Last week I ended my activities scheduling and running calculations for a large subset of the Issue 14 database. Now it's time to check how those calculations ran.

Check QC Calculations

-w flag means ignore lack of WFN files which means WAVE FUNCTION. Optimization calculations opt don't write this type of files.
-x flag means ignore WFX which is a newer version of the WFN file.

Check the calculations from last friday, at a def2-svpd level of theory:

database check g16 0*/*def2svpd/*.log

8 molecules didn't terminate normally, had stability, generate WFN nor WFX -> ID 22:29

database check g16 0*/*def2tzvpd/*.log

8 molecules didn't terminate normally, had stability, generate WFN nor WFX -> ID 22:29

database check g16 0*/*def2qzvpd/*.log

8 molecules didn't terminate normally, had stability, generate WFN nor WFX -> ID 22:29

It seems there is a problem with the input files for molecules 0022:0029, charges are not being taken into. These molecules are methylamines.

See FCHK files of all problematic molecules: head -n 20 002*/00*fchk | less

Input "manually" the charge and multiplicity for these molecules:

database json 0022:C4H12N+:1:1 0023:C3H10N+:1:1 0024:C2H8N+:1:1 0025:CH6N+:1:1 0026:H4N+:1:1 0027:C2H6N+:1:1 0028:CH4N-:-1:1 0029:H2N-:-1:1 -o amines.json

Erase all previous input folders:

rm -r 0023*/*force* 0024*/*force* 0025*/*force* 0026*/*force* 0027*/*force* 0028*/*force* 0029*/*force*

Create new input files using data from JSON file:

database input g16 force uhf def2-SVPD 0022*/00*.fchk 0023*/00*.fchk 0024*/00*.fchk 0025*/00*.fchk 0026*/00*.fchk 0027*/00*.fchk 0028*/00*.fchk 0029*/00*.fchk -j amines.json
database input g16 force uhf def2-TZVPD 0022*/00*.fchk 0023*/00*.fchk 0024*/00*.fchk 0025*/00*.fchk 0026*/00*.fchk 0027*/00*.fchk 0028*/00*.fchk 0029*/00*.fchk -j amines.json
database input g16 force uhf def2-QZVPD 0022*/00*.fchk 0023*/00*.fchk 0024*/00*.fchk 0025*/00*.fchk 0026*/00*.fchk 0027*/00*.fchk 0028*/00*.fchk 0029*/00*.fchk -j amines.json

Generate slurm files for selected input files:

database slurm g16 02-23:00 rrg-ayers-ab 0022*/*def2*/*.com 0023*/*def2*/*.com 0024*/*def2*/*.com 0025*/*def2*/*.com 0026*/*def2*/*.com 0027*/*def2*/*.com 0028*/*def2*/*.com 0029*/*def2*/*.com

Submit jobs to scheduler:

database submit 0022*/*def2*/*.sh 0023*/*def2*/*.sh 0024*/*def2*/*.sh 0025*/*def2*/*.sh 0026*/*def2*/*.sh 0027*/*def2*/*.sh 0028*/*def2*/*.sh 0029*/*def2*/*.sh

After running calculations, check for results of calculations:

database check g16 0*/*def2*/*.log

Files with problems:

0022_C4H12N+/0022_q001_m01_k00_force_uhf_def2qzvpd/0022_q001_m01_k00_force_uhf_def2qzvpd.log
0023_C3H10N+/0023_q001_m01_k00_force_uhf_def2qzvpd/0023_q001_m01_k00_force_uhf_def2qzvpd.log
0024_C2H8N+/0024_q001_m01_k00_force_uhf_def2qzvpd/0024_q001_m01_k00_force_uhf_def2qzvpd.log

:man_facepalming: there was no "problem" itself with these files, but that they were just still running. Now that uhf level of theory is ready, let's move with the levels.

UB3LYP

Create input files for ublyp level of theory.

database input g16 force ub3lyp def2-SVPD 00*/00*.fchk -j amines.json
database input g16 force ub3lyp def2-TZVPD 00*/00*.fchk -j amines.json
database input g16 force ub3lyp def2-QZVPD 00*/00*.fchk -j amines.json

Check for molecules 0022:0029 that got correct charge and multiplicity:

head -n 20 002*/*ub3lyp*/*com | less

Generate slurm files

database slurm g16 01-23:00 rrg-ayers-ab 00*/*ub3lyp*/*.com

Submit files to scheduler

database submit 00*/*ub3lyp*/*.sh

UWB97XD

# Generate input files
database input g16 force uwb97xd def2-SVPD 00*/00*.fchk -j amines.json
database input g16 force uwb97xd def2-TZVPD 00*/00*.fchk -j amines.json
database input g16 force uwb97xd def2-QZVPD 00*/00*.fchk -j amines.json

# Generate SLURM files
database slurm g16 01-23:00 rrg-ayers-ab 00*/*uwb97xd*/*.com

# Submit files to scheduler
database submit 00*/*uwb97xd*/*.sh

NOTE when generating input file, it tells you that charge and mult was taken from FCHK file, but if it was taken from JSON file it doesn't tells you.