the adapter now can recognise through additional information if the job was killed due to exceeding the wall time
it also now has a troubleshoot queue function
when writing the submit file, the function will now attempt to see if the user provided a dictionary of queue(s) with wall times and then place them in the submit file template

Test:
Written a test for the recognition of ServerTimeLimit keyword

…t attempts to consider all the OPT job but does not determine whether the OPT job has a status of done

… string format sometimes. This additional if and regex statement will convert the string to a tuple, if possible

Built a dataframe of possible combinations of basis sets that QChem requires and the correct format for the input file. Additionally, ensured that it is uploaded in the git push. This is a WIP as there may be more basis sets to add or even fix!

Molpro Adapter: Molpro needs a different touch to troubleshooting its memory. Here in setting the input file memory we determine if the MWords was enough per process but the total memory was too high. If that's the case, we reduce the processes req. while maintaining the memory per process
Update
Adjusted the file name to download from input.out to output.out

 QChem Adapter

0. QChem Adapter: Import - Pandas, ARC_PATH, rapidfuzz
1. QChem Adapter: Input Template now supports IRC and {trsh} args and ensures IQMOL_FCHK is false (This can be set to true BUT be aware this .fchk file can be rather large)
2. QChem Adapter: write_input_file - basis set is now matched via the software_input_matching function
3. QChem Adapter: write_input_file - QChem now supports D3 method. We should look at working with other DFT_D methods in the future. More specifically there are other types of D3 methods
4. QChem Adapter: write_input_file - Correctly pass in troubleshooting arguments into the input file
5. QChem Adapter: write_input_file - Capitalised TRUE/FALSE in UNRESTRICTED parameter
6. QChem Adapter: write_input_file - Removed the scan job type and moved it to another section of the input file writing
7. QChem Adapter: write_input_file - If scan is set, the job_type is PES_SCAN. We also set the fine to be XC_GRID 3. However, we may need to look into changing the tolerances later
8. QChem Adapter: write_input_file - We now write correctly the torsional scans for the input file for a scan
9. QChem Adapter: write_input_file - IRC is now supported, however this input file means we run two jobs from the one input file - A  FREQ job and then IRC. This currently works but will need improvements when used more by users
10. QChem Adapter: write_input_file - Ensuring that the SCF CONVERGENCE is 10^-8 for certain job types
11. QChem Adapter: [NEWFUNCTION] generate_scan_angles - to support PES SCAN jobs, we have a function that will look at what the required angle we want to scan, and the step size, and then return a start and end angle between -180, 180 that will ensure we scan the require angle during the stepping
12. QChem Adapter: [NEWFUNCTION] software_input_matching - Since QCHEM has different formatting for basis sets, this function will try take the users format of the basis set and match it against a dataframe (which should always be updated if its missing a format). This uses the new package in the ARC environment called rapidfuzz

Additionally - Updated QChem Tests

TrshQChem: Added in new trsh keywrods

TrshQChem: 'Error within run_minimization with minimization method' - Not certain what this error requires, and also if we should troubleshoot it if the job type is a 'conformer'. For now, we will re-run the job under the same conditions and if it fails again, we will declare it not possible to troubleshoot
remove 'break'

TrshMolpro: Parse new array length memory

Updated Trsh Tests

For future reference

Added QChem for the Normal Mode Displacement parsing and also change the default bool for raise_error

1. Scheduler: Now imports JobError
2. Scheduler: Fixed adding trsh to the args
3. Scheduler: Added JobError exception for determining job status
4. Scheduler: Now removing remote jobs at the end of the scheduler - !!!MAY NEED TO SEE IF THIS HAS AN EFFECT ON NON SSH JOBS!!!
5. Scheduler: Getting the recent opt job name via properly checking if the opt job was considered done (This was not done before)
6. Scheduler: TODO - We attempt to trouble shoot a frequency we deem not okay. Yet, there is no specific troubleshoot method, so why do we do this?
7. Scheduler: Properly troubleshoot an job
8. Scheduler: Fix conformer troubleshoot if it was a TS conformer

For future reference and good to know for SLURM servers

…onal

Needs further development and understanding

The original code did not functional correctly - nor was never used hence why it was passed into production. It has now been changed to properly return the actual number of heavy atoms

Added in rapidfuxx

This function will be required for later use when SSH is updated. For the time being, better to remove. It also causes an error in xTBAdapater (has no attribute remove_remote_files)

Molpro Memory Set Update

Will now limit the memory of Molpro to what is req. by Molpro if the CPU is set 1 core.

If user has both software available for IRC,  it will use go with preferred order

level tests update

Fixed local var min_mem_value

Update core reduction logic test for MP