_{Updated 2023-02-24}

Run CP2K on the Cluster¶

Overview¶

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.
This guide will cover how to run CP2K with a batch script on the cluster.
Here is a link to CP2K's homepage that can provide more information.

Tips¶

Here is a link to the manual provided by CP2K to give more information on different functions.
You can find more exercises and examples other than the one covered in this guide here.

Walkthrough: Run CP2K on the Cluster¶

In this example, we will illustrate how to relax the structure of a system (without changing the cell dimensions) using the relaxation of a water molecule as an example.
This example is directly taken from an exercise posted on CP2K's website. You can visit the link for more information about what each section in the input file means.
Create a basic argon.inp input file with this content:

&GLOBAL
  PROJECT ar108           #Project Name
  RUN_TYPE md             #Calculation Type : MD (molecular dynamics), GEO_OPT (Geometry Optimization), Energy (Energy Calculation)
&END GLOBAL

&MOTION
  &MD
    ENSEMBLE NVE          #The ensemble for MD propagation, NVE (microcanonical), NVT (canonical), NPT_I (NPT with isotropic cell) 
    STEPS 100             #The number of MD steps to perform
    TIMESTEP 5.           #The length of an integration step (fs)
    TEMPERATURE 85.0      #The temperature in K used to initialize the velocities with init and pos restart, and in the NPT/NVT simulations
  &END MD
&END MOTION

&FORCE_EVAL
  METHOD FIST             #Method to calculate force: Fist (Molecular Mechanics), QS or QUICKSTEP (Electronic structure methods, like DFT)
  &MM
    &FORCEFIELD
      &CHARGE             #charge of the MM atoms 
        ATOM Ar           #Defines the atomic kind of the charge
        CHARGE 0.0        #Defines the charge of the MM atom in electron charge unit
      &END
      &NONBONDED
        &LENNARD-JONES    #LENNARD-JONES potential type.Functional form: V(r) = 4.0 * EPSILON * [(SIGMA/r)^12-(SIGMA/r)^6]
          atoms Ar Ar     #Defines the atomic kind involved in the nonbonded potential 
          EPSILON 119.8   #Defines the EPSILON parameter of the LJ potential (K_e) 
          SIGMA 3.405     #Defines the SIGMA parameter of the LJ potential (Angstrom)
          RCUT 8.4        #Defines the cutoff parameter of the LJ potential 
        &END LENNARD-JONES
      &END NONBONDED
    &END FORCEFIELD
    &POISSON              # Poisson solver
      &EWALD
        EWALD_TYPE none
      &END EWALD
    &END POISSON
  &END MM
  &SUBSYS
    &CELL
      ABC 17.1580 17.158 17.158    #Simulation box size
    &END CELL

