<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <meta name="Generator" content="Microsoft Word 15 (filtered medium)"> <style></style> </head> <body lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"> <div class="WordSection1"> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Hi <o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Check your coordinate file and make sure that it fits the MULTIPLE_UNIT_CELLS keyword. Note, that the atomic coordinates from a run using MULTIPLE_UNIT_CELLS are expanded by CP2K to the full set. I guess that you will have to remove/comment the MULTIPLE_UNIT_CELL keyword to get it work.<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">HTH<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Matthias<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <div id="mail-editor-reference-message-container"> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <b><span style="color:black">From: </span></b><span style="color:black">cp2k@googlegroups.com <cp2k@googlegroups.com> on behalf of Niccolò Di Eugenio <niccolodieugenio@gmail.com><br> <b>Date: </b>Monday, 22 July 2024 at 11:08<br> <b>To: </b>cp2k <cp2k@googlegroups.com><br> <b>Subject: </b>Re: [CP2K:20474] CP2K Restart<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Hi,<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">This is the input file I am using:<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">&FORCE_EVAL<br> <br> &PRINT<br> &FORCES<br> <br> &END FORCES<br> <br> &END PRINT<br> METHOD Quickstep<br> &DFT<br> BASIS_SET_FILE_NAME BASIS_MOLOPT_UZH<br> POTENTIAL_FILE_NAME GTH_POTENTIALS<br> &POISSON<br> POISSON_SOLVER PERIODIC<br> PERIODIC XYZ<br> &END POISSON<br> <br> &MGRID<br> NGRIDS 5<br> CUTOFF 400<br> REL_CUTOFF 80<br> <br> &END MGRID<br> &QS<br> METHOD GPW<br> EPS_PGF_ORB 1E-16<br> <br> &END QS<br> &SCF<br> &SMEAR ON<br> ELECTRONIC_TEMPERATURE 2000<br> METHOD FERMI_DIRAC<br> &END SMEAR<br> ADDED_MOS 2000<br> CHOLESKY INVERSE<br> SCF_GUESS RESTART<br> EPS_SCF 1.0E-6<br> MAX_SCF 200<br> <br> &DIAGONALIZATION ON<br> ALGORITHM STANDARD<br> &END DIAGONALIZATION<br> &MIXING T<br> METHOD BROYDEN_MIXING<br> ALPHA 0.2<br> BETA 1.5<br> NBUFFER 15<br> <br> &END MIXING<br> <br> &END SCF<br> &XC<br> &XC_FUNCTIONAL PBE<br> &END XC_FUNCTIONAL<br> &END XC<br> <br> &END DFT<br> &SUBSYS<br> <br> &TOPOLOGY<br> MULTIPLE_UNIT_CELL 4 4 4<br> COORD_FILE_FORMAT XYZ<br> COORD_FILE Ba2Y1Cu3O6_mp-1021507.xyz<br> &END TOPOLOGY<br> &CELL<br> MULTIPLE_UNIT_CELL 4 4 4<br> SYMMETRY CUBIC<br> ABC 3.886234 3.911377 11.840840<br> PERIODIC XYZ<br> &END CELL<br> &KIND Ba<br> BASIS_SET DZVP-MOLOPT-PBE-GTH-q10<br> POTENTIAL GTH-PBE-q10<br> &END KIND<br> &KIND Y<br> BASIS_SET DZVP-MOLOPT-PBE-GTH-q11<br> POTENTIAL GTH-PBE-q11<br> &END KIND<br> &KIND Cu<br> BASIS_SET DZVP-MOLOPT-PBE-GTH-q11<br> POTENTIAL GTH-PBE-q11<br> &END KIND<br> &KIND O<br> BASIS_SET DZVP-MOLOPT-PBE-GTH-q6<br> POTENTIAL GTH-PBE-q6<br> &END KIND<br> &PRINT<br> &CELL HIGH<br> <br> &END CELL<br> &END PRINT<br> <br> &END SUBSYS<br> STRESS_TENSOR ANALYTICAL<br> <br> &END FORCE_EVAL<br> &GLOBAL<br> PROJECT BaYCuOopt<br> RUN_TYPE CELL_OPT<br> PRINT_LEVEL MEDIUM<br> PREFERRED_DIAG_LIBRARY SL<br> <br> &END GLOBAL<br> <br> &MOTION<br> <br> &CELL_OPT<br> <br> KEEP_SYMMETRY .TRUE.<br> OPTIMIZER BFGS<br> KEEP_ANGLES<br> EXTERNAL_PRESSURE 1 0 0 0 1 0 0 0 1<br> <br> &END CELL_OPT<br> <br> &END MOTION<br> <br> Are there any mistakes here? It was working fine before introducing the restart.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Niccolò <o:p></o:p></p> </div> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Il giorno lunedì 22 luglio 2024 alle 11:04:37 UTC+2 Krack Matthias ha scritto:<o:p></o:p></p> </div> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt">Hi</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">There seems to be a problem reading the atomic coordinates. However, without further information, it is difficult to give further guidance.</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Best</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p> </div> </div> <div> <div> <div> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt;margin-left:72.0pt"> <b><span style="color:black">From: </span></b><span style="color:black"><span class="MsoHyperlink">cp...@googlegroups.com</span> <<span class="MsoHyperlink">cp...