Opis

cp2k je aplikacija namijenjena simulaciji fizike čvrstog stanja, tekućina, molekularnih i bioloških sustava korištenjem ab-inito metoda. Osim pružanja tipičnih mogućnosti kvanto-kemijskog modeliranja metodama DFT putem modula QUICKSTEP , cp2k pruža i mogućnosti termodinamičkog simuliranja molekularnih sustava, te miješanog kvantno-kemijskog/termodinamičkog simuliranja.

Verzije

verzijamodulredSupekPadobran
2022.1scientific/cp2k/2022.1-gnucpu(tick) (error) 
2024.3scientific/cp2k/2024.3-gnucpu(tick) (tick) 

Dokumentacija

Primjeri

Ispod je opisan primjer podnošenja posla za jedan od službenih cp2k predložaka (H20-64):

  • H20-64.inp - ulazni podaci
  • H20-64.sh - skripta sustava PBS


CP2K na Padobranu pokreće se sa wrapper-om runcp2k.

Obavezna definicija #PBS -l place=pack.


H2O-64.inp 
&FORCE_EVAL
  METHOD QS
  &DFT
    BASIS_SET_FILE_NAME GTH_BASIS_SETS
    POTENTIAL_FILE_NAME POTENTIAL
    &MGRID
      CUTOFF 280
      REL_CUTOFF 30
    &END MGRID
    &QS
      EPS_DEFAULT 1.0E-12
      WF_INTERPOLATION PS
      EXTRAPOLATION_ORDER 3
    &END QS
    &SCF
      SCF_GUESS ATOMIC
      &OT ON
        MINIMIZER DIIS
      &END OT

