[CP2K-user] [CP2K:20478] CP2K Restart

Krack Matthias matthias.krack at psi.ch
Mon Jul 22 10:05:35 UTC 2024


Can you try to comment the lines COORD_FILE_NAME and COORD_FILE_FORMAT in the .restart file?
Maybe, I am mistaken and the .restart file does not work in all cases as is.

From: cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Niccolò Di Eugenio <niccolodieugenio at gmail.com>
Date: Monday, 22 July 2024 at 11:49
To: cp2k <cp2k at googlegroups.com>
Subject: Re: [CP2K:20478] CP2K Restart
Hi,
I did not, this is how it came out. The files in my folder are:
Ba2Y1Cu3O6_mp-1021507.inp  Ba2Y1Cu3O6.sh          BaYCuOopt-1_3.restart  BaYCuOopt-1_6.restart  BaYCuOopt-1.restart        BaYCuOopt-pos-1.xyz          template.inp
Ba2Y1Cu3O6_mp-1021507.out  BaYCuOopt-1_1.restart  BaYCuOopt-1_4.restart  BaYCuOopt-1_7.restart  BaYCuOopt-1.restart.bak-1  BaYCuOopt-RESTART.wfn
Ba2Y1Cu3O6_mp-1021507.xyz  BaYCuOopt-1_2.restart  BaYCuOopt-1_5.restart  BaYCuOopt-1_8.restart  BaYCuOopt-BFGS.Hessian     BaYCuOopt-RESTART.wfn.bak-1
And I am running the BaYCuOopt-1_8.restart with the command srun /project/ML_YBCO/nic/cp2k/exe/CRAY-XC50-gcc/cp2k.psmp BaYCuOopt-1_8.restart > Ba2Y1Cu3O6_mp-1021507.out

Niccolò

Il giorno lunedì 22 luglio 2024 alle 11:37:46 UTC+2 Krack Matthias ha scritto:
The .restart file written by CP2K should run as is. Did you change that file by hand?

From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Niccolò Di Eugenio <niccolod... at gmail.com>
Date: Monday, 22 July 2024 at 11:28
To: cp2k <cp... at googlegroups.com>
Subject: Re: [CP2K:20476] CP2K Restart
Hi all and thanks Mr. Krack for your kind response,
I am sorry: that was the input file used to run the cp2k calculation before the HPC wall time. When restarting, I am calling the .restart file that looks like this:

# Version information for this restart file
 # current date 2024-07-17 19:40:31.049
 # current working dir /project/ML_YBCO/nic/cp2k/YBCO/Ba2Y1Cu3O6_mp-1021507
 # Program compiled at                              Tue Jul  9 18:29:51 JST 2024
 # Program compiled on                                                      csc3
 # Program compiled for                                            CRAY-XC50-gcc
 # Source code revision number                                       git:b4a17a5
 &GLOBAL
   PREFERRED_DIAG_LIBRARY SCALAPACK
   PRINT_LEVEL MEDIUM
   PROJECT_NAME "BaYCuOopt"
   RUN_TYPE CELL_OPT
 &END GLOBAL
 &MOTION
   &CELL_OPT
     OPTIMIZER BFGS
     STEP_START_VAL 8
     EXTERNAL_PRESSURE  1.0000000000000000E+000  0.0000000000000000E+000  0.0000000000000000E+000  0.0000000000000000E+000 \
       1.0000000000000000E+000  0.0000000000000000E+000  0.0000000000000000E+000  0.0000000000000000E+000  1.0000000000000000E+000
     KEEP_ANGLES T
     KEEP_SYMMETRY T
   &END CELL_OPT
 &END MOTION
 &FORCE_EVAL
   METHOD QS
   STRESS_TENSOR ANALYTICAL
   &DFT
     BASIS_SET_FILE_NAME BASIS_MOLOPT_UZH
     POTENTIAL_FILE_NAME GTH_POTENTIALS
     &SCF
       MAX_SCF 200
       EPS_SCF  9.9999999999999995E-007
       CHOLESKY INVERSE
       SCF_GUESS ATOMIC
       ADDED_MOS 2000
       &DIAGONALIZATION T
         ALGORITHM STANDARD
       &END DIAGONALIZATION
       &SMEAR T
         METHOD FERMI_DIRAC
         ELECTRONIC_TEMPERATURE  2.0000000000000000E+003
       &END SMEAR
       &MIXING T
         METHOD BROYDEN_MIXING
         ALPHA  2.0000000000000001E-001
         BETA  1.5000000000000000E+000
         NBUFFER 15
       &END MIXING
     &END SCF
     &QS
       EPS_PGF_ORB  9.9999999999999998E-017
       METHOD GPW
     &END QS
     &MGRID
       NGRIDS 5
       CUTOFF  4.0000000000000000E+002
REL_CUTOFF  8.0000000000000000E+001
     &END MGRID
     &XC
       DENSITY_CUTOFF  1.0000000000000000E-010
       GRADIENT_CUTOFF  1.0000000000000000E-010
       TAU_CUTOFF  1.0000000000000000E-010
       &XC_FUNCTIONAL NO_SHORTCUT
         &PBE T
         &END PBE
       &END XC_FUNCTIONAL
     &END XC
     &POISSON
       POISSON_SOLVER PERIODIC
       PERIODIC XYZ
     &END POISSON
   &END DFT
   &SUBSYS
     &CELL
       A  2.8184601333333330E+001  0.0000000000000000E+000  0.0000000000000000E+000
       B  0.0000000000000000E+000  2.8184601333333330E+001  0.0000000000000000E+000
       C  0.0000000000000000E+000  0.0000000000000000E+000  2.8184601333333330E+001
       PERIODIC XYZ
       MULTIPLE_UNIT_CELL 1 1 1
       SYMMETRY CUBIC
     &END CELL
     &COORD
       Ba  2.0881355223116063E+000  2.1081336076904886E+000  1.0731644357464377E+001
       Ba  2.1105353811046417E+000  2.1050866536731037E+000  1.9416636361470143E+000
       Y  2.0978449531699890E+000  2.0865232904996378E+000  6.5189374554766406E+000
       Cu -8.5497041237671094E-003 -5.2291919964740198E-003  8.2677063595696030E+000
       Cu -6.1654838371616076E-003 -2.5558110197782817E-003  4.6274667132335576E+000
       Cu  7.2188942183468640E-003 -1.5860703738888510E-002 -2.0735700509928981E-001
       O -9.2063279084127236E-004  2.1144441548333401E+000 -1.0811122621217063E-001
       O  2.0922308957407263E+000  1.1438570991530483E-002  7.9708449287024701E+000
       O  2.0919516195129284E+000  8.4705075099355594E-003  4.8674895316140319E+000
       O -1.4222229365387621E-002  2.1116784982821857E+000  7.8242627460067347E+000
       O  7.0885470607998362E-003 -1.0359230964127018E-003  1.0562381339474765E+001
       O  5.3226273407098415E-004  3.5207032981484435E-003  2.2767440065454108E+000

        [...]

&END COORD
     &KIND "Ba"
       BASIS_SET "DZVP-MOLOPT-PBE-GTH-q10"
       POTENTIAL "GTH-PBE-q10"
       &POTENTIAL
         4 6
           5.4000000000000004E-001 2  2.4526780700000000E+001 -2.4686700099999999E+000
         4
           4.9206839000000002E-001 2  9.5150929999999995E-002  1.1693184000000001E+000
                                                              -1.5095835700000000E+000
           3.9148929999999998E-001 2  8.0018261000000002E-001 -1.6168390699999999E+000
                                                               1.9130697900000000E+000
           6.7217347999999999E-001 1  3.8853100000000002E-001
           3.0049773000000002E-001 1 -1.9653794520000002E+001
         # Potential name: GTH-PBE-Q10 for element symbol: BA
         # Potential read from the potential filename: GTH_POTENTIALS
       &END POTENTIAL
     &END KIND
     &KIND "Y"
       BASIS_SET "DZVP-MOLOPT-PBE-GTH-q11"
       POTENTIAL "GTH-PBE-q11"
       &POTENTIAL
         4 6 1
           4.7499999999999998E-001 2  1.2167769040000000E+001 -2.3285510299999999E+000
         3
           2.4674070000000001E-001 2  2.3450271950000001E+001 -8.3253574799999992E+000
                                                               1.0747990290000001E+001
           2.9656397000000001E-001 2  5.9786340100000004E+000 -5.8523496399999999E+000
                                                               6.9245934800000004E+000
           4.5045569000000002E-001 2  1.1874904799999999E+000 -1.3186733100000001E+000
                                                               1.4952349899999999E+000
         # Potential name: GTH-PBE-Q11 for element symbol: Y
         # Potential read from the potential filename: GTH_POTENTIALS
       &END POTENTIAL
     &END KIND
     &KIND "Cu"
       BASIS_SET "DZVP-MOLOPT-PBE-GTH-q11"
       POTENTIAL "GTH-PBE-q11"
       &POTENTIAL
         1 0 10
           5.3000000000000003E-001 0
         3
           4.3135505000000002E-001 3  9.6938050699999998E+000 -6.4701653500000003E+000  1.9359521500000001E+000
                                                               1.1501773960000000E+001 -4.9986069600000000E+000
                                                                                        3.9675212700000002E+000
           5.6139154999999996E-001 2  2.5454732999999998E+000 -7.8463572999999998E-001
                                                               9.2839351999999997E-001
           2.6455485000000001E-001 1 -1.2828614060000000E+001
         # Potential name: GTH-PBE-Q11 for element symbol: CU
         # Potential read from the potential filename: GTH_POTENTIALS
       &END POTENTIAL
     &END KIND
     &KIND "O"
       BASIS_SET "DZVP-MOLOPT-PBE-GTH-q6"
       POTENTIAL "GTH-PBE-q6"
       &POTENTIAL
2 4
           2.4455430000000000E-001 2 -1.6667214800000000E+001  2.4873113199999999E+000
         2
           2.2095592000000000E-001 1  1.8337458110000000E+001
           2.1133246999999999E-001 0
         # Potential name: GTH-PBE-Q6 for element symbol: O
         # Potential read from the potential filename: GTH_POTENTIALS
       &END POTENTIAL
     &END KIND
     &TOPOLOGY
       COORD_FILE_NAME Ba2Y1Cu3O6_mp-1021507.xyz
       COORD_FILE_FORMAT XYZ
       NUMBER_OF_ATOMS 768
       MULTIPLE_UNIT_CELL 1 1 1
     &END TOPOLOGY
     &PRINT
       &CELL HIGH
       &END CELL
     &END PRINT
   &END SUBSYS
   &PRINT
     &FORCES SILENT
     &END FORCES
   &END PRINT
 &END FORCE_EVAL

