WAVELET &END POISSON &QS METHOD GAPW &END QS &SCF SCF_GUESS ATOMIC EPS_SCF 1.0E-05 MAX_SCF 200 &DIAGONALIZATION T ALGORITHM STANDARD &END DIAGONALIZATION &MIXING T ALPHA 0.5 METHOD PULAY_MIXING NPULAY 5 &END MIXING &PRINT &RESTART OFF &END RESTART &END PRINT &END SCF &XC &XC_FUNCTIONAL &PBE &END &END XC_FUNCTIONAL ! add Grimme D3 correction (without C9 terms, default) &VDW_POTENTIAL POTENTIAL_TYPE PAIR_POTENTIAL &PAIR_POTENTIAL PARAMETER_FILE_NAME dftd3.dat TYPE DFTD3 REFERENCE_FUNCTIONAL PBE R_CUTOFF [angstrom] 16 &END &END VDW_POTENTIAL &END XC &END DFT &SUBSYS &CELL PERIODIC NONE ABC 14.83 14.83 14.83 ALPHA_BETA_GAMMA 60.0 60.0 60.0 &END CELL &TOPOLOGY &CENTER_COORDINATES &END CENTER_COORDINATES COORD_FILE_NAME IPA.xyz COORD_FILE_FORMAT XYZ &END &KIND C BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q4 &END KIND &KIND H BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q1 &END KIND &KIND O BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q6 &END KIND &KIND Zr BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q12 &END KIND &END SUBSYS &END FORCE_EVAL &MOTION &GEO_OPT OPTIMIZER BFGS MAX_ITER 1500 MAX_DR [bohr] 0.003 &BFGS &END &END &PRINT &RESTART BACKUP_COPIES 0 &END RESTART &END PRINT &END Thanks!!! Xin -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: simulation (2).out Type: application/octet-stream Size: 135491 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: IPA.xyz Type: chemical/x-xyz Size: 618 bytes Desc: not available URL: From mada... at gmail.com Tue Jun 30 07:53:37 2020 From: mada... at gmail.com (yulei wang) Date: Tue, 30 Jun 2020 00:53:37 -0700 (PDT) Subject: [CP2K-user] Operation Interrupted Message-ID: <7be27cd8-d679-4636-a795-76d1c75c22b7o@googlegroups.com> Hello all, I am fairly new to cp2k and I had some trouble when I use it. When I use cp2k, the program was interrupted suddenly. The output file did not report an error. But the terminal reported an error. The error message are listed below: *** WARNING in input/input_keyword_types.F:286 :: keyword MEMORY_USAGE *** *** assumed undefined type by default *** *** WARNING in input/input_keyword_types.F:286 :: keyword XC_FUNCTIONALS *** *** assumed undefined type by default *** SIRIUS 6.4.1, git hash: 40eef542d9bf427234f9f7592abc829d2a48b275 -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 0 on node ubuntu exited on signal 9 (Killed). So I want to ask why it will be like this, and how can I solve it. Thank you for your help or advice. Sincerely Yulei Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: From kamak... at gmail.com Tue Jun 30 11:12:11 2020 From: kamak... at gmail.com (wabeck wabeck) Date: Tue, 30 Jun 2020 04:12:11 -0700 (PDT) Subject: [CP2K-user] About compiling "psmp" file Message-ID: <05bdc870-a0ec-4916-b7a8-522209c8a982o@googlegroups.com> Hi. I am a newbie. So I am not familiar with Linux and cp2k. Now, I try to compile cp2k but there is an error. It went well about VERSION="sopt ssmp popt" But an error occurred only about VERSION="psmp", an error said that /cp2k-7.1/src/input_cp2k_pwdft.F:157:60: 153 | DO i = 0, length - 1 | 2 ...... 157 | CALL sirius_option_get_name_and_type(section_name, i, name, ctype) | 1 Error: Variable ?i? at (1) set to undefined value inside loop beginning at (2) as INTENT(OUT) argument to subroutine ?sirius_option_get_name_and_type? Although I checked the file "input_cp2k_pwdft.F", I don't know the cause and the solution of the error. To compile psmp file, what should I do? ps. what are the differences those extensions? How can I use them properly? -------------- next part -------------- An HTML attachment was scrubbed... URL: From hut... at chem.uzh.ch Tue Jun 30 09:27:33 2020 From: hut... at chem.uzh.ch (hut... at chem.uzh.ch) Date: Tue, 30 Jun 2020 11:27:33 +0200 Subject: [CP2K-user] [CP2K:13569] Geo-opt for gas molecule ( In-Reply-To: <89b4d9ea-e7a7-48e1-9899-13e6c6ea8c67o@googlegroups.com> References: <89b4d9ea-e7a7-48e1-9899-13e6c6ea8c67o@googlegroups.com> Message-ID: Hi > Will the cell size affect the geometry optimization results for single-molecule in the gas phase? Yes > and do I have to use a cubic cell? Yes, for the wavelet Poisson solver. regards Juerg Hutter -------------------------------------------------------------- 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: "Xin Wei" Sent by: cp... at googlegroups.com Date: 06/30/2020 06:37AM Subject: [CP2K:13569] Geo-opt for gas molecule ( Hello everyone, I am doing geometry optimization using cp2k for isopropanol alcohol (gas phase). However, I don't know how to fix the error below: Can anyone help me with it? (I centered my molecule using &CENTER_COORDINATES) *** WARNING in pw/ps_wavelet_methods.F:236 :: Density non-zero on the edges of the unit cell: wrong results in WAVELET solver Will the cell size affect the geometry optimization results for single-molecule in the gas phase? and do I have to use a cubic cell? &CELL PERIODIC NONE ABC 14.83 14.83 14.83 ALPHA_BETA_GAMMA 60.0 60.0 60.0 &END CELL Here is my input file: (my output file and xyz file are attached) &GLOBAL PROJECT IPA RUN_TYPE GEO_OPT PRINT_LEVEL LOW &END GLOBAL &FORCE_EVAL METHOD Quickstep &DFT BASIS_SET_FILE_NAME /ihome/crc/build/cp2k/cp2k-6.1-intel-mkl/data/BASIS_MOLOPT &POISSON PERIODIC NONE PSOLVER WAVELET &END POISSON &QS METHOD GAPW &END QS &SCF SCF_GUESS ATOMIC EPS_SCF 1.0E-05 MAX_SCF 200 &DIAGONALIZATION T ALGORITHM STANDARD &END DIAGONALIZATION &MIXING T ALPHA 0.5 METHOD PULAY_MIXING NPULAY 5 &END MIXING &PRINT &RESTART OFF &END RESTART &END PRINT &END SCF &XC &XC_FUNCTIONAL &PBE &END &END XC_FUNCTIONAL ! add Grimme D3 correction (without C9 terms, default) &VDW_POTENTIAL POTENTIAL_TYPE PAIR_POTENTIAL &PAIR_POTENTIAL PARAMETER_FILE_NAME dftd3.dat TYPE DFTD3 REFERENCE_FUNCTIONAL PBE R_CUTOFF [angstrom] 16 &END &END VDW_POTENTIAL &END XC &END DFT &SUBSYS &CELL PERIODIC NONE ABC 14.83 14.83 14.83 ALPHA_BETA_GAMMA 60.0 60.0 60.0 &END CELL &TOPOLOGY &CENTER_COORDINATES &END CENTER_COORDINATES COORD_FILE_NAME IPA.xyz COORD_FILE_FORMAT XYZ &END &KIND C BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q4 &END KIND &KIND H BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q1 &END KIND &KIND O BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q6 &END KIND &KIND Zr BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q12 &END KIND &END SUBSYS &END FORCE_EVAL &MOTION &GEO_OPT OPTIMIZER BFGS MAX_ITER 1500 MAX_DR [bohr] 0.003 &BFGS &END &END &PRINT &RESTART BACKUP_COPIES 0 &END RESTART &END PRINT &END Thanks!!! Xin -- 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 cp... at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/89b4d9ea-e7a7-48e1-9899-13e6c6ea8c67o%40googlegroups.com. [attachment "simulation 2.out" removed by J?rg Hutter/at/UZH] [attachment "IPA.xyz" removed by J?rg Hutter/at/UZH] From goweix... at gmail.com Tue Jun 30 13:05:32 2020 From: goweix... at gmail.com (Xin Wei) Date: Tue, 30 Jun 2020 06:05:32 -0700 (PDT) Subject: [CP2K-user] [CP2K:13569] Geo-opt for gas molecule ( In-Reply-To: References: <89b4d9ea-e7a7-48e1-9899-13e6c6ea8c67o@googlegroups.com> Message-ID: <95e5fdb0-e28d-443b-805d-5e706f3deb24o@googlegroups.com> Hi Juerg Could you explain how the size gonna affect the results and how to choose the cell size? I am trying to calculate the binding energy and the original unit cell is non-orthogonal. I tried several numbers for the cell size of IPA, as long as it's not extremely large, the difference is negligible. Thank you very much! Xin On Tuesday, June 30, 2020 at 5:27:41 AM UTC-4, jgh wrote: > > Hi > > > Will the cell size affect the geometry optimization results for > single-molecule in the gas phase? > > Yes > > > and do I have to use a cubic cell? > > Yes, for the wavelet Poisson solver. > > regards > > Juerg Hutter > -------------------------------------------------------------- > Juerg Hutter Phone : ++41 44 635 4491 > Institut f?r Chemie C FAX : ++41 44 635 6838 > Universit?t Z?rich E-mail: h... at chem.uzh.ch > > Winterthurerstrasse 190 > CH-8057 Z?rich, Switzerland > --------------------------------------------------------------- > > -----c... at googlegroups.com wrote: ----- > To: "cp2k" > > From: "Xin Wei" > Sent by: c... at googlegroups.com > Date: 06/30/2020 06:37AM > Subject: [CP2K:13569] Geo-opt for gas molecule ( > > Hello everyone, > > I am doing geometry optimization using cp2k for isopropanol alcohol (gas > phase). However, I don't know how to fix the error below: Can anyone help > me with it? (I centered my molecule using &CENTER_COORDINATES) > *** WARNING in pw/ps_wavelet_methods.F:236 :: Density non-zero on the > edges of the unit cell: wrong results in WAVELET solver > > Will the cell size affect the geometry optimization results for > single-molecule in the gas phase? and do I have to use a cubic cell? > &CELL > PERIODIC NONE > ABC 14.83 14.83 14.83 > ALPHA_BETA_GAMMA 60.0 60.0 60.0 > &END CELL > > Here is my input file: (my output file and xyz file are attached) > > &GLOBAL > PROJECT IPA > RUN_TYPE GEO_OPT > PRINT_LEVEL LOW > &END GLOBAL > > &FORCE_EVAL > > METHOD Quickstep > &DFT > BASIS_SET_FILE_NAME > /ihome/crc/build/cp2k/cp2k-6.1-intel-mkl/data/BASIS_MOLOPT > &POISSON > PERIODIC NONE > PSOLVER WAVELET > &END POISSON > &QS > METHOD GAPW > &END QS > > > &SCF > SCF_GUESS ATOMIC > EPS_SCF 1.0E-05 > MAX_SCF 200 > &DIAGONALIZATION T > ALGORITHM STANDARD > &END DIAGONALIZATION > &MIXING T > ALPHA 0.5 > METHOD PULAY_MIXING > NPULAY 5 > &END MIXING > &PRINT > &RESTART OFF > &END RESTART > &END PRINT > &END SCF > > > &XC > &XC_FUNCTIONAL > &PBE > &END > &END XC_FUNCTIONAL > ! add Grimme D3 correction (without C9 terms, default) > &VDW_POTENTIAL > POTENTIAL_TYPE PAIR_POTENTIAL > &PAIR_POTENTIAL > PARAMETER_FILE_NAME dftd3.dat > TYPE DFTD3 > REFERENCE_FUNCTIONAL PBE > R_CUTOFF [angstrom] 16 > &END > &END VDW_POTENTIAL > &END XC > > &END DFT > > > &SUBSYS > &CELL > PERIODIC NONE > ABC 14.83 14.83 14.83 > ALPHA_BETA_GAMMA 60.0 60.0 60.0 > &END CELL > > &TOPOLOGY > &CENTER_COORDINATES > &END CENTER_COORDINATES > COORD_FILE_NAME IPA.xyz > COORD_FILE_FORMAT XYZ > &END > > &KIND C > BASIS_SET DZVP-MOLOPT-SR-GTH > POTENTIAL GTH-PBE-q4 > &END KIND > &KIND H > BASIS_SET DZVP-MOLOPT-SR-GTH > POTENTIAL GTH-PBE-q1 > &END KIND > &KIND O > BASIS_SET DZVP-MOLOPT-SR-GTH > POTENTIAL GTH-PBE-q6 > &END KIND > &KIND Zr > BASIS_SET DZVP-MOLOPT-SR-GTH > POTENTIAL GTH-PBE-q12 > &END KIND > &END SUBSYS > &END FORCE_EVAL > > &MOTION > &GEO_OPT > OPTIMIZER BFGS > MAX_ITER 1500 > MAX_DR [bohr] 0.003 > &BFGS > &END > &END > &PRINT > &RESTART > BACKUP_COPIES 0 > &END RESTART > &END PRINT > &END > > Thanks!!! > Xin > > > -- > 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 c... at googlegroups.com . > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/89b4d9ea-e7a7-48e1-9899-13e6c6ea8c67o%40googlegroups.com. > > > > [attachment "simulation 2.out" removed by J?rg Hutter/at/UZH] > [attachment "IPA.xyz" removed by J?rg Hutter/at/UZH] > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ykhua... at gmail.com Tue Jun 30 13:11:12 2020 From: ykhua... at gmail.com (Yike Huang) Date: Tue, 30 Jun 2020 06:11:12 -0700 (PDT) Subject: [CP2K-user] Can't fix atoms in BAND calculation Message-ID: Hi, cp2k experts and users. I try to perform BAND calculations with some atoms fixed. However, after BAND calculation, I find atoms that should have been fixed have some slight displacements and I have no idea about why does it happen. This strange result doesn't appear in GEO_OPT calculation (of optimized structures ini.xyz and fin.xyz). Following is &MOTION section of my input file. Any suggestions will be appreciated. ---------- &MOTION &CONSTRAINT &FIXED_ATOMS COMPONENTS_TO_FIX XYZ LIST 1..56 &END &END &BAND NUMBER_OF_REPLICA 5 NPROC_REP 64 K_SPRING 0.1 &OPTIMIZE_BAND OPT_TYPE DIIS &DIIS MAX_STEPS 50 &END &END BAND_TYPE CI-NEB &CI_NEB NSTEPS_IT 5 &END &REPLICA COORD_FILE_NAME ini.xyz &END &REPLICA COORD_FILE_NAME fin.xyz &END &PROGRAM_RUN_INFO INITIAL_CONFIGURATION_INFO &END &END BAND &END MOTION The version I use is 7.1.0. Best regards, Yike Huang, PhD candidate. Dalian Institute of Chemistry and Physics, CAS, China. From janel... at gmail.com Tue Jun 30 15:48:31 2020 From: janel... at gmail.com (Jan Elsner) Date: Tue, 30 Jun 2020 08:48:31 -0700 (PDT) Subject: [CP2K-user] SCF convergence using PBE+50%HFX on +ve dimer In-Reply-To: References: Message-ID: I solved this by decreasing EPS_PGF_ORB to 1.0E-40 and removing EPS_FILTER_MATRIX. Jan On Friday, June 19, 2020 at 12:08:08 PM UTC+1, Jan Elsner wrote: > > Dear all, > > > > I'm running a single point calculation on a positively charged rubrene (C > 42H28) dimer (spin polarized calculation) using PBE+50%HFX, restarting > from a converged PBE wavefunction. Unfortunately the SCF does not converge > after 350 steps. The "convergence" value jumps to huge values at SCF step 2 > ("convergence" at SCF step1 = *3.3*, "convergence" at SCF step2 = *12281*) > and at longer times (around SCF step 150 onwards), it shows oscillatory > behaviour. The behaviour is the same if I use RESTART ATOMIC. > > > > I note: > > - The SCF also doesn't converge for the neutral dimer > - The SCF *does converges *for both the neutral and cationic *single > rubrene molecule* > - For the dimer, I have tried a number of settings: different mixing > schemes (BROYDEN, DIRECT_P_MIXING), diagonalization and OT method, larger > CUTOFF, smaller EPS_SCHWARZ > - I also can't converge the SCF using PBE0, where I observe similar > behaviour > > I attach the relevant files. Any help would be much appreciated. > > > > Best, > > > > Jan > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From polla... at gmail.com Tue Jun 30 18:47:11 2020 From: polla... at gmail.com (Travis) Date: Tue, 30 Jun 2020 11:47:11 -0700 (PDT) Subject: [CP2K-user] SCF convergence using PBE+50%HFX on +ve dimer In-Reply-To: References: Message-ID: Hi, Do you mean to use the truncated Coulomb method? You have chosen a large screening parameter for omega of 7.0 for a screened Coulomb (HSE-like) method. That's an exceptionally small range for the HF potential. HSE functional variants reduce to PBE0 and PBE50 methods with omega = 0, I'm assuming this is closer to what you're after. Typically PBE0 and similar would be done with a truncated Coulomb method like that applied in the tutorial here, https://www.cp2k.org/exercises:2017_uzh_cp2k-tutorial:hybrid (see 2nd task). You just need to change SCALE_X in &PBE and FRACTION in &HF to 0.5 each for PBE50. -T On Tuesday, June 30, 2020 at 11:48:31 AM UTC-4 Jan Elsner wrote: > I solved this by decreasing EPS_PGF_ORB to 1.0E-40 and removing > EPS_FILTER_MATRIX. > > Jan > > > > > > On Friday, June 19, 2020 at 12:08:08 PM UTC+1, Jan Elsner wrote: >> >> Dear all, >> >> >> >> I'm running a single point calculation on a positively charged rubrene (C >> 42H28) dimer (spin polarized calculation) using PBE+50%HFX, restarting >> from a converged PBE wavefunction. Unfortunately the SCF does not converge >> after 350 steps. The "convergence" value jumps to huge values at SCF step 2 >> ("convergence" at SCF step1 = *3.3*, "convergence" at SCF step2 = *12281*) >> and at longer times (around SCF step 150 onwards), it shows oscillatory >> behaviour. The behaviour is the same if I use RESTART ATOMIC. >> >> >> >> I note: >> >> - The SCF also doesn't converge for the neutral dimer >> - The SCF *does converges *for both the neutral and cationic *single >> rubrene molecule* >> - For the dimer, I have tried a number of settings: different