moved to https://docs.hpc.taltech.ee
NWChem
This manual is work in progress, please check regularly for updates
NWChem short introduction
Make nwchem.slurm batch script for parallel calculations:
#!/bin/bash #SBATCH --job-name=NWChem #SBATCH --mem-per-cpu=2GB #SBATCH --nodes=1 #SBATCH --ntasks=6 #SBATCH -t 1:00:00 #SBATCH --partition=common module load rocky8-spack module load nwchem #Create scratch directory SCRATCH=/state/partition1/$SLURM_JOB_ID mkdir -p $SCRATCH cp $SLURM_SUBMIT_DIR/*.nw $SCRATCH/ cd $SCRATCH/ nwchem job.nw >> job.out #Copy files back to working directory cp $SCRATCH/* $SLURM_SUBMIT_DIR #Clean after yourself rm -rf $SCRATCH
Copy job-input file job.nw.
Submit the job on base:
sbatch nwchem.slurm
Check results using visualization software.
NWChem long version
The North West computational chemistry (NWChem) is an ab initio computational chemistry software package. NWChem offers various approaches: density functional (DFT), second-order Möller–Plesset perturbation theory (MP2), single- and multi-reference (MR), ground-and excited-state and linear-response (LR) coupled-cluster (CC), multi-configuration self-consistent field (MCSCF), selected and full configuration interaction (CI). A broad range of DFT response properties, ground and excited-state molecular dynamics (MD) using either AMBER or CHARMM force fields or methods of quantum mechanics (QM), nudged elastic band (NEB) method, linear-response (LR), and real-time (RT) time-dependent density functional theory (TDDFT) are available in NWChem. Through its modular design, the ab initio methods can be coupled with the classical MD to perform mixed quantum-mechanics and molecular-mechanics simulations (QM/MM). Various solvent models and relativistic approaches are also available. Additionally, python programs may be embedded into the NWChem input and used to control the execution of NWChem. More about the possibilities of NWChem can be found in this article - 10.1063/5.0004997.
the tutorials site at FAccTs - https://nwchemgit.github.io/Home.html
Environment
At HPC is installed 7.0.2 version of NWChem. To start working with NWChem an environment needed to be set up with the commands:
module load rocky8-spack
module load nwche
Input file
water dimer will bi firstly optimized at BP86-D3BJ/def2-SVP level of theory
frequency calculations will be done at the same level of theort
single poin energy will be calculated using larger basis set (def2-TZVPP) and B3LYP functional.
Additionally in example input file are shown inplementation of some useful keywords as print and linopt.
start water # all intermediate files will have this name
title "Water dimer" # title of job
echo # input file will be printed in the beginning of the output file
memory total 3000 mb
charge 0
geometry units angstrom
O -0.093470 -1.154274 0.290542
H 0.329461 -0.566865 -0.340362
H -0.864449 -1.335840 -0.238173
O -0.135461 1.136660 -0.233474
H 0.636237 1.304331 0.298468
H -0.563123 0.545569 0.390712
end
basis
* library Def2-SVP
end
scf
rhf # restricted Hartree-Fock
singlet # multiplicity
maxiter 100 # maximum number of SCF iterations
print low # will minimize output
end
dft
mult 1 # multiplicity
xc becke88 perdew86 # functional BP86
disp vdw 4 # dispersion correction D3BJ
print low # will minimize output
end
driver
maxiter 100 # maximum number of iterations during optimization
linopt 0 # speed up calculations
end
task dft optimize
task dft freq numerical
basis
* library Def2-TZVPP
end
dft
mult 1 # multiplicity
xc b3lyp # functional B3LYP
disp vdw 4 # dispersion correction D3BJ
print low # will minimize output
end
task dft energy
NWChem is well suited for large system calculations or molecular dynamics simulations with subsequent calculation of system properties. Example of an input (job_MD.nw) for MD sinumation with subsequent calculation of dipole moment every 10 steps.
More about NWChem input can be found at NWChem manual.
Running NWChem jobs
NWChem input files are executed by the command nwchem. This command is usually placed in slurm script.
