[CP2K-user] [CP2K:20482] CP2K Restart
Niccolò Di Eugenio
niccolodieugenio at gmail.com
Mon Jul 22 15:49:45 UTC 2024
Hi all,
This was solved, thank you very much!
Niccolò
Il giorno lunedì 22 luglio 2024 alle 12:06:01 UTC+2 Krack Matthias ha
scritto:
> 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: *cp... at googlegroups.com <cp... at googlegroups.com> on behalf of
> Niccolò Di Eugenio <niccolod... at gmail.com>
> *Date: *Monday, 22 July 2024 at 11:49
> *To: *cp2k <cp... 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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