m-julian
commented
5 months ago Not in the menus yet, but added a check function.
from ichor.hpc.main.check_for_missing_files import submit_check_points_directory_for_missing_files
submit_check_points_directory_for_missing_files("pointsdirectory_or_pointsdirectoryparent_path")That will submit a job that checks for aimall and gaussian input/output files. The outputs can be found in the output file .DATA/SCRIPTS/OUTPUTS/check_for_missing_data.sh.o.....
This will only check files and will not move anything.
It is probable that when using the ICHOR_cli to do Gaussian or especially AIMAll, some jobs are essentially ignored by CSF. As of now, we are not sure why but it is safe to check whether the AIMAll has been finished for every geometry before proceeding to make the sqlit3 file. This can be done with a script like:
for i in NAME*; do (cd $i && if ! grep -q "AIMQB Job Completed" $i.aim; then echo $i; fi); donewhere NAME is the name of the molecule that you are studying. Run this in the subdirectories within the parent directory.When the unfinished/faulty calculations are found do not rerun the ICHOR-cli to do the calculation in the parent directory, instead move the faulty subdirectories out of the parent directory and then run ICHOR-cli. If you do not do this and simply resubmit these jobs in the parent directory, a .DATA directory will be made in the subdirectory which will stop the sqlit3 file to be made properly.