mixing >> schemes (BROYDEN, DIRECT_P_MIXING), diagonalization and OT method, larger >> CUTOFF, smaller EPS_SCHWARZ >> - I also can't converge the SCF using PBE0, where I observe similar >> behaviour >> >> I attach the relevant files. Any help would be much appreciated. >> >> >> >> Best, >> >> >> >> Jan >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuva... at gmail.com Mon Jun 29 16:05:55 2020 From: yuva... at gmail.com (Yuvam Bhateja) Date: Mon, 29 Jun 2020 21:35:55 +0530 Subject: [CP2K-user] [CP2K] Looking for colaboration Message-ID: Good evening everyone, I hope everyone is doing fine. My name is Yuvam Bhateja, I am an undergraduate student from the Indian Institute of Engineering Science and Technology, Shibpur, located in Kolkata, India. I am doing my final year bachelor's study (Bachelor of Technology) in the field of Electronics and Telecommunication. I am working on a project of a nanosensor for breath biomarker analysis. I have been working on this project since September of 2019. The project is very well defined and constructed. I was using a cluster of my institute but unfortunately, it went into a horrible accident and cannot be fixed until my college reopens. I am looking for mutual benefits here through this collaboration. I am targeting for journals with high impact factors like ACS. The project will include both theoretical as well as practical (fabrication) approaches. I have some experience in research works. I have presented a paper in ISDCS 2020 (IEEE conference) in Feb 2020 and submitted a journal for review in IEEE Micro this month. I am one of the lead authors in both of my works. I have prerequisite knowledge of DFT codes like Quantum ESPRESSO, CP2K, and SIESTA, but collaboration will help in finishing up the theoretical part of this project sooner. This is the information of my supervisor - Dr. Sanhita Majumdar Center of Green Energy and Sensor System (CEGESS), IIEST Shibpur. emai... at gmail.com Specialization - nanosensors and nanofabrication. She is a member of Material Science Research India (MSRI). If anyone interested, please contact me for detailed information about the project. Official email - yuvamb... at telecom.iiests.ac.in Regards Yuvam Bhateja -------------- next part -------------- An HTML attachment was scrubbed... URL: From sp05... at gmail.com Mon Jun 29 23:25:10 2020 From: sp05... at gmail.com (Sun Peng) Date: Tue, 30 Jun 2020 07:25:10 +0800 Subject: [CP2K-user] [CP2K:13555] Re: Final step of compiling of CP2K-7.1.0 In-Reply-To: <32cbc434-f4d5-4786-a59c-7ab454138f7bo@googlegroups.com> References: <1831bbaf-051c-4303-a21f-41cb480d089bo@googlegroups.com> <32cbc434-f4d5-4786-a59c-7ab454138f7bo@googlegroups.com> Message-ID: OK, Maxim. I will try. Thanks a lot! On Sun, 28 Jun 2020 at 16:45, Maxim Khomenko wrote: > Hello! > > I usually extract the dbcsr-2.0.0.tar.gz archive into directory > $CP2K_DIR/ext/dbcsr/ and it works for me. > > ???????, 27 ???? 2020 ?., 6:44:23 UTC+3 ???????????? Sun Peng ???????: >> >> Hi, everyone. I encountered a problem when I was going to compile >> the CP2K-7.1.0 after I compile all the software using the toolchains method >> and copy the local.popt to arch file.As shown in following picture, it >> said "No DBCSR submodule available, please run 'git submodule update --init >> --recursive'". However, when I run 'git submodule update --init >> --recursive', nothing changed. If anyone has encountered this problem, >> please help me. >> Thanks a lot! >> >> [image: error.png] >> >> -- > 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 cp... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/32cbc434-f4d5-4786-a59c-7ab454138f7bo%40googlegroups.com > > . > -- *?????????* *?? * *+86 15913131189* *???? ????????????????135? 510275* *Your sincerely* *Peng Sun* -------------- next part -------------- An HTML attachment was scrubbed... URL: