Submitting .gjf files to Gaussian or .wfn files to AIMALL using ichor.hpc
Since ICHOR can be used as a library, we can write a separate python script that uses ichor’s modules to do tasks like submitting a lot of gjf files at once.
The ichor.core.files.Trajectory class can be used to convert a trajectory file (such as a .xyz or DLPOLY History that contain a lot of geometries) into individual .xyz files that are the inputs to Gaussian.
from ichor.main.gaussian import submit_points_directory_to_gaussian
from ichor.core.files import Trajectory, PointsDirectory
traj = Trajectory("WATER.xyz")
# make into a directory containing individual .xyz files
traj.to_dir("water_no_angle_change")
pd = PointsDirectory("water_no_angle_change")
submit_points_directory_to_gaussian(pd)
The to_dir method makes a directory containing individual .xyz files that were split from
the trajectory. Then the PointsDirectory can parse this directory and make individual
directories for each .xyz file. Finally, submit_points_directory_to_gaussian submits the
Gaussian array job to a compute cluster.
Submitting AIMALL jobs
Now that we have ran Gaussian, we should have .wfn files which can be passed into AIMALL. After the Gaussian jobs are finished we can do
from ichor.main.aimall import submit_points_directory_to_aimall
submit_points_directory_to_aimall("water_no_angle_change")
This will queue up AIMALL jobs for all the .wfn files that were found in the given directory.
WARNING: The method that is used in Gaussian (e.g. B3LYP) must be written out to the .wfn file otherwise, AIMAll will think that the Gaussians were ran at the Hartree-Fock (HF) level. This is done automatically by ichor when submitting aimalls. By default
B3LYPis written out to the .wfn files, however if you have used a different functional/method, then you will need to pass that into the submit_points_directory_to_aimall` function. If you do not do so, you will get completely wrong results from AIMAll and the IQA energy will not add up to the total energy from Gaussian.