      &PRINT
        &RESTART OFF
        &END
      &END

    # SCF_GUESS        RESTART
    # EPS_SCF      1.0E-7
    &END SCF
    &XC
      &XC_FUNCTIONAL Pade
      &END XC_FUNCTIONAL
    &END XC
  &END DFT
  &SUBSYS
    &CELL
      ABC 12.4138 12.4138 12.4138
    &END CELL
  # 64 H2O (TIP5P,1bar,300K) a = 12.4138
    &COORD
   O      12.235322       1.376642      10.869880
   O       6.445390       3.706940       8.650794
   O       0.085977       2.181322       8.276663
   O      12.052554       2.671366       2.147199
   O      12.250036       4.190930      12.092014
   O       7.187422       0.959062       4.733469
   O       8.346457       7.210040       4.667644
   O      12.361546      11.527875       8.106887
   O       3.299984       4.440816       9.193275
   O       2.855829       3.759909       6.552815
   O       1.392494       6.362753       0.586172
   O       1.858645       8.694013       2.068738
   O       3.770231      12.094519       8.652183
   O       6.432508       3.669828       2.772418
   O       1.998724       1.820217       4.876440
   O       8.248581       2.404730       6.931303
   O       5.753814       3.360029      12.461534
   O      11.322212       5.649239       2.236798
   O       4.277318       2.113956      10.590808
   O       5.405015       3.349247       5.484702
   O       6.493278      11.869958       0.684912
   O       3.275250       2.346576       2.425241
   O       7.981003       6.352512       7.507970
   O       5.985990       6.512854      12.194648
   O      10.636714      11.856872      12.209540
   O       9.312283       3.670384       3.508594
   O       1.106885       5.830301       6.638695
   O       8.008007       3.326363      10.869818
   O      12.403000       9.687405      11.761901
   O       4.219782       7.085315       8.153470
   O       3.781557       8.203821      11.563272
   O      11.088898       4.532081       7.809475
   O      10.387548       8.408890       1.017882
   O       1.979016       6.418091      10.374159
   O       4.660547       0.549666       5.617403
   O       8.745880      12.256257       8.089383
   O       2.662041      10.489890       0.092980
   O       7.241661      10.471815       4.226946
   O       2.276827       0.276647      10.810417
   O       8.887733       0.946877       1.333885
   O       1.943554       8.088552       7.567650
   O       9.667942       8.056759       9.868847
   O      10.905491       8.339638       6.484782
   O       3.507733       4.862402       1.557439
   O       8.010457       8.642846      12.055969
   O       8.374446      10.035932       6.690309
   O       5.635247       6.076875       5.563993
   O      11.728434       1.601906       5.079475
   O       9.771134       9.814114       3.548703
   O       3.944355      10.563450       4.687536
   O       0.890357       6.382287       4.065806
   O       6.862447       6.425182       2.488202
   O       3.813963       6.595122       3.762649
   O       6.562448       8.295463       8.807182
   O       9.809455       0.143325       3.886553
   O       4.117074      11.661225       2.221679
   O       5.295317       8.735561       2.763183
   O       9.971999       5.379339       5.340378
   O      12.254708       8.643874       3.957116
   O       2.344274      10.761274       6.829162
   O       7.013416       0.643488      10.518797
   O       5.152349      10.233624      10.359388
   O      11.184278       5.884064      10.298279
   O      12.252335       8.974142       9.070831
   H      12.415139       2.233125      11.257611
   H      11.922476       1.573799       9.986994
   H       5.608192       3.371543       8.971482
   H       6.731226       3.060851       8.004962
   H      -0.169205       1.565594       7.589645
   H      -0.455440       2.954771       8.118939
   H      12.125168       2.826463       1.205443
   H      12.888828       2.969761       2.504745
   H      11.553255       4.386613      11.465566
   H      12.818281       4.960808      12.067151
   H       7.049495       1.772344       4.247898
   H       6.353019       0.798145       5.174047
   H       7.781850       7.384852       5.420566
   H       9.103203       6.754017       5.035898
   H      12.771232      11.788645       8.931744
   H      12.018035      10.650652       8.276334
   H       3.557245       3.792529       9.848846
   H       2.543844       4.884102       9.577958
   H       2.320235       4.521250       6.329813
   H       2.872128       3.749963       7.509824
   H       1.209685       7.121391       1.140501
   H       2.238885       6.038801       0.894245
   H       2.763109       8.856353       2.336735
   H       1.329379       9.047369       2.783755
   H       4.315639      11.533388       9.203449
   H       3.098742      12.433043       9.244412
   H       5.987369       3.448974       3.590530
   H       5.813096       3.419344       2.086985
   H       1.057126       1.675344       4.969379
   H       2.248496       2.292119       5.670892
   H       8.508264       1.653337       7.464411
   H       8.066015       2.034597       6.067646
   H       5.197835       2.915542      11.821572
   H       6.630900       3.329981      12.079371
   H      10.788986       6.436672       2.127933
   H      11.657923       5.463602       1.359832
   H       3.544476       1.634958      10.977765
   H       4.755770       1.455054      10.087655
   H       4.465371       3.375459       5.665294
   H       5.682663       4.264430       5.524498
   H       6.174815      11.778676       1.582954
   H       5.713640      12.089924       0.174999
   H       3.476076       1.498708       2.028983
   H       2.730229       2.134295       3.182949
   H       7.119624       5.936450       7.474030
   H       8.536492       5.799405       6.958665
   H       5.909499       5.717477      11.667621
   H       6.125402       6.196758      13.087330
   H      11.203499      12.513536      11.804844
   H      10.260930      12.300153      12.970145
   H       9.985036       3.927685       2.878172
   H       8.545584       3.468329       2.972331
   H       1.399882       6.620092       7.093246
   H       0.963561       6.112523       5.735345
   H       8.067363       3.674002       9.979955
   H       8.000737       2.375959      10.756190
   H      11.821629      10.402510      12.020482
   H      12.206854       8.983242      12.379892
   H       3.461473       7.606485       7.889688
   H       3.844478       6.304711       8.560946
   H       3.179884       7.585614      11.148494
   H       4.401957       7.652030      12.039573
   H      11.573777       5.053211       7.169515
   H      10.342076       4.186083       7.320831
   H      10.065640       8.919194       1.760981
   H       9.629585       8.322499       0.439729
   H       1.396302       6.546079       9.625630
   H       1.405516       6.479759      11.138049
   H       4.024008       1.232518       5.405828
   H       4.736858       0.579881       6.571077
   H       9.452293      12.313381       8.732772
   H       8.976559      11.502788       7.545965
   H       1.834701      10.012311       0.153462
   H       3.295197       9.836403      -0.204175
   H       7.056724      11.401702       4.095264
   H       6.499038      10.020287       3.825865
   H       1.365541       0.487338      11.013887
   H       2.501591      -0.428131      11.417871
   H       8.644279       1.812362       1.005409
   H       8.142674       0.388030       1.112955
   H       1.272659       8.365063       8.191888
   H       2.142485       8.877768       7.063867
   H       8.961493       7.826192       9.265523
   H       9.227102       8.487654      10.601118
   H      10.150144       7.758934       6.392768
   H      10.596082       9.187988       6.167290
   H       3.463106       4.096188       2.129414
   H       3.919461       4.539801       0.755791
   H       7.418998       9.394959      12.028876
   H       7.430413       7.883095      12.106546
   H       7.972905      10.220334       5.841196
   H       7.675111       9.631498       7.203725
   H       5.332446       6.381336       6.419473
   H       5.000025       6.434186       4.943466
   H      11.575078       2.271167       4.412540
   H      11.219802       0.847030       4.783357
   H       8.865342       9.721516       3.843998
   H      10.000732      10.719285       3.758898
   H       3.186196      10.476397       5.265333
   H       4.407331      11.335128       5.013723
   H       0.558187       7.255936       3.859331
   H       0.341672       5.789383       3.552346
   H       7.459933       6.526049       3.229193
   H       6.696228       5.483739       2.440372
   H       3.864872       6.313007       2.849385
   H       2.876419       6.621201       3.953862
   H       5.631529       8.079145       8.753997
   H       7.003296       7.568245       8.367822
   H       9.615413       0.527902       3.031755
   H       8.962985       0.109366       4.332162
   H       3.825854      11.139182       1.474087
   H       4.063988      11.063232       2.967211
   H       5.784391       7.914558       2.708486
   H       4.780461       8.655167       3.566110
   H      10.880659       5.444664       5.046607
   H       9.593331       4.687991       4.797350
   H      11.562317       8.960134       3.376765
   H      11.926084       8.816948       4.839320
   H       2.856874      11.297981       7.433660
   H       1.492332      11.195517       6.786033
   H       7.145820       0.090200       9.749009
   H       7.227275       0.077690      11.260665
   H       4.662021       9.538430      10.798155
   H       5.994537       9.833472      10.142985
   H      10.544299       6.595857      10.301445
   H      11.281750       5.653082       9.374494
   H      12.103020       8.841164      10.006916
   H      11.491592       8.576221       8.647557
    &END COORD
    &KIND H
      BASIS_SET TZV2P-GTH
      POTENTIAL GTH-PADE-q1
    &END KIND
    &KIND O
      BASIS_SET TZV2P-GTH
      POTENTIAL GTH-PADE-q6
    &END KIND
  &END SUBSYS
&END FORCE_EVAL
&GLOBAL
  PROJECT H2O-64
  RUN_TYPE MD
  PRINT_LEVEL LOW
&END GLOBAL
&MOTION
  &MD
    ENSEMBLE NVE
    STEPS 10
    TIMESTEP 0.5
    TEMPERATURE 300.0
  &END MD
&END MOTION
H2O-64.sh (Supek) 
#!/bin/bash

#PBS -q cpu
#PBS -l select=4:ncpus=2:mem=10GB
#PBS -l place=pack
#PBS -l walltime=1000

module load cray-pals
module load scientific/cp2k/2024.3-gnu

cd $PBS_O_WORKDIR
mpiexec -d ${OMP_NUM_THREADS} --cpu-bind depth cp2k.psmp -i H2O-64.inp
H2O-64.sh (Padobran) 
#!/bin/bash

#PBS -q cpu
#PBS -l select=4:ncpus=2:mem=10GB
#PBS -l place=pack
#PBS -l walltime=1000

module load scientific/cp2k/2024.3

cd $PBS_O_WORKDIR

runcp2k -bind-to core:${OMP_NUM_THREADS} cp2k.psmp -i H2O-64.inp

Napomena

cp2k u sebi sadrži dva nivoa paralelizacije:

  • MPI - broj procesa (ili rangova)
  • OMP - broj threadova po procesu (ili rangu)

Sintaksa koja će osigurati ispravnu raspodjelu resursa je:

Supek
...
#PBS -l select=<broj_MPI_procesa>:ncpus=<broj_OMP_niti>
...
mpiexec -d ${OMP_NUM_THREADS} --cpu-bind depth cp2k.psmp ...
Padobran
...
#PBS -l select=<broj_MPI_procesa>:ncpus=<broj_OMP_niti>
...
runcp2k -bind-to core:${OMP_NUM_THREADS} cp2k.psmp ...

PBS sustav automatski definira varijablu okoliša OMP_NUM_THREADS, ali za ispravu dodjelu resursa tj. thread-ova procesima, preporuča se korištenje cpu-bind opcije.

Sintaksa za ovakvo podnošenje poslova razlikuje se ovisno o MPI implementaciji.