From matthias.krack at psi.ch Tue Oct 1 07:52:21 2024 From: matthias.krack at psi.ch (Krack Matthias) Date: Tue, 1 Oct 2024 07:52:21 +0000 Subject: [CP2K-user] [CP2K:20734] Adsorption of organic molecules on metal surface In-Reply-To: <29df6ea1-a061-4ee5-af17-aa4cd407dee0n@googlegroups.com> References: <29df6ea1-a061-4ee5-af17-aa4cd407dee0n@googlegroups.com> Message-ID: Hi The input file ?molecule.input? has a syntax error. The ?&END KIND? for the ?&KIND O? section is missing as indicated by the the indentation. Further issues are: (1) the pseudo potential for C should end with ?q4?, (2) EPS_DEFAULT should be smaller, e.g. 1.0E-12, (3) the cutoff should be larger, e.g. 400 Ry, (4) CHO has an odd number of electrons which requires LSD. HTH Matthias From: cp2k at googlegroups.com on behalf of Hanaa Sari Date: Tuesday, 1 October 2024 at 03:33 To: cp2k Subject: [CP2K:20733] Adsorption of organic molecules on metal surface Dear All, I am a new user of CP2K. I am trying to study the adsorption of organic molecules on metal surface. When I run the input file (in attachment) to optimize the molecule I have this message: invoking MPI_ABORT causes Open MPI to kill all MPI processes. ? You may or may not see output from other processes, depending on exactly when Open MPI kills them ? In the other side I try to optimize Ni(111) bulk and slab consisiting layers ? and the only calculation that converge is that of the elementary cell . As soon as I increase the number of atoms the calculation do not converge. Could someone provide an example input file? knowing that I am using the version cp2k 2024.1 Thank you. ? -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/29df6ea1-a061-4ee5-af17-aa4cd407dee0n%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 cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/ZRAP278MB0827FD87F7FBE1001384A562F4772%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM. -------------- next part -------------- An HTML attachment was scrubbed... URL: From belizsertcan at gmail.com Tue Oct 1 15:51:55 2024 From: belizsertcan at gmail.com (=?UTF-8?Q?Beliz_G=C3=B6kmen?=) Date: Tue, 1 Oct 2024 08:51:55 -0700 (PDT) Subject: [CP2K-user] [CP2K:20736] Re: Polarizability calculation In-Reply-To: <14b6a4b8-369f-4967-aaab-d99ac550305fn@googlegroups.com> References: <14b6a4b8-369f-4967-aaab-d99ac550305fn@googlegroups.com> Message-ID: <2e6aba77-0eda-41ff-bc73-41d896510047n@googlegroups.com> Hi Simone, Usually CP2K prints asterisks when the value is too large to be printed. Could you please attach your input and output? Best, Beliz On Wednesday 25 September 2024 at 00:18:24 UTC+2 Simone Ritarossi wrote: > Hi, I'm calculating the Raman spectrum of a system and in the output I > have that some values of the polarizability tensor are asterisks > (divergences?). What problem could there be? > Thank you for any help or suggestions. > > Simone > -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/2e6aba77-0eda-41ff-bc73-41d896510047n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bnzmichela at gmail.com Wed Oct 2 17:02:15 2024 From: bnzmichela at gmail.com (Michela Benazzi) Date: Wed, 2 Oct 2024 10:02:15 -0700 (PDT) Subject: [CP2K-user] [CP2K:20737] 6-31+G(d) basis set? + anion questions In-Reply-To: References: Message-ID: <7ece4ffc-0c3d-4bfc-92cb-9dd17b3f2de5n@googlegroups.com> Thank you, Dr. Krack, I really appreciate it! This worked :) On Monday, September 30, 2024 at 3:19:27?AM UTC-4 Krack Matthias wrote: > Dear Michela > > > > You can download these basis sets from Basis Set Exchange > in CP2K format. If I am not mistaken, > the 631++G basis set includes also a diffuse function for the first row > elements H and He by contrast to 6-31+G as the only difference. > > > > You need to set CHARGE -1, if you want to simulate an CH3O- anion. This > will add automatically a compensating background charge of +1 for periodic > calculation (?PERIODIC xyz? which is the default). For a non-periodic > calculation with ?PERIODIC none? in the &CELL and &POISSON sections, select > an appropriate POISSION_SOLVER > > like MT. > > > > HTH > > > > Matthias > > > > *From: *cp... at googlegroups.com on behalf of > Michela Benazzi > *Date: *Sunday, 29 September 2024 at 15:43 > *To: *cp2k > *Subject: *[CP2K:20732] 6-31+G(d) basis set? + anion questions > > Good morning everyone, > > I was able to find the 6-31G and 6-31++G basis set in > data/EMSL_BASIS_SETS, but not the single + basis set (6-31+G(d)). Can > anyone show me where to find it?? > > Another question is about representing the methoxide anion for a geometry > opt job - is it enough to make coordinate for CH3O? Do I have to add a > CHARGE? I am generally confused about setting up simulations with ions and > I would love someone to verify. > > > > Thank you so much for your time - I appreciate the help! > > Michela > > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+uns... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/a502cc1f-8ef7-4e5f-8725-7138d3bda977n%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 cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/7ece4ffc-0c3d-4bfc-92cb-9dd17b3f2de5n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bnzmichela at gmail.com Wed Oct 2 17:27:59 2024 From: bnzmichela at gmail.com (Michela Benazzi) Date: Wed, 2 Oct 2024 10:27:59 -0700 (PDT) Subject: [CP2K-user] [CP2K:20738] Gallium + CO2 lack of convergence Message-ID: <01922cb9-0de8-4887-bacb-da4a2ed78a28n@googlegroups.com> Good morning dear CP2K community, how are you? You may know me from previous posts on liquid Al (+CO2) MD troubleshooting. All of your responses have been super helpful so far, and I am coming here again for a different liquid metal. My simulations with pure liquid Gallium have been less troublesome than all of my liquid Al simulations, but the MD with 1 CO2 molecule won't converge. Can I please get some help troubleshooting? Thank you, Michela -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/01922cb9-0de8-4887-bacb-da4a2ed78a28n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Ga64C1.in Type: application/octet-stream Size: 2729 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Ga64C1.xyz Type: chemical/x-xyz Size: 2574 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 29620709.out Type: application/octet-stream Size: 40985 bytes Desc: not available URL: From mayank.dodia at gmail.com Thu Oct 3 03:25:18 2024 From: mayank.dodia at gmail.com (mayank...@gmail.com) Date: Wed, 2 Oct 2024 20:25:18 -0700 (PDT) Subject: [CP2K-user] [CP2K:20739] Setting up time dependent MM partial charges Message-ID: Hi, I have a solute-solvent in which the solute is excited via external radiation and I track the resultant solvent dynamics due to evolution of the electronic density on the solute (~100 atoms). A simple and cost-effective way for mimicing this process is to transform the evolving electronic density into time-dependent partial atomic charges on the solute at a suitable timestep \delta_t (~25 a.u.) The current implementation I have is: 1) setting the partial charges in cp2k input at t=n*\delta_t (n=0,1,2..) 2) running cp2k simulation for t+\delta_t 3) stop cp2k run 4) update the input file for MM charges for t+(n+1)*\delta_t 5) redo 2) until the simulation is done The main issue here is that I have to keep on running and stopping cp2k at every 5 steps to update the MM charges, which is a significant overhead on the calculation cost. Is there a more efficient way to do so within the cp2k output? Best Regards, Mayank -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/c2be5e6f-440f-4fb9-af1a-20bf480d7c6en%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From marci.akira at gmail.com Thu Oct 3 12:23:26 2024 From: marci.akira at gmail.com (Marcella Iannuzzi) Date: Thu, 3 Oct 2024 05:23:26 -0700 (PDT) Subject: [CP2K-user] [CP2K:20740] Re: Gallium + CO2 lack of convergence In-Reply-To: <01922cb9-0de8-4887-bacb-da4a2ed78a28n@googlegroups.com> References: <01922cb9-0de8-4887-bacb-da4a2ed78a28n@googlegroups.com> Message-ID: <6d229766-9b30-422f-8ce5-154ace7da6f8n@googlegroups.com> Dear Michela, The basis set you are using is of poor quality. The coordinates you sent show a rather strange C-O bond length The cell is very small, but still there is vacuum space among the replicas in all directions, it is a rather weird choice of coordinates. Is there a reason why you are using GAPW? Regards Marcella On Wednesday, October 2, 2024 at 7:27:59?PM UTC+2 bnzmi... at gmail.com wrote: > Good morning dear CP2K community, > > how are you? You may know me from previous posts on liquid Al (+CO2) MD > troubleshooting. All of your responses have been super helpful so far, and > I am coming here again for a different liquid metal. > > My simulations with pure liquid Gallium have been less troublesome than > all of my liquid Al simulations, but the MD with 1 CO2 molecule won't > converge. Can I please get some help troubleshooting? > > Thank you, > > Michela > -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/6d229766-9b30-422f-8ce5-154ace7da6f8n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bnzmichela at gmail.com Thu Oct 3 13:02:10 2024 From: bnzmichela at gmail.com (Michela Benazzi) Date: Thu, 3 Oct 2024 06:02:10 -0700 (PDT) Subject: [CP2K-user] [CP2K:20741] Re: Gallium + CO2 lack of convergence In-Reply-To: <6d229766-9b30-422f-8ce5-154ace7da6f8n@googlegroups.com> References: <01922cb9-0de8-4887-bacb-da4a2ed78a28n@googlegroups.com> <6d229766-9b30-422f-8ce5-154ace7da6f8n@googlegroups.com> Message-ID: <1342769e-8153-4387-b5a8-b18c6b084635n@googlegroups.com> Hi Marcella, thank you for your kind response and your time. 1) I just switched to double zeta quality a few hours ago, but my MD just crashed because, weirdly, it converged for the first few SCF loops, but then it stopped converging (attached the output file here to explain). 2) I am using GAPW because I found that augmented plane waves method worked really well with my liquid Al systems before. that method is also reported in DFT literature for liquid Ga. Rationalizing it, I think it works because it samples regions of space with different charge densities with more accuracy. Do you think I should consider something else? 3) I used a cell size to represent the density of liquid Ga with the # of atoms I have. I prepared my coordinates with a Python script, then relaxed the geometry in Avogadro2 software and inserted CO2 such that it was a distance of min 2.5 A to minimize initial repulsion with Ga atoms. Do you have any suggestions to prepare a structure? I am leaving 1-2 A on all sides from the unit cell boundaries because I have been worried about Ga atoms being too close to neighbors across periodic boundaries. Michela On Thursday, October 3, 2024 at 8:23:26?AM UTC-4 Marcella Iannuzzi wrote: > Dear Michela, > > The basis set you are using is of poor quality. > The coordinates you sent show a rather strange C-O bond length > The cell is very small, but still there is vacuum space among the replicas > in all directions, it is a rather weird choice of coordinates. > > Is there a reason why you are using GAPW? > > Regards > Marcella > On Wednesday, October 2, 2024 at 7:27:59?PM UTC+2 bnzmi... at gmail.com > wrote: > >> Good morning dear CP2K community, >> >> how are you? You may know me from previous posts on liquid Al (+CO2) MD >> troubleshooting. All of your responses have been super helpful so far, and >> I am coming here again for a different liquid metal. >> >> My simulations with pure liquid Gallium have been less troublesome than >> all of my liquid Al simulations, but the MD with 1 CO2 molecule won't >> converge. Can I please get some help troubleshooting? >> >> Thank you, >> >> Michela >> > -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/1342769e-8153-4387-b5a8-b18c6b084635n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 44553907.out Type: application/octet-stream Size: 167407 bytes Desc: not available URL: From marci.akira at gmail.com Thu Oct 3 14:20:25 2024 From: marci.akira at gmail.com (Marcella Iannuzzi) Date: Thu, 3 Oct 2024 07:20:25 -0700 (PDT) Subject: [CP2K-user] [CP2K:20742] Re: Gallium + CO2 lack of convergence In-Reply-To: <1342769e-8153-4387-b5a8-b18c6b084635n@googlegroups.com> References: <01922cb9-0de8-4887-bacb-da4a2ed78a28n@googlegroups.com> <6d229766-9b30-422f-8ce5-154ace7da6f8n@googlegroups.com> <1342769e-8153-4387-b5a8-b18c6b084635n@googlegroups.com> Message-ID: <30f8cec8-8b86-4dc1-a499-4f2af91e947an@googlegroups.com> Dear Michela, The procedure you describe does not sound very appropriate to me. You should first obtain a liquid system, without solute. I suppose you should check for density and other properties and have a sufficiently large box. Then you can create a cavity in the equilibrated liquid and insert the solute, still with the right C-O bond length. If the SCF does not converge anymore after a few steps it is probably because of the coordinates. The concentration of CO2 seems rather high. You can use GAPW. It is more commonly used for all electron calculations. With PP, GPW is as accurate. Regards Marcella On Thursday, October 3, 2024 at 3:02:10?PM UTC+2 bnzmi... at gmail.com wrote: > Hi Marcella, > > thank you for your kind response and your time. > > 1) I just switched to double zeta quality a few hours ago, but my MD just > crashed because, weirdly, it converged for the first few SCF loops, but > then it stopped converging (attached the output file here to explain). > > 2) I am using GAPW because I found that augmented plane waves method > worked really well with my liquid Al systems before. that method is also > reported in DFT literature for liquid Ga. Rationalizing it, I think it > works because it samples regions of space with different charge densities > with more accuracy. Do you think I should consider something else? > > 3) I used a cell size to represent the density of liquid Ga with the # of > atoms I have. I prepared my coordinates with a Python script, then relaxed > the geometry in Avogadro2 software and inserted CO2 such that it was a > distance of min 2.5 A to minimize initial repulsion with Ga atoms. Do you > have any suggestions to prepare a structure? I am leaving 1-2 A on all > sides from the unit cell boundaries because I have been worried about Ga > atoms being too close to neighbors across periodic boundaries. > > Michela > On Thursday, October 3, 2024 at 8:23:26?AM UTC-4 Marcella Iannuzzi wrote: > >> Dear Michela, >> >> The basis set you are using is of poor quality. >> The coordinates you sent show a rather strange C-O bond length >> The cell is very small, but still there is vacuum space among the >> replicas in all directions, it is a rather weird choice of coordinates. >> >> Is there a reason why you are using GAPW? >> >> Regards >> Marcella >> On Wednesday, October 2, 2024 at 7:27:59?PM UTC+2 bnzmi... at gmail.com >> wrote: >> >>> Good morning dear CP2K community, >>> >>> how are you? You may know me from previous posts on liquid Al (+CO2) MD >>> troubleshooting. All of your responses have been super helpful so far, and >>> I am coming here again for a different liquid metal. >>> >>> My simulations with pure liquid Gallium have been less troublesome than >>> all of my liquid Al simulations, but the MD with 1 CO2 molecule won't >>> converge. Can I please get some help troubleshooting? >>> >>> Thank you, >>> >>> Michela >>> >> -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/30f8cec8-8b86-4dc1-a499-4f2af91e947an%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bnzmichela at gmail.com Thu Oct 3 15:02:46 2024 From: bnzmichela at gmail.com (Michela Benazzi) Date: Thu, 3 Oct 2024 08:02:46 -0700 (PDT) Subject: [CP2K-user] [CP2K:20743] Re: Gallium + CO2 lack of convergence In-Reply-To: <30f8cec8-8b86-4dc1-a499-4f2af91e947an@googlegroups.com> References: <01922cb9-0de8-4887-bacb-da4a2ed78a28n@googlegroups.com> <6d229766-9b30-422f-8ce5-154ace7da6f8n@googlegroups.com> <1342769e-8153-4387-b5a8-b18c6b084635n@googlegroups.com> <30f8cec8-8b86-4dc1-a499-4f2af91e947an@googlegroups.com> Message-ID: <335efca4-9014-4d60-8c0e-42d4ab964000n@googlegroups.com> Hi Marcella, Thank you again! 1) should I run GEO_OPT on the pure Ga liquid, then add CO2? 2) How should I form a cavity artificially without disrupting the newly equilibrated Ga structure? 3) I only have one molecule of CO2 in there - How should I go about lowering the concentration? Should I just increase my #Ga atoms and add 1 CO2 molecule? Best, Michela On Thursday, October 3, 2024 at 10:20:25?AM UTC-4 Marcella Iannuzzi wrote: > > Dear Michela, > > The procedure you describe does not sound very appropriate to me. > You should first obtain a liquid system, without solute. > I suppose you should check for density and other properties and have a > sufficiently large box. > Then you can create a cavity in the equilibrated liquid and insert the > solute, still with the right C-O bond length. > If the SCF does not converge anymore after a few steps it is probably > because of the coordinates. > The concentration of CO2 seems rather high. > > You can use GAPW. It is more commonly used for all electron calculations. > With PP, GPW is as accurate. > > Regards > Marcella > > > > On Thursday, October 3, 2024 at 3:02:10?PM UTC+2 bnzmi... at gmail.com wrote: > >> Hi Marcella, >> >> thank you for your kind response and your time. >> >> 1) I just switched to double zeta quality a few hours ago, but my MD just >> crashed because, weirdly, it converged for the first few SCF loops, but >> then it stopped converging (attached the output file here to explain). >> >> 2) I am using GAPW because I found that augmented plane waves method >> worked really well with my liquid Al systems before. that method is also >> reported in DFT literature for liquid Ga. Rationalizing it, I think it >> works because it samples regions of space with different charge densities >> with more accuracy. Do you think I should consider something else? >> >> 3) I used a cell size to represent the density of liquid Ga with the # of >> atoms I have. I prepared my coordinates with a Python script, then relaxed >> the geometry in Avogadro2 software and inserted CO2 such that it was a >> distance of min 2.5 A to minimize initial repulsion with Ga atoms. Do you >> have any suggestions to prepare a structure? I am leaving 1-2 A on all >> sides from the unit cell boundaries because I have been worried about Ga >> atoms being too close to neighbors across periodic boundaries. >> >> Michela >> On Thursday, October 3, 2024 at 8:23:26?AM UTC-4 Marcella Iannuzzi wrote: >> >>> Dear Michela, >>> >>> The basis set you are using is of poor quality. >>> The coordinates you sent show a rather strange C-O bond length >>> The cell is very small, but still there is vacuum space among the >>> replicas in all directions, it is a rather weird choice of coordinates. >>> >>> Is there a reason why you are using GAPW? >>> >>> Regards >>> Marcella >>> On Wednesday, October 2, 2024 at 7:27:59?PM UTC+2 bnzmi... at gmail.com >>> wrote: >>> >>>> Good morning dear CP2K community, >>>> >>>> how are you? You may know me from previous posts on liquid Al (+CO2) MD >>>> troubleshooting. All of your responses have been super helpful so far, and >>>> I am coming here again for a different liquid metal. >>>> >>>> My simulations with pure liquid Gallium have been less troublesome than >>>> all of my liquid Al simulations, but the MD with 1 CO2 molecule won't >>>> converge. Can I please get some help troubleshooting? >>>> >>>> Thank you, >>>> >>>> Michela >>>> >>> -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/335efca4-9014-4d60-8c0e-42d4ab964000n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From marci.akira at gmail.com Thu Oct 3 17:22:47 2024 From: marci.akira at gmail.com (Marcella Iannuzzi) Date: Thu, 3 Oct 2024 10:22:47 -0700 (PDT) Subject: [CP2K-user] [CP2K:20744] Re: Gallium + CO2 lack of convergence In-Reply-To: <335efca4-9014-4d60-8c0e-42d4ab964000n@googlegroups.com> References: <01922cb9-0de8-4887-bacb-da4a2ed78a28n@googlegroups.com> <6d229766-9b30-422f-8ce5-154ace7da6f8n@googlegroups.com> <1342769e-8153-4387-b5a8-b18c6b084635n@googlegroups.com> <30f8cec8-8b86-4dc1-a499-4f2af91e947an@googlegroups.com> <335efca4-9014-4d60-8c0e-42d4ab964000n@googlegroups.com> Message-ID: <8cb7ec66-c7da-4798-b626-d9f93489be9en@googlegroups.com> Hi If you have a good equilibrated Ga liquid box (right density and low stress tensor) I wouldn't run GEO_OPT Obviously introducing CO2 is going to change the conditions, but I would anyway start with a NVT run for a first equilibration and then run NPT to re-equilibrate the volume. I would add the CO2 molecule and remove all the Ga atoms within a certain radius from the center of mass of the molecule, and then run the equilibrations as described above. The only way to lower the concentration is to increase the amount of Ga, i.e., increase the box. Regards Marcella On Thursday, October 3, 2024 at 5:02:46?PM UTC+2 bnzmi... at gmail.com wrote: > Hi Marcella, > > Thank you again! > > 1) should I run GEO_OPT on the pure Ga liquid, then add CO2? > 2) How should I form a cavity artificially without disrupting the newly > equilibrated Ga structure? > 3) I only have one molecule of CO2 in there - How should I go about > lowering the concentration? Should I just increase my #Ga atoms and add 1 > CO2 molecule? > > Best, > > Michela > On Thursday, October 3, 2024 at 10:20:25?AM UTC-4 Marcella Iannuzzi wrote: > >> >> Dear Michela, >> >> The procedure you describe does not sound very appropriate to me. >> You should first obtain a liquid system, without solute. >> I suppose you should check for density and other properties and have a >> sufficiently large box. >> Then you can create a cavity in the equilibrated liquid and insert the >> solute, still with the right C-O bond length. >> If the SCF does not converge anymore after a few steps it is probably >> because of the coordinates. >> The concentration of CO2 seems rather high. >> >> You can use GAPW. It is more commonly used for all electron calculations. >> With PP, GPW is as accurate. >> >> Regards >> Marcella >> >> >> >> On Thursday, October 3, 2024 at 3:02:10?PM UTC+2 bnzmi... at gmail.com >> wrote: >> >>> Hi Marcella, >>> >>> thank you for your kind response and your time. >>> >>> 1) I just switched to double zeta quality a few hours ago, but my MD >>> just crashed because, weirdly, it converged for the first few SCF loops, >>> but then it stopped converging (attached the output file here to explain). >>> >>> 2) I am using GAPW because I found that augmented plane waves method >>> worked really well with my liquid Al systems before. that method is also >>> reported in DFT literature for liquid Ga. Rationalizing it, I think it >>> works because it samples regions of space with different charge densities >>> with more accuracy. Do you think I should consider something else? >>> >>> 3) I used a cell size to represent the density of liquid Ga with the # >>> of atoms I have. I prepared my coordinates with a Python script, then >>> relaxed the geometry in Avogadro2 software and inserted CO2 such that it >>> was a distance of min 2.5 A to minimize initial repulsion with Ga atoms. Do >>> you have any suggestions to prepare a structure? I am leaving 1-2 A on all >>> sides from the unit cell boundaries because I have been worried about Ga >>> atoms being too close to neighbors across periodic boundaries. >>> >>> Michela >>> On Thursday, October 3, 2024 at 8:23:26?AM UTC-4 Marcella Iannuzzi wrote: >>> >>>> Dear Michela, >>>> >>>> The basis set you are using is of poor quality. >>>> The coordinates you sent show a rather strange C-O bond length >>>> The cell is very small, but still there is vacuum space among the >>>> replicas in all directions, it is a rather weird choice of coordinates. >>>> >>>> Is there a reason why you are using GAPW? >>>> >>>> Regards >>>> Marcella >>>> On Wednesday, October 2, 2024 at 7:27:59?PM UTC+2 bnzmi... at gmail.com >>>> wrote: >>>> >>>>> Good morning dear CP2K community, >>>>> >>>>> how are you? You may know me from previous posts on liquid Al (+CO2) >>>>> MD troubleshooting. All of your responses have been super helpful so far, >>>>> and I am coming here again for a different liquid metal. >>>>> >>>>> My simulations with pure liquid Gallium have been less troublesome >>>>> than all of my liquid Al simulations, but the MD with 1 CO2 molecule won't >>>>> converge. Can I please get some help troubleshooting? >>>>> >>>>> Thank you, >>>>> >>>>> Michela >>>>> >>>> -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/8cb7ec66-c7da-4798-b626-d9f93489be9en%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From l.cvitkovich at gmail.com Thu Oct 3 22:18:02 2024 From: l.cvitkovich at gmail.com (Lukas C) Date: Thu, 3 Oct 2024 15:18:02 -0700 (PDT) Subject: [CP2K-user] [CP2K:20745] Re: cp2k V_XC_CUBE In-Reply-To: <4323ee22-7159-48ed-a1c8-f8cba2ed5abcn@googlegroups.com> References: <4323ee22-7159-48ed-a1c8-f8cba2ed5abcn@googlegroups.com> Message-ID: <18dd0059-8b5a-41e1-af74-09a9f30cba27n@googlegroups.com> Dear CP2K users, I want to understand the XC contribution to the overall potential in detail. Therefore I would like to come back to the Andres' question above. I have the same problem. There is no separate cube file for V_XC using: &V_XC_CUBE ON ADD_LAST NUMERIC &END V_XC_CUBE The section &V_HARTREE_CUBE is set to OFF. If it is ON *v_hartree-1_0.cube appears. I use a PBE0 functional with the following setup: &XC &XC_FUNCTIONAL &PBE SCALE_X 1.0 SCALE_C 1.0 &END &PBE_HOLE_T_C_LR CUTOFF_RADIUS 2.0 SCALE_X 0.0 &END &END XC_FUNCTIONAL &HF &SCREENING EPS_SCHWARZ 1.0E-6 SCREEN_ON_INITIAL_P Y &END &MEMORY MAX_MEMORY 1000 EPS_STORAGE_SCALING 0.1 &END &INTERACTION_POTENTIAL POTENTIAL_TYPE TRUNCATED CUTOFF_RADIUS 2.0 T_C_G_DATA ${fdir}t_c_g.dat &END FRACTION 0.00 &END &END XC Am I missing something? Is there an alternative way to find out the XC potential? Thanks for your help! Best, Lukas oandr... at gmail.com schrieb am Mittwoch, 14. September 2022 um 17:51:22 UTC+2: > Dear Cp2k group, > > I am trying to print both Hartree and xc as cube files. > > I am using > > &V_XC_CUBE > > STRIDE 2 2 2 > > &END V_XC_CUBE > > > &V_HARTREE_CUBE > > STRIDE 2 2 2 > > &END V_HARTREE_CUBE > > > However, I only get the Hartree. cube file. I removed the V_HARTREE_CUBE > section and left the V_XC_CUBE but I still get a file as Hartree and not > the xc cube file. > > is this correct? am I misunderstanding something? should I obtain two > independent cube files for Hartree and xc.? > > I was wondering if you could give me advice on this. > > I am using cp2k 9.1 in daint, > > > best, > > > Andres Ortega-Guerrero > > > -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/18dd0059-8b5a-41e1-af74-09a9f30cba27n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From angus.gentles at gmail.com Fri Oct 4 13:33:12 2024 From: angus.gentles at gmail.com (Angus Gentles) Date: Fri, 4 Oct 2024 06:33:12 -0700 (PDT) Subject: [CP2K-user] [CP2K:20745] cp2k Hybrids + Smearing Message-ID: <81dcc10c-a50b-48d9-b60b-f98f0dfc933en@googlegroups.com> Dear all, Does anyone know if there are plans to implement smearing in hybrid functional calculations? cheers Angus Gentles -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/81dcc10c-a50b-48d9-b60b-f98f0dfc933en%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hutter at chem.uzh.ch Sat Oct 5 08:31:25 2024 From: hutter at chem.uzh.ch (=?iso-8859-1?Q?J=FCrg_Hutter?=) Date: Sat, 5 Oct 2024 08:31:25 +0000 Subject: [CP2K-user] [CP2K:20746] cp2k Hybrids + Smearing In-Reply-To: <81dcc10c-a50b-48d9-b60b-f98f0dfc933en@googlegroups.com> References: <81dcc10c-a50b-48d9-b60b-f98f0dfc933en@googlegroups.com> Message-ID: Hi can you specify in more detail what combination of options you are missing? I don't have any problems to run hybrid functionals together with the option SMEAR. regards JH ________________________________________ From: cp2k at googlegroups.com on behalf of Angus Gentles Sent: Friday, October 4, 2024 3:33 PM To: cp2k Subject: [CP2K:20745] cp2k Hybrids + Smearing Dear all, Does anyone know if there are plans to implement smearing in hybrid functional calculations? cheers Angus Gentles -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/81dcc10c-a50b-48d9-b60b-f98f0dfc933en%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 cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/ZR0P278MB0759365C1998B07B01C304A59F732%40ZR0P278MB0759.CHEP278.PROD.OUTLOOK.COM. From hanaa.sarimohammed at gmail.com Sun Oct 6 22:20:33 2024 From: hanaa.sarimohammed at gmail.com (Hanaa Sari) Date: Sun, 6 Oct 2024 15:20:33 -0700 (PDT) Subject: [CP2K-user] [CP2K:20747] Optimization of Bulk and slab Message-ID: <8ceba3a5-8747-46b8-a307-3341f95c9adcn@googlegroups.com> Dear All, I am a new user of CP2K. I am trying to to optimize Ru(111) bulk and slab consisiting 4 layers. When I run the input file (in attachment) the only calculation that converge is that of the elementary cell . As soon as I increase the number of atoms (slab) the calculation do not converge. Could someone please point out my mistakes? knowing that I am using the version cp2k 2024.1 Thank you. -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/8ceba3a5-8747-46b8-a307-3341f95c9adcn%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Ru-slab.inp Type: chemical/x-gamess-input Size: 11311 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Ru-Bulk.inp Type: chemical/x-gamess-input Size: 1820 bytes Desc: not available URL: From shivam-gupta at pharmafoods.co.jp Mon Oct 7 08:24:57 2024 From: shivam-gupta at pharmafoods.co.jp (Shivam Gupta) Date: Mon, 7 Oct 2024 01:24:57 -0700 (PDT) Subject: [CP2K-user] [CP2K:20748] start with CP2k Message-ID: Hello everyone, I'm new to CP2K and would like to use it to study antigen-antibody interactions. As I'm unsure how to begin, could anyone recommend a tutorial or beginner-friendly protocol to help me get started? Thank you! -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/bdfd896b-8d8b-4f7a-9354-f52d4e38e401n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthias.krack at psi.ch Mon Oct 7 08:46:30 2024 From: matthias.krack at psi.ch (Krack Matthias) Date: Mon, 7 Oct 2024 08:46:30 +0000 Subject: [CP2K-user] [CP2K:20749] Optimization of Bulk and slab In-Reply-To: <8ceba3a5-8747-46b8-a307-3341f95c9adcn@googlegroups.com> References: <8ceba3a5-8747-46b8-a307-3341f95c9adcn@googlegroups.com> Message-ID: Hi in Ru-slab.inp, cell size and atomic positions should match. The slab atoms do not fit into the defined simulation cell. Moreover, the atomic coordinates seem to be not scaled coordinates which typically range between 0 and 1. HTH Matthias From: cp2k at googlegroups.com on behalf of Hanaa Sari Date: Monday, 7 October 2024 at 07:55 To: cp2k Subject: [CP2K:20747] Optimization of Bulk and slab Dear All, I am a new user of CP2K. I am trying to to optimize Ru(111) bulk and slab consisiting 4 layers. When I run the input file (in attachment) the only calculation that converge is that of the elementary cell . As soon as I increase the number of atoms (slab) the calculation do not converge. Could someone please point out my mistakes? knowing that I am using the version cp2k 2024.1 Thank you. -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/8ceba3a5-8747-46b8-a307-3341f95c9adcn%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 cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/ZRAP278MB0827ABE1A97DD65DB1A732E0F47D2%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bamaz.97 at gmail.com Mon Oct 7 13:10:09 2024 From: bamaz.97 at gmail.com (bartosz mazur) Date: Mon, 7 Oct 2024 06:10:09 -0700 (PDT) Subject: [CP2K-user] [CP2K:20750] slow slurm regtests Message-ID: Hi all, I am trying to run regtests using the slurm sbatch script, but what I am observing is their extremely slow execution. After looking at the task, I can see that only 4 CPUs are being used (out of 48 set). It looks as if each task is run one after the other, i.e. 2 MPI x 2 OMP = 4 CPU. I have already tried different `mpiexec` command settings and changed the `srun` command, but this did not help. When using 4 nodes the task also runs on only 4 CPU of a single node. I don't quite understand why the system reports 2 GPUs when the `nvidia-smi --query-gpu=gpu_name --format=csv,noheader | wc -l` command is called, so I modified do_regtest.py to force 0 GPUs, but that didn't change anything either. The instructions at https://www.cp2k.org/dev:regtesting#run_with_sbatch are out of date, so maybe something else needs to be changed in the script? I would appreciate any help! Here is my sbatch script: ``` #!/bin/bash -l #SBATCH --time=06:00:00 #SBATCH --nodes=1 #SBATCH --ntasks-per-node=24 #SBATCH --cpus-per-task=2 #SBATCH --ntasks-per-core=1 #SBATCH --mem=180G set -o errexit set -o nounset set -o pipefail export MPICH_OFI_STARTUP_CONNECT=1 export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK} # export OMP_PROC_BIND=close # export OMP_PLACES=cores module load intel/2022b module load GCC/12.2.0 # Let the user see the currently loaded modules in the slurm log for completeness: module list CP2K_BASE_DIR="/lustre/pd01/hpc-kuchta-1716987452/software/cp2k" CP2K_TEST_DIR=${TMPDIR} CP2K_VERSION="psmp" NTASKS_SINGLE_TEST=2 NNODES_SINGLE_TEST=1 SRUN_CMD="srun --cpu-bind=verbose,cores" # to run tests across nodes (to check for communication effects), use: # NNODES_SINGLE_TEST=4 # SRUN_CMD="srun --cpu-bind=verbose,cores --ntasks-per-node 2" # the following should be sufficiently generic: mkdir -p "${CP2K_TEST_DIR}" cd "${CP2K_TEST_DIR}" cp2k_rel_dir=$(realpath --relative-to="${CP2K_TEST_DIR}" "${CP2K_BASE_DIR}/exe/local") # srun does not like `-np`, override the complete command instead: export cp2k_run_prefix="${SRUN_CMD} -N ${NNODES_SINGLE_TEST} -n ${NTASKS_SINGLE_TEST}" "${CP2K_REGEST_SCRIPT_DIR:-${CP2K_BASE_DIR}/tests}/do_regtest.py" \ --mpiranks ${NTASKS_SINGLE_TEST} \ --ompthreads ${OMP_NUM_THREADS} \ --maxtasks ${SLURM_NTASKS} \ --num_gpus 0 \ --workbasedir "${CP2K_TEST_DIR}" \ --mpiexec "mpiexec -n {N}" \ --debug \ "${cp2k_rel_dir}" \ "${CP2K_VERSION}" \ |& tee "${CP2K_TEST_DIR}/${CP2K_ARCH}.${CP2K_VERSION}.log" ``` and output after 1h of execution: ``` Loading intel/2022b Loading requirement: GCCcore/12.2.0 zlib/1.2.12-GCCcore-12.2.0 binutils/2.39-GCCcore-12.2.0 intel-compilers/2022.2.1 numactl/2.0.16-GCCcore-12.2.0 UCX/1.13.1-GCCcore-12.2.0 impi/2021.7.1-intel-compilers-2022.2.1 imkl/2022.2.1 iimpi/2022b imkl-FFTW/2022.2.1-iimpi-2022b Currently Loaded Modulefiles: 1) GCCcore/12.2.0 7) impi/2021.7.1-intel-compilers-2022.2.1 2) zlib/1.2.12-GCCcore-12.2.0 8) imkl/2022.2.1 3) binutils/2.39-GCCcore-12.2.0 9) iimpi/2022b 4) intel-compilers/2022.2.1 10) imkl-FFTW/2022.2.1-iimpi-2022b 5) numactl/2.0.16-GCCcore-12.2.0 11) intel/2022b 6) UCX/1.13.1-GCCcore-12.2.0 12) GCC/12.2.0 *************************** Testing started **************************** Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] ('--version',) ----------------------------- Settings --------------------------------- MPI ranks: 2 OpenMP threads: 2 GPU devices: 2 Workers: 6 Timeout [s]: 400 Work base dir: /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41 MPI exec: mpiexec -n {N} Smoke test: False Valgrind: False Keepalive: False Flag slow: False Debug: True Binary dir: /lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local VERSION: psmp Flags: omp,libint,fftw3,libxc,libgrpp,pexsi,elpa,parallel,scalapack,mpi_f08,cosma,xsmm,plumed2,spglib,mkl,sirius,libvori,libbqb,libvdwxc,hdf5 ------------------------------------------------------------------------ Copying test files ... done Skipping UNIT/nequip_unittest because its requirements are not satisfied. Skipping TMC/regtest_ana_on_the_fly because its requirements are not satisfied. Skipping QS/regtest-cusolver because its requirements are not satisfied. Skipping QS/regtest-dlaf because its requirements are not satisfied. Skipping Fist/regtest-nequip because its requirements are not satisfied. Skipping Fist/regtest-allegro because its requirements are not satisfied. Skipping QS/regtest-dft-vdw-corr-4 because its requirements are not satisfied. Skipping Fist/regtest-deepmd because its requirements are not satisfied. Skipping Fist/regtest-quip because its requirements are not satisfied. Launched 362 test directories and 6 worker... Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/dbt_tas_unittest.psmp'] ('/lustre/pd01/hpc-kuchta-1716987452/software/cp2k',) Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/dbt_unittest.psmp'] ('/lustre/pd01/hpc-kuchta-1716987452/software/cp2k',) Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/grid_unittest.psmp'] ('/lustre/pd01/hpc-kuchta-1716987452/software/cp2k',) Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/libcp2k_unittest.psmp'] ('/lustre/pd01/hpc-kuchta-1716987452/software/cp2k',) Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/memory_utilities_unittest.psmp'] ('/lustre/pd01/hpc-kuchta-1716987452/software/cp2k',) Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/parallel_rng_types_unittest.psmp'] ('/lustre/pd01/hpc-kuchta-1716987452/software/cp2k',) Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] ('RPA_SIGMA_H2O_clenshaw.inp',) >>> /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/memory_utilities_unittest memory_utilities_unittest - OK ( 0.29 sec) <<< /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/memory_utilities_unittest (1 of 362) done in 0.29 sec Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] ('H2O_ref.inp',) >>> /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/dbt_unittest dbt_unittest - RUNTIME FAIL ( 1.61 sec) <<< /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/dbt_unittest (2 of 362) done in 1.61 sec Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] ('h2o_f01_coulomb_only.inp',) >>> /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/dbt_tas_unittest dbt_tas_unittest - RUNTIME FAIL ( 1.84 sec) <<< /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/dbt_tas_unittest (3 of 362) done in 1.84 sec Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] ('test01.inp',) >>> /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/parallel_rng_types_unittest parallel_rng_types_unittest - OK ( 2.04 sec) <<< /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/parallel_rng_types_unittest (4 of 362) done in 2.04 sec Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] ('h2o_f21.inp',) >>> /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/grid_unittest grid_unittest - OK ( 2.53 sec) <<< /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/grid_unittest (5 of 362) done in 2.53 sec Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] ('h2o_dip12.inp',) >>> /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/libcp2k_unittest libcp2k_unittest - OK ( 19.03 sec) <<< /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/libcp2k_unittest (6 of 362) done in 19.03 sec Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] ('RPA_SIGMA_H2O_minimax.inp',) Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] ('RPA_SIGMA_H_minimax.inp',) Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] ('H2O_pao_exp.inp',) Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] ('RPA_SIGMA_H_clenshaw.inp',) Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] ('RPA_SIGMA_H2O_minimax_NUM_INTEG_GROUPS.inp',) Creating subprocess: ['mpiexec', '-n', '2', '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] ('H2O-5.inp',) >>> /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/QS/regtest-rpa-sigma RPA_SIGMA_H2O_clenshaw.inp -17.19226814 OK ( 83.42 sec) RPA_SIGMA_H2O_minimax.inp -17.18984039 OK ( 83.59 sec) RPA_SIGMA_H_minimax.inp -0.5150377917 OK ( 63.64 sec) RPA_SIGMA_H_clenshaw.inp -0.5150909069 OK ( 65.65 sec) RPA_SIGMA_H2O_minimax_NUM_INTEG_GROUPS.inp -17.18984039 OK ( 86.54 sec) <<< /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/QS/regtest-rpa-sigma (7 of 362) done in 382.84 sec ``` -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/d9ed484a-b9aa-4b0a-89cc-138343328848n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hanaa.sarimohammed at gmail.com Mon Oct 7 19:05:29 2024 From: hanaa.sarimohammed at gmail.com (Hanaa Sari) Date: Mon, 7 Oct 2024 12:05:29 -0700 (PDT) Subject: [CP2K-user] [CP2K:20751] Optimization of Bulk and slab In-Reply-To: References: <8ceba3a5-8747-46b8-a307-3341f95c9adcn@googlegroups.com> Message-ID: <61a5a8ea-76a6-4fac-a4ba-245784cf5db1n@googlegroups.com> Thanks a lot for your response. I will make the necessary adjustments. Le lundi 7 octobre 2024 ? 