Should I follow the same advice you gave me before?
Thanks again,

Niccolò Di Eugenio


Il giorno lunedì 22 luglio 2024 alle 11:17:04 UTC+2 Krack Matthias ha scritto:

Hi



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.



HTH



Matthias



From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Niccolò Di Eugenio <niccolod... at gmail.com>
Date: Monday, 22 July 2024 at 11:08
To: cp2k <cp... at googlegroups.com>
Subject: Re: [CP2K:20474] CP2K Restart

Hi,

This is the input file I am using:



&FORCE_EVAL

&PRINT
&FORCES

&END FORCES

&END PRINT
  METHOD Quickstep
  &DFT
    BASIS_SET_FILE_NAME BASIS_MOLOPT_UZH
    POTENTIAL_FILE_NAME GTH_POTENTIALS
     &POISSON
                POISSON_SOLVER PERIODIC
                PERIODIC XYZ
                &END POISSON

 &MGRID
      NGRIDS 5
      CUTOFF 400
                REL_CUTOFF 80

    &END MGRID
    &QS
      METHOD GPW
      EPS_PGF_ORB 1E-16

    &END QS
    &SCF
      &SMEAR ON
      ELECTRONIC_TEMPERATURE 2000
      METHOD FERMI_DIRAC
      &END SMEAR
      ADDED_MOS 2000
      CHOLESKY INVERSE
      SCF_GUESS RESTART
      EPS_SCF 1.0E-6
      MAX_SCF 200

      &DIAGONALIZATION  ON
              ALGORITHM STANDARD
            &END DIAGONALIZATION
            &MIXING  T
                    METHOD BROYDEN_MIXING
                    ALPHA 0.2
                                    BETA 1.5
                    NBUFFER 15

                   &END MIXING

    &END SCF
    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
    &END XC

  &END DFT
  &SUBSYS

    &TOPOLOGY
MULTIPLE_UNIT_CELL 4 4 4
COORD_FILE_FORMAT XYZ
COORD_FILE Ba2Y1Cu3O6_mp-1021507.xyz
    &END TOPOLOGY
    &CELL
MULTIPLE_UNIT_CELL 4 4 4
    SYMMETRY CUBIC
      ABC 3.886234 3.911377 11.840840
      PERIODIC XYZ
    &END CELL
    &KIND Ba
        BASIS_SET DZVP-MOLOPT-PBE-GTH-q10
        POTENTIAL GTH-PBE-q10
      &END KIND
      &KIND Y
        BASIS_SET DZVP-MOLOPT-PBE-GTH-q11
        POTENTIAL GTH-PBE-q11
      &END KIND
      &KIND Cu
        BASIS_SET DZVP-MOLOPT-PBE-GTH-q11
        POTENTIAL GTH-PBE-q11
      &END KIND
      &KIND O
        BASIS_SET DZVP-MOLOPT-PBE-GTH-q6
        POTENTIAL GTH-PBE-q6
      &END KIND
&PRINT
&CELL HIGH

