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

Niccolò Di Eugenio niccolodieugenio at gmail.com
Mon Jul 22 09:49:24 UTC 2024


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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