10:46:45 UTC+2, Krack Matthias a ?crit : > Hi > > > > in Ru-slab.inp, cell size and atomic positions should match. The slab > atoms do not fit into the defined simulation cell. Moreover, the atomic > coordinates seem to be not scaled coordinates which typically range between > 0 and 1. > > > > HTH > > > > Matthias > > > > *From: *cp... at googlegroups.com on behalf of > Hanaa Sari > *Date: *Monday, 7 October 2024 at 07:55 > *To: *cp2k > *Subject: *[CP2K:20747] Optimization of Bulk and slab > > Dear All, > > I am a new user of CP2K. > > I am trying to to optimize Ru(111) bulk and slab consisiting 4 layers. > > When I run the input file (in attachment) the only calculation that > converge is that of the elementary cell . As soon as I increase the number > of atoms (slab) the calculation do not converge. > > Could someone please point out my mistakes? > > knowing that I am using the version cp2k 2024.1 > > Thank you. > > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+uns... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/8ceba3a5-8747-46b8-a307-3341f95c9adcn%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 cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/61a5a8ea-76a6-4fac-a4ba-245784cf5db1n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From xw97259 at gmail.com Tue Oct 8 06:22:46 2024 From: xw97259 at gmail.com (xuan wang) Date: Mon, 7 Oct 2024 23:22:46 -0700 (PDT) Subject: [CP2K-user] [CP2K:20752] about molden file for MO visualization Message-ID: Dear cp2k users, I am now trying to dump the information from MO_molden file for MO visualization, and trying to transform the information into datagrid in the form of cube with python. I am the newer about this and want to learn about how this process can be performed, with the basic chemical princible. Is there some manu about how to teach the transformation with the asistance of python? Thank you very much. Best regards, Xuan -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/ebc40d5d-52fa-489e-94b8-52e9daf81362n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bamaz.97 at gmail.com Tue Oct 8 10:58:00 2024 From: bamaz.97 at gmail.com (bartosz mazur) Date: Tue, 8 Oct 2024 03:58:00 -0700 (PDT) Subject: [CP2K-user] [CP2K:20753] compilation problems - LHS and RHS of an assignment statement have incompatible types Message-ID: Hi all, I recently managed to compile cp2k on our cluster, but regtests showed several errors. Most of the failures are due to the error `forrtl: severe (189): LHS and RHS of an assignment statement have incompatible types` or `forrtl: severe (153): allocatable array or pointer is not allocated`. After looking at the output from `make` I noticed that there are quite a few similar warnings there: ``` /lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exts/dbcsr/src/mpi/dbcsr_mpiwrap.F(1930): warning #8100: The actual argument is an array section or assumed-shape array, corresponding dummy argument that has either the VOLATILE or ASYNCHRONOUS attribute shall be an assumed-shape array. [MSGIN] CALL mpi_isend(msgin, msglen, MPI_LOGICAL, dest, my_tag, & ------------------------^ ``` For compilation I used GCC 12.2.0 and intel 2022.2.1. My toolchain command was `./install_cp2k_toolchain.sh --mpi-mode=intelmpi --with-intel --with-gcc=system --with-plumed --with-quip --with-pexsi --with-ptscotch --with-superlu --with-fftw=no --with-hdf5`. In the attachment I provide all outputs from toolchain, make, and regtests. I'm not sure what went wrong and how should I proceed so any help will be much appreciated! Best Bartosz -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/f23087e8-772f-4484-9f38-1f2aa0874058n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: bem_compilation_warnings.zip Type: application/x-zip Size: 351812 bytes Desc: not available URL: From f.stein at hzdr.de Tue Oct 8 12:07:14 2024 From: f.stein at hzdr.de (Frederick Stein) Date: Tue, 8 Oct 2024 05:07:14 -0700 (PDT) Subject: [CP2K-user] [CP2K:20755] Re: compilation problems - LHS and RHS of an assignment statement have incompatible types In-Reply-To: References: Message-ID: <17064317-728e-4164-b086-edd664bd8d28n@googlegroups.com> Dear Bartosz, If you want to compile with Intel, then drop the "--with-gcc" flag. Regarding Intel, we do not test Intel 2022.2 anymore. You should try the IntelOneAPI containing more recent compilers instead. We are currently testing version 2024.2. The warnings can be ignored for now, but we are aware of that issue and will make adjustments later after dropping some older compilers. Regarding the runtime errors. The error "LHS and RHS of an assignment statement have incompatible types" could be a compiler bug (see https://community.intel.com/t5/Intel-Fortran-Compiler/Segmentation-fault-due-to-assignment-of-derived-type-variable/td-p/1489823). The allocation error may also be a compiler bug as the respective array is always allocated and the routine is left directly after deallocating the array earlier in the routine. Best, Frederick bartosz mazur schrieb am Dienstag, 8. Oktober 2024 um 13:17:08 UTC+2: > Hi all, > > I recently managed to compile cp2k on our cluster, but regtests showed > several errors. Most of the failures are due to the error `forrtl: severe > (189): LHS and RHS of an assignment statement have incompatible types` or `forrtl: > severe (153): allocatable array or pointer is not allocated`. After > looking at the output from `make` I noticed that there are quite a few > similar warnings there: > > ``` > /lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exts/dbcsr/src/mpi/dbcsr_mpiwrap.F(1930): > warning #8100: The actual argument is an array section or assumed-shape > array, corresponding dummy argument that has either the VOLATILE or > ASYNCHRONOUS attribute shall be an assumed-shape array. [MSGIN] > CALL mpi_isend(msgin, msglen, MPI_LOGICAL, dest, my_tag, & > ------------------------^ > ``` > > For compilation I used GCC 12.2.0 and intel 2022.2.1. My toolchain command > was `./install_cp2k_toolchain.sh --mpi-mode=intelmpi --with-intel > --with-gcc=system --with-plumed --with-quip --with-pexsi --with-ptscotch > --with-superlu --with-fftw=no --with-hdf5`. In the attachment I provide > all outputs from toolchain, make, and regtests. > > I'm not sure what went wrong and how should I proceed so any help will be > much appreciated! > > Best > Bartosz > -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/17064317-728e-4164-b086-edd664bd8d28n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bamaz.97 at gmail.com Tue Oct 8 12:43:18 2024 From: bamaz.97 at gmail.com (bartosz mazur) Date: Tue, 8 Oct 2024 05:43:18 -0700 (PDT) Subject: [CP2K-user] [CP2K:20756] Re: compilation problems - LHS and RHS of an assignment statement have incompatible types In-Reply-To: <17064317-728e-4164-b086-edd664bd8d28n@googlegroups.com> References: <17064317-728e-4164-b086-edd664bd8d28n@googlegroups.com> Message-ID: <21825b1f-9a66-4d63-a223-e958db74d714n@googlegroups.com> Hi Frederick, Thank you for your quick response! Just to be sure, if I compile the latest version of cp2k using Intel 2021 (https://www.cp2k.org/dev:compiler_support), I should no longer have the problems described? I ask because I don't see a module with Intel OneAPI 2024 on our HPC, so I am considering using either an older module or asking the admins to provide a newer one. Best Bartosz wtorek, 8 pa?dziernika 2024 o 14:07:15 UTC+2 Frederick Stein napisa?