CP2K running slow

Tanmoy Paul tanmo... at gmail.com
Tue Oct 28 14:20:07 UTC 2014


 Thanks Samuel for a quick reply. Here is the input file.............
&FORCE_EVAL
 METHOD QMMM
  &DFT
   CHARGE 0
   BASIS_SET_FILE_NAME ../BASIS_SET
   BASIS_SET_FILE_NAME ../BASIS_MOLOPT
   POTENTIAL_FILE_NAME  ../POTENTIAL
   
   &MGRID
    COMMENSURATE
    CUTOFF 250
   &END MGRID
   &QS
    EXTRAPOLATION PS
    EXTRAPOLATION_ORDER 3
    METHOD GPW
    PW_GRID NS-FULLSPACE
   &END QS
   &SCF 
    SCF_GUESS ATOMIC
    MAX_SCF 300
    EPS_SCF 1.0E-06
    &OUTER_SCF
     EPS_SCF 1.0E-06
     MAX_SCF 20
    &END OUTER_SCF
    &OT
     PRECONDITIONER FULL_ALL
     ENERGY_GAP 0.001
     MINIMIZER CG
    &END OT
   &END SCF
   &POISSON                
    POISSON_SOLVER PERIODIC 
    PERIODIC XYZ             
   &END POISSON             
   &XC
    &XC_GRID
     XC_SMOOTH_RHO NN10
     XC_DERIV SPLINE2_SMOOTH
    &END XC_GRID
    &XC_FUNCTIONAL BLYP
    &END XC_FUNCTIONAL 
   &END XC
  &END DFT
  &MM
   &FORCEFIELD
    PARMTYPE CHM
    PARM_FILE_NAME par_all27_prot_lipid.inp 
      EI_SCALE14 1.0
      VDW_SCALE14 1.0
      &SPLINE
        EMAX_SPLINE 5.00000000E-01
        RCUT_NB 15.0         
      &END SPLINE 
    &END FORCEFIELD
    &POISSON
     &EWALD
      EWALD_TYPE PME
      ALPHA 0.20
      GMAX 100
      RCUT 15.0
     &END EWALD
    &END POISSON
  &END MM
  &QMMM
    &CELL
      ABC 20.0 20.0 20.0
    &END CELL
    E_COUPL GAUSS 
    &INTERPOLATOR 
      EPS_R 1.0e-15
      EPS_X 1.0e-15
      MAXITER 100 
    &END INTERPOLATOR
    &PERIODIC
     GMAX 1.0
     &MULTIPOLE ON
      ANALYTICAL_GTERM TRUE
      NGRIDS 60 60 60
      RCUT 50.0
     &END MULTIPOLE
    &END PERIODIC
    &PRINT
      &PERIODIC_INFO
      &END PERIODIC_INFO
      &POTENTIAL
      &END POTENTIAL
    &END PRINT
    &QM_KIND H
      MM_INDEX 43 42 46 48 56 58 54 52 73 74 77 79
      MM_INDEX 82 84 86 941 942 946 947 967 969  
      MM_INDEX 971 962 963 1014 1015 1010 1009 1398 
      MM_INDEX 1399 1393 1394 1427 1428 1436 1430  
      MM_INDEX 1433 1473 1464 1465 1467 1470 1820  
      MM_INDEX 1818 1816 1811 1812 3040 3038 3054
      MM_INDEX 3052 25438 25437 41848 41847 11184  
      MM_INDEX 11185 45760 45759 10410 10411 4078 
      MM_INDEX 4077 4093 4092 4075 4074 
    &END QM_KIND
    &QM_KIND O
      MM_INDEX 81 944 1012 1396 3039 3053 11183  
      MM_INDEX 41846 25436 10409 4076 4091 4073 
      MM_INDEX 45758
    &END QM_KIND
    &QM_KIND C      
      MM_INDEX 41 44 45 49 55 57 53 51 50 72 75 76 
      MM_INDEX 78 80 85 83 943 940 961 965 970 966 
      MM_INDEX 1008 1011 1395 1392 1426 1431 1432  
      MM_INDEX 1435 1472 1468 1469 1815 1819 1814  
      MM_INDEX 1810 3037 3051 1463 
    &END QM_KIND
    &QM_KIND N
      MM_INDEX 47 945 968 964 1013 1397 1434 1429  
      MM_INDEX 1466 1817 1813 1471
    &END QM_KIND
    &QM_KIND ZN 
     MM_INDEX 4072
    &END QM_KIND
    &LINK
     MM_INDEX 39
     QM_INDEX 41
     QM_KIND H
     ALPHA_IMOMM 1.322 
    &END LINK
    &LINK
     MM_INDEX 70
     QM_INDEX 72
     QM_KIND H
     ALPHA_IMOMM 1.363
    &END LINK
    &LINK
     MM_INDEX 938
     QM_INDEX 940
     QM_KIND H
     ALPHA_IMOMM 1.369
    &END LINK
    &LINK
     MM_INDEX 959
     QM_INDEX 961
     QM_KIND H
     ALPHA_IMOMM 1.423
    &END LINK
    &LINK
     MM_INDEX 1006
     QM_INDEX 1008
     QM_KIND H
     ALPHA_IMOMM 1.407
    &END LINK 
    &LINK
     MM_INDEX 1389
     QM_INDEX 1392
     QM_KIND H
     ALPHA_IMOMM 1.290
    &END LINK
    &LINK
     MM_INDEX 1424
     QM_INDEX 1426
     QM_KIND H
     ALPHA_IMOMM 1.411
    &END LINK
    &LINK
     MM_INDEX 1461
     QM_INDEX 1463
     QM_KIND H
     ALPHA_IMOMM 1.286
    &END LINK
    &LINK
     MM_INDEX 1808
     QM_INDEX 1810
     QM_KIND H
     ALPHA_IMOMM 1.454
    &END LINK
    &LINK
     MM_INDEX 3041
     QM_INDEX 3037
     QM_KIND H
     ALPHA_IMOMM 1.373
    &END LINK
    &LINK
     MM_INDEX 3035
     QM_INDEX 3037
     QM_KIND H
     ALPHA_IMOMM 1.391
    &END LINK
    &LINK
     MM_INDEX 3055
     QM_INDEX 3051
     QM_KIND H
     ALPHA_IMOMM 1.378
    &END LINK
    &LINK
     MM_INDEX 3049
     QM_INDEX 3051
     QM_KIND H
     ALPHA_IMOMM 1.387
    &END LINK
  &END QMMM 
  &SUBSYS
    &CELL
      ABC 77.18 74.44 85.17
      PERIODIC XYZ
    &END CELL
    &KIND H
      BASIS_SET DZVP-GTH-BLYP
      POTENTIAL GTH-BLYP-q1 
    &END KIND
    &KIND O
      BASIS_SET DZVP-GTH-BLYP
      POTENTIAL GTH-BLYP-q6
    &END KIND
    &KIND C
      BASIS_SET DZVP-GTH-BLYP
      POTENTIAL GTH-BLYP-q4
    &END KIND
    &KIND N
      BASIS_SET DZVP-GTH-BLYP
      POTENTIAL GTH-BLYP-q5
    &END KIND
    &KIND ZN
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-BLYP-q12
    &END KIND
    &TOPOLOGY
     CONN_FILE_FORMAT UPSF
     CONN_FILE_NAME HCA_in_final.psf
     COORD_FILE_FORMAT PDB
     COORD_FILE_NAME HCA_no_co2_cp2k.pdb
    &END TOPOLOGY
  &END SUBSYS
&END FORCE_EVAL
&GLOBAL
  PROJECT HCA_qmmm_min_cp2k_no_co2
  PRINT_LEVEL MEDIUM
  RUN_TYPE MD
&END GLOBAL
&MOTION
  &MD
    ENSEMBLE NVE
    STEPS 50000
    TIMESTEP 0.5
    TEMPERATURE 310
   &THERMOSTAT 
    REGION GLOBAL
    TYPE NOSE
    &NOSE
    LENGTH 4
    YOSHIDA 9
    TIMECON 1000
    &END NOSE
   &END THERMOSTAT
   &PRINT
      &ENERGY
        &EACH
          MD 1
        &END EACH
      &END ENERGY
   &END PRINT
  &END MD
  &PRINT
    &RESTART
      &EACH
        MD 10000
      &END EACH
    &END RESTART
    &RESTART_HISTORY OFF
    &END RESTART_HISTORY
    &TRAJECTORY SILENT
      FORMAT DCD
      &EACH
        MD 100
      &END EACH
    &END TRAJECTORY
    &VELOCITIES OFF
          LOG_PRINT_KEY T
          FORMAT XYZ
          UNIT angstrom
          &EACH
            MD 100
          &END EACH
          ADD_LAST NUMERIC
    &END VELOCITIES
    &FORCES OFF
    &END FORCES
  &END PRINT
&END MOTION

On Tuesday, October 28, 2014 7:44:43 PM UTC+5:30, Samuel Andermatt wrote:
>
> Could you post your input file, knowing which parameters you chose (e.g. 
> for the PW cutoff and the basis set) would help.
>
> On Tuesday, October 28, 2014 3:10:44 PM UTC+1, Tanmoy Paul wrote:
>>
>>
>>  Hello CP2K users,
>>                             I am new to this field . I have installed 
>> cp2k using "sudo apt-get install cp2k" . I am trying to run a QM/MM 
>> minimization for 40000 steps using command "mpirun -np 8 cp2k.popt -i 
>> inputfile -o outputfile ". It does not show any error message but the 
>> problem is it is terribly slow ( around 100 steps per day ) .My system is 
>> quite large (~48000 atoms are there ) and the QM-selection contains 150 
>> atoms .I can understand that something has gone wrong with cp2k 
>> installation or my understanding about how it works, but I don't know 
>> what's going wrong . This may really be an aw-coward question to ask and I 
>> am really sorry about that . Can I have your kind suggestions on this topic.
>>                                                                           
>>                        Regards
>>                                                                           
>>                        Tanmoy          
>>
>
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