segmentation fault - hydrogen bonded system

m-ymgc m-y... at jcom.home.ne.jp
Tue Jul 30 02:41:12 CEST 2013


Thank you for your help. By removing the localization section the job 
worked fine but Wannier functions are necessary for simulation of 
vibrational spectra.
The problem was solved by tightening two epsilons in the QS section from 
1E-12 to 1E-14, I did not test this before posting this topic as I just 
thought these values are already small enough but actually their settings 
were crucial and larger values (e.g. 1E-10) made the job being stopped 
immediately.

Regards,

Makoto 

2013年7月27日土曜日 2時34分32秒 UTC+9 Matt W:
>
> This isn't an answer, but remove the localization stuff...and see if it 
> runs...
>
> Your (default) convergence criteria on the SCF is very loose - maybe 
> EPS_SCF 1.0E-6. You could have very large forces causing problems, though 
> with the tiny timestep, this would be unlikely.
>
> Also,using GAPW for this run, is maybe less tested.
>
> Basically debug. It is impossible to tell if it is a problem with the 
> stability of the trajectory, or something else from what you've sent.
>
> Matt
>
> On Thursday, 25 July 2013 00:03:27 UTC+1, m-ymgc wrote:
>>
>> Dear cp2k group members,
>>
>> Recently I got a problem with running MD simulations: I am using both 
>> locally compiled by gfortran and the OpenMP binary on linux x86-64 
>> machines. I am trying to do simulation of IR spectra of hydrogen bonded 
>> systems and the input files are based on the one listed in the recently 
>> uploaded document by Prof. Kirchner's group. The jobs stops after reaching 
>> certain geometries with segmentation fault. The error message also appears 
>> when I restart another MD run by setting the last geometry as an initial 
>> geometry in the input file.
>>
>> This is an input file
>>
>> &GLOBAL
>>   PROJECT t2w2
>>   PRINT_LEVEL LOW
>>   RUN_TYPE MD
>> &END GLOBAL
>> &FORCE_EVAL
>>   METHOD Quickstep
>>   &DFT
>>     BASIS_SET_FILE_NAME /home/yamaguti/cp2k-2.4/tests/QS/BASIS_MOLOPT
>>     POTENTIAL_FILE_NAME /home/yamaguti/cp2k-2.4/tests/QS/POTENTIAL
>>     &MGRID
>>       CUTOFF 280
>>       REL_CUTOFF 50
>>       NGRIDS 5
>>     &END MGRID
>>     &QS
>>       METHOD GAPW
>>       EPS_FILTER_MATRIX 1.0E-12
>>       EPS_PGF_ORB 1.0E-12
>>     &END QS
>>     &SCF
>>       SCF_GUESS ATOMIC
>>       MAX_SCF 200
>>       &OT
>>         MINIMIZER DIIS
>>         PRECONDITIONER FULL_ALL
>>       &END
>>       &PRINT
>>         &RESTART
>>           &EACH
>>             MD 0
>>           &END
>>         &END
>>       &END
>>     &END SCF
>>     &LOCALIZE
>>       METHOD JACOBI
>>       MAX_ITER 10000
>>       &PRINT
>>         &WANNIER_CENTERS 
>>           IONS+CENTERS
>>           FILENAME =t2w2_wannier.xyz
>>           &EACH
>>             MD 5
>>           &END
>>         &END
>>       &END
>>     &END
>>     &XC
>>       &XC_FUNCTIONAL PBE
>>       &END XC_FUNCTIONAL
>>       &XC_GRID
>>         XC_DERIV NN10_SMOOTH
>>         XC_SMOOTH_RHO NN10
>>       &END
>>       &VDW_POTENTIAL
>>         DISPERSION_FUNCTIONAL PAIR_POTENTIAL
>>         &PAIR_POTENTIAL
>>           TYPE DFTD3
>>           PARAMETER_FILE_NAME /home/yamaguti/cp2k-2.4/tests/QS/dftd3.dat
>>           REFERENCE_FUNCTIONAL PBE
>>         &END
>>       &END
>>     &END XC
>>   &END DFT
>>   &SUBSYS
>>     &CELL
>>       ABC 14.0 14.0 14.0
>>     &END
>>     &COORD
>>   S        -2.2142972451       -2.9301020672       -1.7868817159
>>   C        -4.1143788911       -2.9080311721       -1.6594602736
>>   O        -1.9603585719       -1.4223988788       -1.6100212352
>>   O        -1.9237112535       -3.4880179501       -3.1062952014
>>   O        -1.6837714859       -3.5669369762       -0.6059877320
>>   F        -4.6513022715       -4.0882072061       -1.9360349753
>>   F        -4.4128418293       -2.1216482404       -2.6635660253
>>   F        -4.5526869429       -2.4071250953       -0.5253867513
>>   S         1.3510503362        0.6035280707       -0.9906320418
>>   C         3.0771087088        1.2462159133       -0.7130631578
>>   O         0.6420948929        1.2841777235       -2.0646513289
>>   O         0.7294924782        0.5776620616        0.3056773055
>>   O         1.7707528694       -0.8416817161       -1.4049090763
>>   F         3.7739327792        0.5574724880        0.2158258484
>>   F         2.8850487080        2.5723123785       -0.2839271390
>>   F         3.8165588985        1.2238166764       -1.8889602835
>>   H        -1.5232549971       -0.1264383431       -4.2892222990
>>   O        -1.4908555749        0.2406897543       -3.4169473059
>>   H        -1.8478856441       -0.7667078085       -2.4042984017
>>   H        -0.6827635921        0.7757075991       -3.2751540434
>>   H         1.4792713316       -1.6202279080       -0.7424100509
>>   O         1.0009947110       -2.8892822226        0.0212840022
>>   H         1.5449312315       -3.7292092505        0.1226208428
>>   H         0.0649028840       -3.1917212778        0.0813336304
>>   &END
>>   &KIND H
>>    BASIS_SET DZVP-MOLOPT-SR-GTH
>>    POTENTIAL GTH-PBE-q1
>>   &END
>>   &KIND O
>>    BASIS_SET DZVP-MOLOPT-SR-GTH
>>    POTENTIAL GTH-PBE-q6
>>   &END
>>   &KIND C
>>    BASIS_SET DZVP-MOLOPT-SR-GTH
>>    POTENTIAL GTH-PBE-q4
>>   &END
>>   &KIND F
>>    BASIS_SET DZVP-MOLOPT-SR-GTH
>>    POTENTIAL GTH-PBE-q7
>>   &END
>>   &KIND S
>>    BASIS_SET DZVP-MOLOPT-SR-GTH
>>    POTENTIAL GTH-PBE-q6
>>   &END
>>   &END SUBSYS
>> &END FORCE_EVAL
>> &MOTION
>>  &MD
>>   ENSEMBLE NVT
>>   STEPS 20000
>>   TIMESTEP 0.25
>>   &THERMOSTAT
>>    REGION GLOBAL
>>    TYPE NOSE
>>    &NOSE
>>     TIMECON 100
>>    &END NOSE
>>   &END THERMOSTAT
>>   TEMPERATURE 300
>>  &END MD
>>  &PRINT
>>   &RESTART
>>    &EACH
>>     MD 1
>>    &END EACH
>>   &END RESTART
>>  &END PRINT
>> &END MOTION
>>
>> Following error messages appeared after the job by the precompiled binary.
>>
>> ----
>>
>> Program received signal SIGSEGV: Segmentation fault - invalid memory 
>> reference.
>>
>> Backtrace for this error:
>> #0  0x1DB74DD in _gfortrani_show_backtrace at backtrace.c:260
>> #1  0x1D93CA6 in _gfortrani_backtrace_handler at compile_options.c:129
>> #2  0x40BAEF in _L_unlock_16 at bar.c:0
>> #3  0x18384D8 in dgemm_
>> #4  0xB12748 in __ai_moments_MOD_contract_cossin at ai_moments.F:83
>> #5  0x11D9834 in __qs_loc_utils_MOD_get_berry_operator at 
>> qs_loc_utils.F:889
>> #6  0x11DCB54 in __qs_loc_utils_MOD_qs_loc_env_init at qs_loc_utils.F:653
>> #7  0x11DDA40 in __qs_loc_utils_MOD_qs_loc_init at qs_loc_utils.F:1407
>> #8  0x7DFDEF in __qs_scf_post_gpw_MOD_scf_post_calculation_gpw at 
>> qs_scf_post_gpw.F:460
>> #9  0x7BB735 in __qs_scf_MOD_scf at qs_scf.F:419
>> #10  0x69B434 in __qs_energy_MOD_qs_energies_scf at qs_energy.F:148
>> #11  0x6BA417 in __qs_force_MOD_qs_forces at qs_force.F:233
>> #12  0x4740D9 in __force_env_methods_MOD_force_env_calc_energy_force at 
>> force_env_methods.F:244
>> #13  0x5AC7F5 in __md_run_MOD_qs_mol_dyn_low at md_run.F:366
>> #14  0x5ADAC6 in __md_run_MOD_qs_mol_dyn at md_run.F:152
>> #15  0x4133F3 in __cp2k_runs_MOD_cp2k_run at cp2k_runs.F:397
>> #16  0x416F6B in __cp2k_runs_MOD_run_input at cp2k_runs.F:1161
>> #17  0x40D7B7 in cp2k at cp2k.F:307
>>
>> Best regards,
>>
>> Makoto Yamaguchi
>> Fuel Cell Cutting-edge Research Center, Tokyo, Japan
>>
>>
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