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NWChem

§ NWChem provides many different methods to compute the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density. In addition, NWChem has the capability to perform classical molecular dynamics and free energy simulations. These approaches may be combined to perform mixed quantum-mechanics and molecular-mechanics simulations.

Available

  • Puhti: 6.8.1
  • Mahti: 7.0.0

License

Usage

Check which versions are recommended:

module avail nwchem

Batch script example for Puhti

#!/bin/bash
#SBATCH --partition=test
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=40 # MPI tasks per node
#SBATCH --account=<project>  # insert here the project to be billed 
#SBATCH --time=00:10:00           # time as hh:mm:ss

module load nwchem/6.8.1
export NWCHEM_RUN=$PWD/NWCHEM_RUN_$SLURM_JOB_ID
mkdir -p $NWCHEM_RUN
export SCRATCH_DIR=$NWCHEM_RUN
srun $NWCHEM_EXE test.nw > test_$SLURM_NPROCS.out
seff $SLURM_JOBID

Note

Particularly some of the more advanced electron correlation calculations can be very disk I/O intensive. Such jobs benefit from using the fast local storage on Puhti. Using local disk for such jobs will also reduce the load on the Lustre parallel file system.

Batch script example for Puhti using local disk

#!/bin/bash
#SBATCH --partition=large
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=40 # MPI tasks per node
#SBATCH --account=<project>  # insert here the project to be billed
#SBATCH --time=00:10:00      # time as hh:mm:ss
#SBATCH --gres=nvme:100      # requested local disk space in GB 

module load nwchem/6.8.1
export NWCHEM_RUN=$LOCAL_SCRATCH
mkdir -p $NWCHEM_RUN
export SCRATCH_DIR=$NWCHEM_RUN
srun $NWCHEM_EXE test.nw > test_$SLURM_NPROCS.out
seff $SLURM_JOBID

Batch script example for Mahti

#!/bin/bash -l
#SBATCH --partition=test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=128
#SBATCH --account=<project>  # insert here the project to be billed
#SBATCH --time=00:10:00      # time as hh:mm:ss

module load nwchem/7.0.0
export NWCHEM_RUN=$PWD/NWCHEM_RUN_$SLURM_JOB_ID
mkdir -p $NWCHEM_RUN
export SCRATCH_DIR=$NWCHEM_RUN
srun $NWCHEM_EXE test.nw > test_$SLURM_NPROCS.out

Submit the batch job with:

sbatch nwchem_job.bash

References

Please cite the following reference when publishing results obtained with NWChem:

E. Aprà, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski, T. P. Straatsma, M. Valiev, H. J. J. van Dam, Y. Alexeev, J. Anchell, V. Anisimov, F. W. Aquino, R. Atta-Fynn, J. Autschbach, N. P. Bauman, J. C. Becca, D. E. Bernholdt, K. Bhaskaran-Nair, S. Bogatko, P. Borowski, J. Boschen, J. Brabec, A. Bruner, E. Cauët, Y. Chen, G. N. Chuev, C. J. Cramer, J. Daily, M. J. O. Deegan, T. H. Dunning Jr., M. Dupuis, K. G. Dyall, G. I. Fann, S. A. Fischer, A. Fonari, H. Früchtl, L. Gagliardi, J. Garza, N. Gawande, S. Ghosh, K. Glaesemann, A. W. Götz, J. Hammond, V. Helms, E. D. Hermes, K. Hirao, S. Hirata, M. Jacquelin, L. Jensen, B. G. Johnson, H. Jónsson, R. A. Kendall, M. Klemm, R. Kobayashi, V. Konkov, S. Krishnamoorthy, M. Krishnan, Z. Lin, R. D. Lins, R. J. Littlefield, A. J. Logsdail, K. Lopata, W. Ma, A. V. Marenich, J. Martin del Campo, D. Mejia-Rodriguez, J. E. Moore, J. M. Mullin, T. Nakajima, D. R. Nascimento, J. A. Nichols, P. J. Nichols, J. Nieplocha, A. Otero-de-la-Roza, B. Palmer, A. Panyala, T. Pirojsirikul, B. Peng, R. Peverati, J. Pittner, L. Pollack, R. M. Richard, P. Sadayappan, G. C. Schatz, W. A. Shelton, D. W. Silverstein, D. M. A. Smith, T. A. Soares, D. Song, M. Swart, H. L. Taylor, G. S. Thomas, V. Tipparaju, D. G. Truhlar, K. Tsemekhman, T. Van Voorhis, Á. Vázquez-Mayagoitia, P. Verma, O. Villa, A. Vishnu, K. D. Vogiatzis, D. Wang, J. H. Weare, M. J. Williamson, T. L. Windus, K. Woliński, A. T. Wong, Q. Wu, C. Yang, Q. Yu, M. Zacharias, Z. Zhang, Y. Zhao, and R. J. Harrison, “NWChem: Past, present, and future”, The Journal of Chemical Physics 152, 184102 (2020). DOI: 10.1063/5.0004997

More information

Last edited Tue Aug 18 2020