&END CELL
&END PRINT

  &END SUBSYS
  STRESS_TENSOR ANALYTICAL

&END FORCE_EVAL
&GLOBAL
  PROJECT     BaYCuOopt
  RUN_TYPE    CELL_OPT
  PRINT_LEVEL MEDIUM
PREFERRED_DIAG_LIBRARY SL

  &END GLOBAL

&MOTION

                &CELL_OPT

                KEEP_SYMMETRY .TRUE.
                OPTIMIZER BFGS
                KEEP_ANGLES
                EXTERNAL_PRESSURE 1 0 0 0 1 0 0 0 1

                &END CELL_OPT

&END MOTION

Are there any mistakes here? It was working fine before introducing the restart.



Niccolò

Il giorno lunedì 22 luglio 2024 alle 11:04:37 UTC+2 Krack Matthias ha scritto:

Hi



There seems to be a problem reading the atomic coordinates. However, without further information, it is difficult to give further guidance.



Best



Matthias



From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Niccolò Di Eugenio <niccolod... at gmail.com>
Date: Monday, 22 July 2024 at 10:45
To: cp2k <cp... at googlegroups.com>
Subject: [CP2K:20471] CP2K Restart

Dear all,

I am trying to restart a DFT calculation. I am currently doing so by running the .restart file instead of the .inp file, as:



srun /project/ML_YBCO/nic/cp2k/exe/CRAY-XC50-gcc/cp2k.psmp BaYCuOopt-1_8.restart > Ba2Y1Cu3O6_mp-1021507.out



However, I am getting the following error:



Rank 0 [Sat Jul 20 21:02:42 2024] [c0-0c0s1n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:
#0  0x7fffeb5b849f in ???
#1  0x7fffeb5b8420 in ???
#2  0x7fffeb5b9a00 in ???
#3  0x7fffecb8a267 in ???
#4  0x7fffeca975e5 in ???
#5  0x7fffecadea84 in ???
#6  0x20d10af in __message_passing_MOD_mp_abort
        at /project/ML_YBCO/nic/cp2k/src/mpiwrap/message_passing.F:1270
#7  0x20d3d24 in __base_hooks_MOD_cp_abort
        at /project/ML_YBCO/nic/cp2k/obj/CRAY-XC50-gcc/psmp/base_hooks.F90:76
#8  0x20d3ed0 in __base_hooks_MOD_cp__a
        at /project/ML_YBCO/nic/cp2k/obj/CRAY-XC50-gcc/psmp/base_hooks.F90:163
#9  0xba743b in __atoms_input_MOD_read_atoms_input
        at /project/ML_YBCO/nic/cp2k/src/atoms_input.F:122
#10  0x7b82c0 in coordinate_control
        at /project/ML_YBCO/nic/cp2k/src/topology.F:588
#11  0x7b82c0 in __topology_MOD_topology_control
        at /project/ML_YBCO/nic/cp2k/src/topology.F:197
#12  0xa49e9c in __cp_subsys_methods_MOD_cp_subsys_create
        at /project/ML_YBCO/nic/cp2k/src/cp_subsys_methods.F:161
#13  0x90b5fa in __qs_subsys_methods_MOD_qs_subsys_create
        at /project/ML_YBCO/nic/cp2k/src/qs_subsys_methods.F:98
#14  0x8d2610 in __qs_environment_MOD_qs_init
        at /project/ML_YBCO/nic/cp2k/src/qs_environment.F:317
#15  0xafbda4 in __f77_interface_MOD_create_force_env
        at /project/ML_YBCO/nic/cp2k/src/f77_interface.F:805
#16  0x410d22 in cp2k_run
        at /project/ML_YBCO/nic/cp2k/src/start/cp2k_runs.F:314
#17  0x41464e in __cp2k_runs_MOD_run_input
        at /project/ML_YBCO/nic/cp2k/src/start/cp2k_runs.F:983
#18  0x40b4c6 in cp2k
        at /project/ML_YBCO/nic/cp2k/src/start/cp2k.F:379
#19  0x40988c in main
        at /project/ML_YBCO/nic/cp2k/obj/CRAY-XC50-gcc/psmp/cp2k.F90:44
srun: error: nid00007: task 0: Aborted
srun: launch/slurm: _step_signal: Terminating StepId=1303919.0
slurmstepd: error: *** STEP 1303919.0 ON nid00007 CANCELLED AT 2024-07-20T21:02:43 ***
srun: error: nid00007: task 1: Terminated
srun: error: nid00008: tasks 2-3: Terminated
srun: Force Terminated StepId=1303919.0



How could I solve this? Thank you very much.

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