@googlegroups.com</span>> on behalf of Niccolò Di Eugenio <<span class="MsoHyperlink">niccolod...@gmail.com</span>><br> <b>Date: </b>Monday, 22 July 2024 at 10:45<br> <b>To: </b>cp2k <<span class="MsoHyperlink">cp...@googlegroups.com</span>><br> <b>Subject: </b>[CP2K:20471] CP2K Restart</span><o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> Dear all, <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> I am trying to restart a DFT calculation. I am currently doing so by running the .restart file instead of the .inp file, as:<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> srun /project/ML_YBCO/nic/cp2k/exe/CRAY-XC50-gcc/cp2k.psmp BaYCuOopt-1_8.restart > Ba2Y1Cu3O6_mp-1021507.out<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> However, I am getting the following error:<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> Rank 0 [Sat Jul 20 21:02:42 2024] [c0-0c0s1n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0<br> <br> Program received signal SIGABRT: Process abort signal.<br> <br> Backtrace for this error:<br> #0 0x7fffeb5b849f in ???<br> #1 0x7fffeb5b8420 in ???<br> #2 0x7fffeb5b9a00 in ???<br> #3 0x7fffecb8a267 in ???<br> #4 0x7fffeca975e5 in ???<br> #5 0x7fffecadea84 in ???<br> #6 0x20d10af in __message_passing_MOD_mp_abort<br> at /project/ML_YBCO/nic/cp2k/src/mpiwrap/message_passing.F:1270<br> #7 0x20d3d24 in __base_hooks_MOD_cp_abort<br> at /project/ML_YBCO/nic/cp2k/obj/CRAY-XC50-gcc/psmp/base_hooks.F90:76<br> #8 0x20d3ed0 in __base_hooks_MOD_cp__a<br> at /project/ML_YBCO/nic/cp2k/obj/CRAY-XC50-gcc/psmp/base_hooks.F90:163<br> #9 0xba743b in __atoms_input_MOD_read_atoms_input<br> at /project/ML_YBCO/nic/cp2k/src/atoms_input.F:122<br> #10 0x7b82c0 in coordinate_control<br> at /project/ML_YBCO/nic/cp2k/src/topology.F:588<br> #11 0x7b82c0 in __topology_MOD_topology_control<br> at /project/ML_YBCO/nic/cp2k/src/topology.F:197<br> #12 0xa49e9c in __cp_subsys_methods_MOD_cp_subsys_create<br> at /project/ML_YBCO/nic/cp2k/src/cp_subsys_methods.F:161<br> #13 0x90b5fa in __qs_subsys_methods_MOD_qs_subsys_create<br> at /project/ML_YBCO/nic/cp2k/src/qs_subsys_methods.F:98<br> #14 0x8d2610 in __qs_environment_MOD_qs_init<br> at /project/ML_YBCO/nic/cp2k/src/qs_environment.F:317<br> #15 0xafbda4 in __f77_interface_MOD_create_force_env<br> at /project/ML_YBCO/nic/cp2k/src/f77_interface.F:805<br> #16 0x410d22 in cp2k_run<br> at /project/ML_YBCO/nic/cp2k/src/start/cp2k_runs.F:314<br> #17 0x41464e in __cp2k_runs_MOD_run_input<br> at /project/ML_YBCO/nic/cp2k/src/start/cp2k_runs.F:983<br> #18 0x40b4c6 in cp2k<br> at /project/ML_YBCO/nic/cp2k/src/start/cp2k.F:379<br> #19 0x40988c in main<br> at /project/ML_YBCO/nic/cp2k/obj/CRAY-XC50-gcc/psmp/cp2k.F90:44<br> srun: error: nid00007: task 0: Aborted<br> srun: launch/slurm: _step_signal: Terminating StepId=1303919.0<br> slurmstepd: error: *** STEP 1303919.0 ON nid00007 CANCELLED AT 2024-07-20T21:02:43 ***<br> srun: error: nid00007: task 1: Terminated<br> srun: error: nid00008: tasks 2-3: Terminated<br> srun: Force Terminated StepId=1303919.0<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> How could I solve this? Thank you very much.<o:p></o:p></p> </div> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <span class="MsoHyperlink">cp2k+uns...@googlegroups.com</span>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/d488ed99-a3a2-446a-b2bc-f21abb9865bbn%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank"> https://groups.google.com/d/msgid/cp2k/d488ed99-a3a2-446a-b2bc-f21abb9865bbn%40googlegroups.com</a>.<o:p></o:p></p> </div> </div> </div> </div> </blockquote> </div> <p class="MsoNormal" style="margin-left:36.0pt">-- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/78230b66-fb84-4739-b3cf-8fb4891ac81bn%40googlegroups.com?utm_medium=email&utm_source=footer"> https://groups.google.com/d/msgid/cp2k/78230b66-fb84-4739-b3cf-8fb4891ac81bn%40googlegroups.com</a>.<o:p></o:p></p> </div> </div> </div> </body> </html> <p></p> -- <br /> You received this message because you are subscribed to the Google Groups "cp2k" group.<br /> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br /> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/ZRAP278MB08274557A85F488DF791DB97F4A82%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/ZRAP278MB08274557A85F488DF791DB97F4A82%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM</a>.<br />