    &COORD
   Ar -8.53869012951987116 -15.5816257770688615 2.85663672298278293
   Ar 1.53007304829383051 9.28528179040142554 11.1777824543317941
   Ar 11.9910225119590699 -7.48825329565798015 -9.96545306345559823
   Ar -12.6782400030290496 -3.34105872014234606 4.07471097818485806
   Ar -1.77046254278594462 -0.232459464264201887 13.2012946017273016
   Ar 8.01761371186688443 -2.57249587730733298 -4.12720554747711432
   Ar 8.57849517232300052 4.01396664624232002 5.57368821983998419
   Ar -3.89200679277030925 -10.2930917801117356 -6.98640232289045482
   Ar -3.35457160564444568 -16.1119619276890056 16.1358515626317427
   Ar 9.78957155103081966 -16.2628264194939263 -5.69790857071688350
   Ar 0.505143495414835719 -4.22978415759568183 12.4854171634357307
   Ar 15.5632243939617503 -7.98048905093276240 2.20994708545912832
   Ar -5.40741643995084953 -2.64764457113743079 -0.681485212640798199
   Ar -0.983719068448489081E-01 -1.73674004862212694 -7.11915545117132265
   Ar 7.52655781331927187 -5.52969969672439632 -12.8886150439489313
   Ar -5.45655410995716128 0.564445754429787061 2.03902510096247536
   Ar -11.8590998267164665 3.40407446386207724 3.72687933934436399
   Ar 16.7175362589401821 -7.47132377347522780 -1.02274476672697889
   Ar -20.4572129717055340 -5.73700807719791683 4.81845086375497811
   Ar 14.8485522289272627 -1.41608633045414667 -16.0839111490847451
   Ar 8.04379470511429595 -8.14033814842439263 -4.75543123809189261
   Ar 12.2738439612049568 -1.70589834674486429 12.9622486199573572
   Ar -0.421851806372696092 -11.1177490353157999 20.4545363332536283
   Ar 2.28194341698637571 5.92083917539752136 -11.1732449877738436
   Ar -13.9648466918215064 8.77923885764231926 8.07373370482465091
   Ar  -10.3147439499058429 6.38529561240966004 -15.3411964215061527
   Ar  -2.71899964647918457 -21.4890074469143855 10.8678096818980006
   Ar  -17.7923879123397271 -10.7840901151121251 -4.83954996524571968
   Ar  5.23494138507746420 -6.79222906792632841 -6.07187690814296133
   Ar  3.52448750638480446 -10.1225951872349782 2.96829048662758721
   Ar  -16.1586602901979361 -5.18274316385346445 8.57072694078649455
   Ar  -5.80982824422251287 4.32640193501643733 2.55599101868223322
   Ar  6.29160109084684382 27.5741337288405717 15.0246410590392632
   Ar  -3.18741711710350684 23.2996469099840624 -16.8034854143018748
   Ar  -4.20225755039435622 9.36037725943080190 16.5891306154890081
   Ar  -7.64392908749747946 -9.52432384411045341 -29.8228731471089645
   Ar  0.545352525792712428 13.9240554617015260 -0.383786780333776500
   Ar  -5.27432886808646906 -5.53813781787395865 -20.3014703747109415
   Ar  22.9921850152838871 6.78619371666398941 -1.98289905290632484
   Ar  19.7720034229251880 -10.2373337687313679 -3.33081818566269172
   Ar  0.156776902886395425 6.59630118110908725 8.90749062505743083
   Ar  5.57937381862174053 0.233106223140015806 1.02752287819280941
   Ar  -3.64343561800208793 3.96448881012491006 25.8752124557059595
   Ar  -0.248491698112870391 20.4489725648023182 -2.51220445353457666
   Ar  2.93626708600658270 0.859812213376437984 9.96743307236779508
   Ar  3.30384315693043895 -2.92421266591109408 -6.34927042371499883
   Ar  -6.15490235244551265 -6.84961480075890883 -6.46204144605644260
   Ar  -23.2388291761596619 -28.1213094673208666 7.13721047187827917
   Ar  4.11526291325474780 2.71564143367947342 -0.852030043744060328
   Ar  14.6194148692240713 2.80815182256426210 1.93601975975151541
   Ar  18.9667954753247869 16.5700888519293095 13.3423444868082761
   Ar  -28.6124161416877705 2.84353637083477562 -9.23601973326721648
   Ar  -5.97004594556101331 -16.2230172568109978 -9.22928061840017477
   Ar  10.0481077882725955 16.3854819569745231 5.12578711346205651
   Ar  -7.22508507825336643 6.34615422233080650 -0.680757463730119028
   Ar  -12.0138912984383506 -10.4653110276797570 -6.43434787584580103
   Ar  -8.53169926903037457 12.8976589212818862 -0.890361252446473683
   Ar  -25.3700692950848676 3.33119906434656077 -7.93917685683272722
   Ar  2.90163480643285920 -12.9668181360039672 -7.94907759259854707
   Ar  -13.5963940986222074 11.9896580951935974 -3.55068754869933789
   Ar  13.1416029517342476 4.97143783446568488 -3.50841252726170705
   Ar  -13.3295460955805254 16.0410015777677764 7.05282797577515375
   Ar  -4.15068335494176122 -19.5111913798076593 21.0255971827539376
   Ar  -8.42944270819351793 16.3065160593537009 -18.2887817284733885
   Ar  0.788636333898691255 9.59016836817029095 22.1772606194495872
   Ar  -2.92606778628861974 -7.97408054890791007 -21.3519900334304964
   Ar  -6.39959865978756426 -4.56280461803643256 2.75533571094951402
   Ar  -4.04423878093174860 -14.9275965394452506 -5.58561473738824965
   Ar  -27.8524912514281482 0.802052180719123098 -3.02663789713126441
   Ar  -2.83966529645897792 7.11627121253196915 6.18547332762273783
   Ar  -8.68327887612401739 -6.67088300493855879 -9.15815450219801264
   Ar  -11.9620847111198501 -2.20956249614563038 -1.83979975374852245
   Ar  22.6848553724304907 12.2047209420099971 1.01238797839832362
   Ar  6.29501012040417507 -0.769712471349173866 -6.91454332254278281
   Ar  3.49995546789933476 -8.00704920137973453 -0.426526631939732892
   Ar  0.385154812289867643 17.8769740351009112 -17.4065226240143041
   Ar  21.2288869131365736 10.2327102035561044 -13.0872200859088803
   Ar  1.22082587001210396 5.83597435065779457 16.8450099266840283
   Ar  -7.08754036219628425 6.03412971863339109 -22.3251445579668015
   Ar  -0.244265849036998037E-01 17.4693605251376454 7.37116730966604194
   Ar  15.0981822679441553 9.88940516251130397 -8.49382740142986670
   Ar  -6.57877688336587152 -15.0484532074656290 14.7230359830473887
   Ar  -2.22666666633409394 -4.18421900331013674 -2.47007887105670587
   Ar  5.20621069851729867 -22.6565181989138011 7.39475674805799521
   Ar  -8.85828800414884299 -2.47510661993999781 2.35441398531938617
   Ar  6.75202354538700167 0.430391383628436597 5.43492495261394382
   Ar  11.9263127546080856 8.13267254152258445 2.40081132956567966
   Ar  -14.5507562394484040 -0.471540677239574602 -13.7058431104765983
   Ar  14.1157692422228553 -2.98968593175088149 24.6842798176059546
   Ar  -3.35107336204723527 -0.681362546744063047 -7.37039916831594510
   Ar  7.79269876443546838 3.30687615091469800 -0.732378021069576002E-01
   Ar  -1.13289059102623746 -17.1672835835708497 -12.9126466371968966
   Ar  -9.21054349522787241 -10.4846510042527843 -8.38485797788161591
   Ar  -6.47848777956778044 -3.90736653076878993 -10.6499668409808841
   Ar  0.987874979233200667 13.7363585340729077 5.07209659800543733
   Ar  8.86097814789463278 9.96103887786039799 1.09373795795780060
   Ar  -6.58068766844202013 -20.4019345282015756 -7.28935608176262662
   Ar  -0.448977062720621045 19.5862520159664086 11.0351198968750293
   Ar  7.36056937465398153 -2.69594281683156067 7.26081874603436361
   Ar  13.8791344546872004 12.1903465249438128 1.24889885444881155
   Ar  -3.65782753722175302 19.7829061761924159 -11.8161510229542408
   Ar  1.49729450944005649 -5.39289977250827679 1.92445849672255198
   Ar  18.5861605633917577 3.00868366398259690 2.06440131010935168
   Ar  6.20730767975507014 -9.47418398815358032 5.54930507752316249
   Ar  3.65054837888884753 3.43181054126032858 -4.31160813615129435
   Ar  2.67862616463048520 2.29300605146530545 5.98502962150055051
   Ar 24.5113122275150914 4.00733170976478448 13.1412501215423774
   Ar -0.600233262008137092 3.62825631372324597 6.38411284716526772
    &END COORD
    &TOPOLOGY
    &END TOPOLOGY
  &END SUBSYS
&END FORCE_EVAL