(a): > Dear Bartosz, > If you want to compile with Intel, then drop the "--with-gcc" flag. > Regarding Intel, we do not test Intel 2022.2 anymore. You should try the > IntelOneAPI containing more recent compilers instead. We are currently > testing version 2024.2. > The warnings can be ignored for now, but we are aware of that issue and > will make adjustments later after dropping some older compilers. > Regarding the runtime errors. The error "LHS and RHS of an assignment > statement have incompatible types" could be a compiler bug (see > https://community.intel.com/t5/Intel-Fortran-Compiler/Segmentation-fault-due-to-assignment-of-derived-type-variable/td-p/1489823). > The allocation error may also be a compiler bug as the respective array is > always allocated and the routine is left directly after deallocating the > array earlier in the routine. > Best, > Frederick > > bartosz mazur schrieb am Dienstag, 8. Oktober 2024 um 13:17:08 UTC+2: > >> Hi all, >> >> I recently managed to compile cp2k on our cluster, but regtests showed >> several errors. Most of the failures are due to the error `forrtl: >> severe (189): LHS and RHS of an assignment statement have incompatible >> types` or `forrtl: severe (153): allocatable array or pointer is not >> allocated`. After looking at the output from `make` I noticed that there >> are quite a few similar warnings there: >> >> ``` >> /lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exts/dbcsr/src/mpi/dbcsr_mpiwrap.F(1930): >> warning #8100: The actual argument is an array section or assumed-shape >> array, corresponding dummy argument that has either the VOLATILE or >> ASYNCHRONOUS attribute shall be an assumed-shape array. [MSGIN] >> CALL mpi_isend(msgin, msglen, MPI_LOGICAL, dest, my_tag, & >> ------------------------^ >> ``` >> >> For compilation I used GCC 12.2.0 and intel 2022.2.1. My toolchain >> command was `./install_cp2k_toolchain.sh --mpi-mode=intelmpi >> --with-intel --with-gcc=system --with-plumed --with-quip --with-pexsi >> --with-ptscotch --with-superlu --with-fftw=no --with-hdf5`. In the >> attachment I provide all outputs from toolchain, make, and regtests. >> >> I'm not sure what went wrong and how should I proceed so any help will be >> much appreciated! >> >> Best >> Bartosz >> > -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/21825b1f-9a66-4d63-a223-e958db74d714n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cp2k at googlegroups.com Tue Oct 8 12:24:02 2024 From: cp2k at googlegroups.com ('daniel Storm' via cp2k) Date: Tue, 8 Oct 2024 05:24:02 -0700 (PDT) Subject: [CP2K-user] [CP2K:20756] Inconsistent geometry optimisations Message-ID: Hi everyone, Just to provide some context, in our group we use CP2k to model molecular reactivity in the solid state, so slightly different than ?standard? solid state chemistry. We run optimisations for minima and transition states (TS), whose character we confirm by running phonon calculations. Now, to the issue. I am working with a crystal structure of an iridium organometallic salt, [Ir(PONOP)(H)Me][BArF4], however, I am encountering issues with achieving consistent optimisations. Despite starting from the same experimental structure, I am getting very different SCF energies (up to 3 kcal/mol) and I have observed minor differences in the resulting geometries. I think that those geometries are close enough to not show that big of an SCF difference, but my main worry is the fact that the starting point is always the same. The convergence criteria that I am currently using is MAX_FORCE 1.0 x 10-4. I have attempted to improve this by tightening the criteria (MAX_FORCE, MAX_DR, RMS_DR and RMS_FORCE) to 1.0 x 10-6, but this didn?t fix the issue. All the optimisations are done with the PBE-D3 functional and DZVP-MOLOPT-SR-GTH basis set. So, to sum up, I run optimisations with the same starting geometry that converge to different structures, and I am not sure why or which criterion to use to select one structure over the other, etc. I have worked with other organometallic salts in the past, and this is the first time I find this issue. I am using CP2k version 2023.2 in the HPC cluster Archer-2. Has anyone seen this before? Any advice on how to proceed? Thanks in advance, Daniel. -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/d50cb0ef-42e9-465d-81c7-2fdacdab6d41n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthias.krack at psi.ch Tue Oct 8 13:34:46 2024 From: matthias.krack at psi.ch (Krack Matthias) Date: Tue, 8 Oct 2024 13:34:46 +0000 Subject: [CP2K-user] [CP2K:20757] Inconsistent geometry optimisations In-Reply-To: References: Message-ID: Hi Daniel Did you try to decrease EPS_DEFAULT and to increase the PW cutoff? These input parameters mainly determine the accuracy of the atomic forces rather than the convergence thresholds for the force calculation like MAX_FORCE or MAX_DR which can also show convergence for poor forces. HTH Matthias From: 'daniel Storm' via cp2k Date: Tuesday, 8 October 2024 at 14:50 To: cp2k Subject: [CP2K:20756] Inconsistent geometry optimisations Hi everyone, Just to provide some context, in our group we use CP2k to model molecular reactivity in the solid state, so slightly different than ?standard? solid state chemistry. We run optimisations for minima and transition states (TS), whose character we confirm by running phonon calculations. Now, to the issue. I am working with a crystal structure of an iridium organometallic salt, [Ir(PONOP)(H)Me][BArF4], however, I am encountering issues with achieving consistent optimisations. Despite starting from the same experimental structure, I am getting very different SCF energies (up to 3 kcal/mol) and I have observed minor differences in the resulting geometries. I think that those geometries are close enough to not show that big of an SCF difference, but my main worry is the fact that the starting point is always the same. The convergence criteria that I am currently using is MAX_FORCE 1.0 x 10-4. I have attempted to improve this by tightening the criteria (MAX_FORCE, MAX_DR, RMS_DR and RMS_FORCE) to 1.0 x 10-6, but this didn?t fix the issue. All the optimisations are done with the PBE-D3 functional and DZVP-MOLOPT-SR-GTH basis set. So, to sum up, I run optimisations with the same starting geometry that converge to different structures, and I am not sure why or which criterion to use to select one structure over the other, etc. I have worked with other organometallic salts in the past, and this is the first time I find this issue. I am using CP2k version 2023.2 in the HPC cluster Archer-2. Has anyone seen this before? Any advice on how to proceed? Thanks in advance, Daniel. -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/d50cb0ef-42e9-465d-81c7-2fdacdab6d41n%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 cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/ZRAP278MB0827F79512B3329F4B818BCEF47E2%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM. -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.stein at hzdr.de Tue Oct 8 13:46:14 2024 From: f.stein at hzdr.de (Frederick Stein) Date: Tue, 8 Oct 2024 06:46:14 -0700 (PDT) Subject: [CP2K-user] [CP2K:20759] Re: compilation problems - LHS and RHS of an assignment statement have incompatible types In-Reply-To: <21825b1f-9a66-4d63-a223-e958db74d714n@googlegroups.com> References: <17064317-728e-4164-b086-edd664bd8d28n@googlegroups.com> <21825b1f-9a66-4d63-a223-e958db74d714n@googlegroups.com> Message-ID: Hi Bartosz, No, Intel 2021 will be probably not work, it is older than Intel 2022. I meant something like Intel OneAPI 2023 or 2024. Best, Frederick bartosz mazur schrieb am Dienstag, 8. Oktober 2024 um 14:43:19 UTC+2: > Hi Frederick, > > Thank you for your quick response! Just to be sure, if I compile the > latest version of cp2k using Intel 2021 ( > https://www.cp2k.org/dev:compiler_support), I should no longer have the > problems described? I ask because I don't see a module with Intel OneAPI > 2024 on our HPC, so I am considering using either an older module or asking > the admins to provide a newer one. > > Best > Bartosz > > wtorek, 8 pa?dziernika 2024 o 14:07:15 UTC+2 Frederick Stein napisa?(a): > >> Dear Bartosz, >> If you want to compile with Intel, then drop the "--with-gcc" flag. >> Regarding Intel, we do not test Intel 2022.2 anymore. You should try the >> IntelOneAPI containing more recent compilers instead. We are currently >> testing version 2024.2. >> The warnings can be ignored for now, but we are aware of that issue and >> will make adjustments later after dropping some older compilers. >> Regarding the runtime errors. The error "LHS and RHS of an assignment >> statement have incompatible types" could be a compiler bug (see >> https://community.intel.com/t5/Intel-Fortran-Compiler/Segmentation-fault-due-to-assignment-of-derived-type-variable/td-p/1489823). >> The allocation error may also be a compiler bug as the respective array is >> always allocated and the routine is left directly after deallocating the >> array earlier in the routine. >> Best, >> Frederick >> >> bartosz mazur schrieb am Dienstag, 8. Oktober 2024 um 13:17:08 UTC+2: >> >>> Hi all, >>> >>> I recently managed to compile cp2k on our cluster, but regtests showed >>> several errors. Most of the failures are due to the error `forrtl: >>> severe (189): LHS and RHS of an assignment statement have incompatible >>> types` or `forrtl: severe (153): allocatable array or pointer is not >>> allocated`. After looking at the output from `make` I noticed that >>> there are quite a few similar warnings there: >>> >>> ``` >>> /lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exts/dbcsr/src/mpi/dbcsr_mpiwrap.F(1930): >>> warning #8100: The actual argument is an array section or assumed-shape >>> array, corresponding dummy argument that has either the VOLATILE or >>> ASYNCHRONOUS attribute shall be an assumed-shape array. [MSGIN] >>> CALL mpi_isend(msgin, msglen, MPI_LOGICAL, dest, my_tag, & >>> ------------------------^ >>> ``` >>> >>> For compilation I used GCC 12.2.0 and intel 2022.2.1. My toolchain >>> command was `./install_cp2k_toolchain.sh --mpi-mode=intelmpi >>> --with-intel --with-gcc=system --with-plumed --with-quip --with-pexsi >>> --with-ptscotch --with-superlu --with-fftw=no --with-hdf5`. In the >>> attachment I provide all outputs from toolchain, make, and regtests. >>> >>> I'm not sure what went wrong and how should I proceed so any help will >>> be much appreciated! >>> >>> Best >>> Bartosz >>> >> -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/f73fa281-30c2-445e-b0c1-3278a7b82f41n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From pototschnig.johann at gmail.com Tue Oct 8 14:35:13 2024 From: pototschnig.johann at gmail.com (Johann Pototschnig) Date: Tue, 8 Oct 2024 07:35:13 -0700 (PDT) Subject: [CP2K-user] [CP2K:20760] Re: slow slurm regtests In-Reply-To: References: Message-ID: <58256d55-fe8c-47e3-b1ec-144a10c33982n@googlegroups.com> Hi, The combination of regtest with slurm leads to all workers being run on the same processors. (This of course leads to resource starvation if there are several workers) The tests are rather small so more than 2 MPI processes are not useful and can lead to failing tests. Regarding OpenMP threads you can go a bit larger. but too large doesn't make sense as the test are quite small. Due to these limitations the tests take time, but it should be a bit faster than your setup where the workers are fighting for resources. They should finish within 10 h. I would suggest something like: #SBATCH --nodes=1 #SBATCH --ntasks-per-node=2 #SBATCH --cpus-per-task=8 The assignment of workers to different CPU's is not straightforward. best, Johann On Monday, October 7, 2024 at 3:11:45?PM UTC+2 bartosz mazur wrote: > Hi all, > > I am trying to run regtests using the slurm sbatch script, but what I am > observing is their extremely slow execution. After looking at the task, I > can see that only 4 CPUs are being used (out of 48 set). It looks as if > each task is run one after the other, i.e. 2 MPI x 2 OMP = 4 CPU. > > I have already tried different `mpiexec` command settings and changed the > `srun` command, but this did not help. When using 4 nodes the task also > runs on only 4 CPU of a single node. I don't quite understand why the > system reports 2 GPUs when the `nvidia-smi --query-gpu=gpu_name > --format=csv,noheader | wc -l` command is called, so I modified > do_regtest.py to force 0 GPUs, but that didn't change anything either. The > instructions at https://www.cp2k.org/dev:regtesting#run_with_sbatch are > out of date, so maybe something else needs to be changed in the script? > > I would appreciate any help! > > Here is my sbatch script: > > ``` > > #!/bin/bash -l > > #SBATCH --time=06:00:00 > > #SBATCH --nodes=1 > > #SBATCH --ntasks-per-node=24 > > #SBATCH --cpus-per-task=2 > > #SBATCH --ntasks-per-core=1 > > #SBATCH --mem=180G > > > > set -o errexit > > set -o nounset > > set -o pipefail > > > > export MPICH_OFI_STARTUP_CONNECT=1 > > export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK} > > # export OMP_PROC_BIND=close > > # export OMP_PLACES=cores > > > > module load intel/2022b > > module load GCC/12.2.0 > > > > # Let the user see the currently loaded modules in the slurm log for > completeness: > > module list > > > > CP2K_BASE_DIR="/lustre/pd01/hpc-kuchta-1716987452/software/cp2k" > > CP2K_TEST_DIR=${TMPDIR} > > > > CP2K_VERSION="psmp" > > > > NTASKS_SINGLE_TEST=2 > > NNODES_SINGLE_TEST=1 > > SRUN_CMD="srun --cpu-bind=verbose,cores" > > > > # to run tests across nodes (to check for communication effects), use: > > # NNODES_SINGLE_TEST=4 > > # SRUN_CMD="srun --cpu-bind=verbose,cores --ntasks-per-node 2" > > > # the following should be sufficiently generic: > > > > mkdir -p "${CP2K_TEST_DIR}" > > cd "${CP2K_TEST_DIR}" > > > > cp2k_rel_dir=$(realpath --relative-to="${CP2K_TEST_DIR}" > "${CP2K_BASE_DIR}/exe/local") > > # srun does not like `-np`, override the complete command instead: > > export cp2k_run_prefix="${SRUN_CMD} -N ${NNODES_SINGLE_TEST} -n > ${NTASKS_SINGLE_TEST}" > > > > "${CP2K_REGEST_SCRIPT_DIR:-${CP2K_BASE_DIR}/tests}/do_regtest.py" \ > > --mpiranks ${NTASKS_SINGLE_TEST} \ > > --ompthreads ${OMP_NUM_THREADS} \ > > --maxtasks ${SLURM_NTASKS} \ > > --num_gpus 0 \ > > --workbasedir "${CP2K_TEST_DIR}" \ > > --mpiexec "mpiexec -n {N}" \ > > --debug \ > > "${cp2k_rel_dir}" \ > > "${CP2K_VERSION}" \ > > |& tee "${CP2K_TEST_DIR}/${CP2K_ARCH}.${CP2K_VERSION}.log" > > > ``` > > and output after 1h of execution: > > ``` > > Loading intel/2022b > > Loading requirement: GCCcore/12.2.0 zlib/1.2.12-GCCcore-12.2.0 > > binutils/2.39-GCCcore-12.2.0 intel-compilers/2022.2.1 > > numactl/2.0.16-GCCcore-12.2.0 UCX/1.13.1-GCCcore-12.2.0 > > impi/2021.7.1-intel-compilers-2022.2.1 imkl/2022.2.1 iimpi/2022b > > imkl-FFTW/2022.2.1-iimpi-2022b > > Currently Loaded Modulefiles: > > 1) GCCcore/12.2.0 7) > impi/2021.7.1-intel-compilers-2022.2.1 > > 2) zlib/1.2.12-GCCcore-12.2.0 8) imkl/2022.2.1 > > > 3) binutils/2.39-GCCcore-12.2.0 9) iimpi/2022b > > > 4) intel-compilers/2022.2.1 10) imkl-FFTW/2022.2.1-iimpi-2022b > > > 5) numactl/2.0.16-GCCcore-12.2.0 11) intel/2022b > > > 6) UCX/1.13.1-GCCcore-12.2.0 12) GCC/12.2.0 > > > *************************** Testing started **************************** > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] > ('--version',) > > > ----------------------------- Settings --------------------------------- > > MPI ranks: 2 > > OpenMP threads: 2 > > GPU devices: 2 > > Workers: 6 > > Timeout [s]: 400 > > Work base dir: /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41 > > MPI exec: mpiexec -n {N} > > Smoke test: False > > Valgrind: False > > Keepalive: False > > Flag slow: False > > Debug: True > > Binary dir: /lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local > > VERSION: psmp > > Flags: > omp,libint,fftw3,libxc,libgrpp,pexsi,elpa,parallel,scalapack,mpi_f08,cosma,xsmm,plumed2,spglib,mkl,sirius,libvori,libbqb,libvdwxc,hdf5 > > ------------------------------------------------------------------------ > > Copying test files ... done > > Skipping UNIT/nequip_unittest because its requirements are not satisfied. > > Skipping TMC/regtest_ana_on_the_fly because its requirements are not > satisfied. > > Skipping QS/regtest-cusolver because its requirements are not satisfied. > > Skipping QS/regtest-dlaf because its requirements are not satisfied. > > Skipping Fist/regtest-nequip because its requirements are not satisfied. > > Skipping Fist/regtest-allegro because its requirements are not satisfied. > > Skipping QS/regtest-dft-vdw-corr-4 because its requirements are not > satisfied. > > Skipping Fist/regtest-deepmd because its requirements are not satisfied. > > Skipping Fist/regtest-quip because its requirements are not satisfied. > > Launched 362 test directories and 6 worker... > > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/dbt_tas_unittest.psmp'] > ('/lustre/pd01/hpc-kuchta-1716987452/software/cp2k',) > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/dbt_unittest.psmp'] > ('/lustre/pd01/hpc-kuchta-1716987452/software/cp2k',) > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/grid_unittest.psmp'] > ('/lustre/pd01/hpc-kuchta-1716987452/software/cp2k',) > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/libcp2k_unittest.psmp'] > ('/lustre/pd01/hpc-kuchta-1716987452/software/cp2k',) > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/memory_utilities_unittest.psmp'] > ('/lustre/pd01/hpc-kuchta-1716987452/software/cp2k',) > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/parallel_rng_types_unittest.psmp'] > ('/lustre/pd01/hpc-kuchta-1716987452/software/cp2k',) > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] > ('RPA_SIGMA_H2O_clenshaw.inp',) > > >>> > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/memory_utilities_unittest > > memory_utilities_unittest > - OK ( 0.29 sec) > > <<< > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/memory_utilities_unittest > (1 of 362) done in 0.29 sec > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] > ('H2O_ref.inp',) > > >>> > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/dbt_unittest > > dbt_unittest > - RUNTIME FAIL ( 1.61 sec) > > <<< > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/dbt_unittest > (2 of 362) done in 1.61 sec > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] > ('h2o_f01_coulomb_only.inp',) > > >>> > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/dbt_tas_unittest > > dbt_tas_unittest > - RUNTIME FAIL ( 1.84 sec) > > <<< > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/dbt_tas_unittest > (3 of 362) done in 1.84 sec > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] > ('test01.inp',) > > >>> > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/parallel_rng_types_unittest > > parallel_rng_types_unittest > - OK ( 2.04 sec) > > <<< > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/parallel_rng_types_unittest > (4 of 362) done in 2.04 sec > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] > ('h2o_f21.inp',) > > >>> > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/grid_unittest > > grid_unittest > - OK ( 2.53 sec) > > <<< > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/grid_unittest > (5 of 362) done in 2.53 sec > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] > ('h2o_dip12.inp',) > > >>> > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/libcp2k_unittest > > libcp2k_unittest > - OK ( 19.03 sec) > > <<< > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/UNIT/libcp2k_unittest > (6 of 362) done in 19.03 sec > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] > ('RPA_SIGMA_H2O_minimax.inp',) > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] > ('RPA_SIGMA_H_minimax.inp',) > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] > ('H2O_pao_exp.inp',) > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] > ('RPA_SIGMA_H_clenshaw.inp',) > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] > ('RPA_SIGMA_H2O_minimax_NUM_INTEG_GROUPS.inp',) > > Creating subprocess: ['mpiexec', '-n', '2', > '/lustre/pd01/hpc-kuchta-1716987452/software/cp2k/exe/local/cp2k.psmp'] > ('H2O-5.inp',) > > >>> > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/QS/regtest-rpa-sigma > > RPA_SIGMA_H2O_clenshaw.inp > -17.19226814 OK ( 83.42 sec) > > RPA_SIGMA_H2O_minimax.inp > -17.18984039 OK ( 83.59 sec) > > RPA_SIGMA_H_minimax.inp > -0.5150377917 OK ( 63.64 sec) > > RPA_SIGMA_H_clenshaw.inp > -0.5150909069 OK ( 65.65 