- Created by Marko Kvakić, last modified on Oct 18, 2023
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
| verzija | modul | red |
|---|---|---|
| 2022.1 | scientific/cp2k/2022.1-gnu | cpu |
Dokumentacija
- Službena stranica - https://www.cp2k.org
- Priručnik za korištenje - https://manual.cp2k.org
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
H2O-64.inp Expand source
&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 Expand source
#!/bin/bash #PBS -q cray_cpu #PBS -l select=4:ncpus=8:mem=10GB #PBS -l place=scatter #PBS -l walltime=1000 module load cray-pals module load scientific/cp2k/2022.1-gnu cd $PBS_O_WORKDIR mpiexec -n 4 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:
... #PBS -l select=<broj_MPI_procesa>:ncpus=<broj_OMP_niti> ... mpiexec -np <broj_MPI_procesa> cp2k.psmp ...
Jer će ovim načinom sustav PBS automatski definirati varijablu okoliša OMP_NUM_THREADS
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