Q-Chem¶
Q-Chem is a comprehensive ab initio quantum chemistry package for accurate predictions of molecular structures, reactivities, and spectra. It provides a wide variety of options for molecular modeling, including over 200 DFT functionals; excited-state modeling with TDDFT; wavefunction theory methods such as coupled cluster and perturbation theory; implicit and explicit solvation modeling; QM/MM simulations; and more.
Users are strongly encouraged to review the Q-Chem manual for more information on constructing input files, running jobs, and available features. The Q-Chem website also contains many useful learning materials, including lab exercises, webinars, and workshops.
Q-Chem also offers a free open-source molecule builder and visualizer, IQmol. For more information please see the website, https://www.q-chem.com/try/iqmol/.
Using Q-Chem At NERSC¶
Q-Chem is available to all NERSC users on Perlmutter via NERSC’s site license; a separate Q-Chem license is not required for individual users, unless some additional functionality not covered by the site license (such as BrianQC) is required.
Q-Chem is available as a module, and can be loaded using:
module load qchem
A list of available Q-Chem versions can be obtained by running the command:
module avail qchem
Sample Q-Chem Batch Job Script¶
A simple example of a batch job script for running a Q-Chem job on Perlmutter is found below:
#!/bin/bash
#SBATCH --job-name=h2.in
#SBATCH --qos=shared
#SBATCH --account=<account>
#SBATCH --time=24:00:00
#SBATCH -C cpu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --output=h2.err
#SBATCH --error=h2.err
module load qchem
export QCLOCALSCR=$QCSCRATCH
export OMP_NUM_THREADS=16
export QC_THREADS=16
###run q-chem
qchem -save -nt 16 h2.in h2.out h220240503112508 > h2.err
rm -rf $QCSCRATCH/h220240503112508
###
echo "Finished running "
echo "================="
echo " "
echo "Job ended at :"
date
Users can copy the script to their own directory and specify a default account to use by modifying the script, if desired.
Additional Tips & Suggestions¶
Choice of QCSCRATCH directory
The scratch directory that Q-Chem uses is defined by the QCSCRATCH environment variable. For optimal performance, is important to choose a directory which has fast I/O to the node on which you are running the calculation. On Perlmutter, it is generally best to use Perlmutter Scratch, outlined in NERSC’s documentation. This can be done in the input sbatch script by adding the line:
export QCSCRATCH=$PSCRATCH
Please note that files are Perlmutter Scratch are purged 8 weeks after creation. If retaining the scratch files is desirable, one should copy the files over to a more permanent location after the calculation is complete.
General Running Instructions¶
General instructions for running Q-Chem jobs can be found in the general usage section of the Q-Chem manual under General Usage. Additional instructions for Q-Chem input file setup are also available in the Q-Chem manual Overview. Further details on running specific job types, as well as sample jobs, can also be found in the Q-Chem manual.
Support¶
Q-Chem users are encouraged to post on the Q-Chem Talk forum with any questions. They can also reach out to the Q-Chem support team via email at support@q-chem.com.