Single core & parallel calculations
NWChem jobs can be calculated on one thread, in parallel on one node or using several nodes at once. Depending on the size of job, the corresponging parameters must be modified in slurm file:
#SBATCH --ntasks=6
#SBATCH --nodes=1
Below is given an example of slurm script for NWChem parallel run on 1 node and 6 threads with allocated memory of 3 GB:
#!/bin/bash
#SBATCH --job-name=NWChem
#SBATCH --mem=3GB
#SBATCH --nodes=1
#SBATCH --ntasks=6
#SBATCH -t 1:00:00
#SBATCH --partition=common
module load rocky8-spack
module load nwchem
#Create scratch directory
SCRATCH=/state/partition1/$SLURM_JOB_ID
mkdir -p $SCRATCH
cp $SLURM_SUBMIT_DIR/*.nw $SCRATCH/
cd $SCRATCH/
nwchem job.nw > job.out
#Copy files back to working directory
cp $SCRATCH/* $SLURM_SUBMIT_DIR
#Clean after yourself
rm -rf $SCRATCH
NB! in example of slurm script calculations will be done on a single node, thus partition is common. If several nodes will be use than partition should be green-ib.
#SBATCH --nodes=2
#SBATCH --ntasks=120
#SBATCH --partition=green-ib
NB! to be able to restart calculations, they must be done in the $HOME catalog, and not in $SCRATCH directory.
Restarting a failed/interrupted calculation
NWChem does not give message about normal ternination. If calculation terminated normally, otput will have this end:
AUTHORS
-------
E. Apra, E. J. Bylaska, N. Govind, K. Kowalski, M. Valiev, W. A. de Jong,
T. P. Straatsma, H. J. J. van Dam, D. Wang, T. L. Windus, N. P. Bauman,
A. Panyala, J. Hammond, J. Autschbach, K. Bhaskaran-Nair, J. Brabec,
K. Lopata, S. A. Fischer, S. Krishnamoorthy, M. Jacquelin, W. Ma, M. Klemm,
O. Villa, Y. Chen, V. Anisimov, F. Aquino, S. Hirata, M. T. Hackler,
Eric Hermes, L. Jensen, J. E. Moore, J. C. Becca, V. Konjkov,
D. Mejia-Rodriguez, T. Risthaus, M. Malagoli, A. Marenich,
A. Otero-de-la-Roza, J. Mullin, P. Nichols, R. Peverati, J. Pittner, Y. Zhao,
P.-D. Fan, A. Fonari, M. J. Williamson, R. J. Harrison, J. R. Rehr,
M. Dupuis, D. Silverstein, D. M. A. Smith, J. Nieplocha, V. Tipparaju,
M. Krishnan, B. E. Van Kuiken, A. Vazquez-Mayagoitia, M. Swart, Q. Wu,
T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby, E. Brown, G. Cisneros,
G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. A. Kendall, J. A. Nichols,
K. Tsemekhman, K. Wolinski, J. Anchell, D. E. Bernholdt, P. Borowski,
T. Clark, D. Clerc, H. Dachsel, M. J. O. Deegan, K. Dyall, D. Elwood,
E. Glendening, M. Gutowski, A. C. Hess, J. Jaffe, B. G. Johnson, J. Ju,
R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng,
T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,
M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.
Total times cpu: 56.9s wall: 57.2s
If job was not terminated normally, it can be restarted. However, to do this, calculations must be done in the $HOME catalog, and not in $SCRATCH directory.
To restart calculation just change start command to restart in initial input file and run slurm script again.
NB! we recommend to change the restart output file name so it was possible to compare progress in the end of calculations.
Memory
At the beginning of the NWChem input file the amount of memory requested for the entire job must be specified. If amount of memory requested is insufficient, the job can crash. Memory usage in NWChem is controlled by the memory total keywords.
memory total 3000 mb
There is no golden rule for memory requests, since they are basis set and calculation type dependant. Usually, 1-5 GB per 1 CPU is sufficient. Data from a slurm-JOBID.stat file can be useful to determine the amount of memory required for a computation. In slurm-JOBID.stat file the efficiency of memory utilization is shown.
Bad example:
Memory Utilized: 3.08 GB
Memory Efficiency: 11.83% of 26.00 GB
Good example:
Memory Utilized: 63.12 GB
Memory Efficiency: 98.62% of 64.00 GB
Time
Time limits depend on time partition used, see taltech user-guides. If the calculation time exceeds the time limit requested in the slurm script, then the job will be killed. Therefore, it is recommended to request more time than is usually needed for calculation.
How to cite:
Please cite DOI:10.1063/5.0004997 when publishing results obtained with NWChem:
And also look at the NWChem manual on the relevant topic, more detailed information on citing will be given there.