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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