SBATCH Script: cp2k.sbatch
You can transfer the files to your account on the cluster to follow along. The file transfer guide may be helpful.

Part : The SBATCH Script¶

#!/bin/bash
#SBATCH -Jcp2kTest
#SBATCH -A phx-pace-staff
#SBATCH -N1 --ntasks-per-node=24
#SBATCH -t15
#SBATCH -qinferno
#SBATCH -oReport-%j.out

cd $SLURM_SUBMIT_DIR
module load gcc/10.3.0
module load openmpi/4.1.4
module load cp2k/2022.1

cp2k.popt -i argon.inp -o argon.out

The #SBATCH directives request 15 minutes of walltime with 1 node and 24 cores. More on #SBATCH directives can be found in the Using Slurm on Phoenix Guide)
$SLURM_SUBMIT_DIR is a variable that represents the directory you submit the SBATCH script from. Make sure the files you want to use are in the same directory you put the SBATCH script.
Output Files will also show up in this directory as well.
module load cp2k/2022.1 loads the 2022.1 version of CP2K. To see what CP2K versions are available, run module spider cp2k, and load the one you want. The other modules are dependencies for the cp2k module and must be loaded prior to loading the cp2k module.
cp2k.popt -o argon.out argon.inp & passes the argon.inp input file to the cp2k.popt function to run the program.

Part 2: Submit Job and check status¶

Make sure you're in the dir that contains the SBATCH Script as well as the CP2K file
Submit as normal, with sbatch < script name>. In this case sbatch cp2k.sbatch
Check job status with squeue --job <jobID>, replacing with the jobid returned after running sbatch
You can delete the job with scancel <jobID> , replacing with the jobid returned after running sbatch.

Part 3: Collecting Results¶

In the directory where you submitted the SBATCH script, you should see the following files generated from the job:
- argon.out
- ar108-1.ener
- ar108-pos-1.xyz
- ar108-1.restart
- ar108-1.restart.bak-1
- ar108-1.restart.bak-2
- ar108-1.restart.bak-3
Use cat or open the file in a text editor to take a look.
After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
Congratulations! You successfully ran CP2K on the cluster.