sec) > > RPA_SIGMA_H2O_minimax_NUM_INTEG_GROUPS.inp > -17.18984039 OK ( 86.54 sec) > > <<< > /lustre/tmp/slurm/3090305/TEST-psmp-2024-10-07_13-58-41/QS/regtest-rpa-sigma > (7 of 362) done in 382.84 sec > ``` > -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/58256d55-fe8c-47e3-b1ec-144a10c33982n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hsupright at gmail.com Wed Oct 9 03:49:22 2024 From: hsupright at gmail.com (sh X) Date: Tue, 8 Oct 2024 20:49:22 -0700 (PDT) Subject: [CP2K-user] [CP2K:20760] Dipole of PIMD in CP2K Message-ID: <81d9b16f-e86a-433e-8fa3-ab30e1bf6e91n@googlegroups.com> Dear all, The dipole moments output by CP2K when doing a PIMD simulation seem to be the dipole moments of all the beads individually defined. If I want to get the dipole moment of the centroid, how should I set it up? Thank you all in advance for any help. Best regards, hsuh -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/81d9b16f-e86a-433e-8fa3-ab30e1bf6e91n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cp2k at googlegroups.com Wed Oct 9 09:25:28 2024 From: cp2k at googlegroups.com ('daniel Storm' via cp2k) Date: Wed, 9 Oct 2024 02:25:28 -0700 (PDT) Subject: [CP2K-user] [CP2K:20762] Inconsistent geometry optimisations In-Reply-To: References: Message-ID: <07149c81-16d2-414a-9816-aeafe65595afn@googlegroups.com> Hi Matthias, I did have a look at the cutoff and EPS_DEFAULT at the start of my project but that was for a different issue. So I haven't tried running consecutive optimisations with these parameters but I will give that a go and get back to you. Thanks for your help, Daniel On Tuesday, October 8, 2024 at 2:35:01?PM UTC+1 Krack Matthias wrote: > Hi Daniel > > > > Did you try to decrease EPS_DEFAULT and to increase the PW cutoff? These > input parameters mainly determine the accuracy of the atomic forces rather > than the convergence thresholds for the force calculation like MAX_FORCE or > MAX_DR which can also show convergence for poor forces. > > > > HTH > > > > Matthias > > > > *From: *'daniel Storm' via cp2k > *Date: *Tuesday, 8 October 2024 at 14:50 > *To: *cp2k > *Subject: *[CP2K:20756] Inconsistent geometry optimisations > > Hi everyone, > > Just to provide some context, in our group we use CP2k to model molecular > reactivity in the solid state, so slightly different than ?standard? solid > state chemistry. We run optimisations for minima and transition states > (TS), whose character we confirm by running phonon calculations. > > Now, to the issue. I am working with a crystal structure of an iridium > organometallic salt, [Ir(PONOP)(H)Me][BArF4], however, I am encountering > issues with achieving consistent optimisations. Despite starting from the > same experimental structure, I am getting very different SCF energies (up > to 3 kcal/mol) and I have observed minor differences in the resulting > geometries. I think that those geometries are close enough to not show that > big of an SCF difference, but my main worry is the fact that the starting > point is always the same. > > The convergence criteria that I am currently using is MAX_FORCE 1.0 x 10-4. > I have attempted to improve this by tightening the criteria (MAX_FORCE, > MAX_DR, RMS_DR and RMS_FORCE) to 1.0 x 10-6, but this didn?t fix the > issue. All the optimisations are done with the PBE-D3 functional and > DZVP-MOLOPT-SR-GTH basis set. > > So, to sum up, I run optimisations with the same starting geometry that > converge to different structures, and I am not sure why or which criterion > to use to select one structure over the other, etc. > > I have worked with other organometallic salts in the past, and this is the > first time I find this issue. I am using CP2k version 2023.2 in the HPC > cluster Archer-2. > > Has anyone seen this before? Any advice on how to proceed? > > Thanks in advance, > > Daniel. > > -- > You received this message because you are subscribed to the Google Groups > "cp2k" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to cp2k+uns... at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/cp2k/d50cb0ef-42e9-465d-81c7-2fdacdab6d41n%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 cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/07149c81-16d2-414a-9816-aeafe65595afn%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... 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URL: From souvikkondal03 at gmail.com Wed Oct 9 23:52:36 2024 From: souvikkondal03 at gmail.com (Souvik Mondal) Date: Wed, 9 Oct 2024 16:52:36 -0700 (PDT) Subject: [CP2K-user] [CP2K:20762] Segmentation Fault (SIGSEGV) when Using RESP in Geometry Optimization Message-ID: <8dbb754c-93a9-416c-847e-ee2fa9c75c4an@googlegroups.com> Hello CP2K community, I am encountering a *segmentation fault (SIGSEGV)* while performing a geometry optimization on a protein system with a catalytic Zn site using CP2K. The geometry optimization runs successfully without the *RESP* section, but when I include the RESP section, I receive the following error after the first geometry optimization step: Program received signal SIGSEGV: Segmentation fault - invalid memory reference. -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/8dbb754c-93a9-416c-847e-ee2fa9c75c4an%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: qm-mm-en-resp.inp Type: chemical/x-gamess-input Size: 4691 bytes Desc: not available URL: From ucapca1 at ucl.ac.uk Thu Oct 10 12:11:03 2024 From: ucapca1 at ucl.ac.uk (uca...@ucl.ac.uk) Date: Thu, 10 Oct 2024 05:11:03 -0700 (PDT) Subject: [CP2K-user] [CP2K:20764] Re: Segmentation fault with Hirshfeld CDFT In-Reply-To: References: <184bd67e-d61f-4efc-9fe7-09e04d18cdcdn@googlegroups.com> Message-ID: <0224492e-965f-47d7-bd30-58dd66b63743n@googlegroups.com> For future reference, the bug causing a segmentation fault when calculating CDFT forces with a large number of constraints has been fixed in the latest version of CP2K. See https://github.com/cp2k/cp2k/pull/3711 On Friday 2 December 2022 at 23:49:13 UTC+8 Leili Rassouli wrote: > Dear Chris, > Thanks for your reply. > Finally, I need to apply 7 constraints. The energy calculation with seven > constraints has been tested, and it worked fine. However, the final spins > in Hirshfeld analysis are not quite what I have defined as constraints. The > files related to this calculation are attached. > I read the " Electron and Hole Mobilities in Bulk Hematite from Spin- > Constrained Density Functional Theory" paper by Christian S. Ahart, Kevin > M. Rosso, and Jochen Blumberger. And it seems they employed 2 constraints > for geometry optimization using cDFT. I am not sure why it doesn't work for > my case. > As you requested, I have attached the xyz file. > Thank you so much for your assistance, I really appreciate it. > Please let me know if you need any other information. > Lili > > On Friday, December 2, 2022 at 9:05:52 AM UTC-5 uca... at ucl.ac.uk wrote: > >> Hi Lili, >> >> I had a look at your input files and the issue is likely related to the >> use of 2 constraints (your unsuccessful job) instead of 1 constraint (your >> successful job). Optimising multiple constraints is very challenging, and >> therefore this has not been tested extensively. >> >> If you provide your structure 'ex1-geo.xyz' then I can check your job >> and perhaps implement a bug fix if needed. >> >> Regards, >> Chris >> >> On Thursday, 1 December 2022 at 23:13:27 UTC rassoul... at gmail.com wrote: >> >>> Dear all, >>> I am using 2022.1 version of cp2k. But I have the same problem as Chris. >>> I want to optimize the geometry of a periodic system using cDFT. I received >>> Segmentation fault error ("Program received signal SIGSEGV: Segmentation >>> fault - invalid memory reference.") with Hirshfeld constraints. Same as >>> Chris, it is sensitive to the combinations of atoms I use in &ATOM_GROUP. >>> In my case, it only works fine for one combination of atoms and not any >>> other combinations. The input and output files for the successful and >>> unsuccessful jobs are attached. Only the ATOM GROUP in the input files was >>> altered. >>> I Changed the number of nodes, cores, and memory, but it didn't solve >>> the problem. >>> Any advice or tips on how to solve this issue would be greatly valued. >>> Best regards, >>> Lili >>> >>> On Tuesday, March 31, 2020 at 12:21:31 PM UTC-4 uca... at ucl.ac.uk wrote: >>> >>>> This bug has now been fixed in the latest development version of CP2K. >>>> See https://github.com/cp2k/cp2k/issues/847 >>>> >>>> >>>> >>>> On Thursday, 19 March 2020 18:31:58 UTC, Chris Ahart wrote: >>>>> >>>>> Dear all, >>>>> >>>>> When performing CDFT with Hirshfeld I am getting the following error: >>>>> "Program received signal SIGSEGV: Segmentation fault - invalid memory >>>>> reference." This appears to be an issue reported previously ( >>>>> https://github.com/cp2k/cp2k/issues/560), however I am encountering >>>>> it again in CP2K 7.1. This error occurs on both my local machine and on a >>>>> cluster. >>>>> >>>>> I have found this error to be sensitive to the system and to the atoms >>>>> included in &ATOM_GROUP, as for certain combinations of atoms CP2K runs >>>>> while with other combinations it crashes. Becke constraint runs in all >>>>> cases, so this is isolated to Hirshfeld. I have attached two example input >>>>> and output files, one with an atom combination that runs while another >>>>> which fails. I have confirmed that Hirshfeld runs for the input files >>>>> included in the CP2K CDFT tutorial. >>>>> >>>>> Any guidance or insight to resolve this problem would be greatly >>>>> appreciated. >>>>> >>>>> Thank you for your help and time. >>>>> >>>>> Regards, >>>>> Chris >>>>> >>>> -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/0224492e-965f-47d7-bd30-58dd66b63743n%40googlegroups.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: