Fix the normal mode displacement TS check

[alongd]

The normal model displacement check was fixed, a new module for this check was added.
Tests added, though more thorough testing for the overall functionality are still needed.

[codecov]

Codecov Report

Attention: Patch coverage is 94.43609% with 37 lines in your changes missing coverage. Please review.

Project coverage is 74.35%. Comparing base (66134b3) to head (0f27b38).
Report is 5 commits behind head on main.

Files with missing lines	Patch %	Lines
arc/checks/nmd.py	89.11%	13 Missing and 8 partials ⚠️
arc/species/converter.py	82.75%	5 Missing ⚠️
arc/checks/ts.py	62.50%	1 Missing and 2 partials ⚠️
arc/species/species.py	75.00%	3 Missing ⚠️
arc/checks/nmd_test.py	99.25%	1 Missing and 1 partial ⚠️
arc/reaction.py	96.66%	0 Missing and 2 partials ⚠️
arc/scheduler.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #768      +/-   ##
==========================================
+ Coverage   74.03%   74.35%   +0.32%     
==========================================
  Files         101      103       +2     
  Lines       28030    28490     +460     
  Branches     5870     5945      +75     
==========================================
+ Hits        20752    21185     +433     
- Misses       5803     5826      +23     
- Partials     1475     1479       +4     

Flag	Coverage Δ
unittests	74.35% <94.43%> (+0.32%)	⬆️

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[calvinp0]

Currently it appears the branch has an issue when it comes to parsing the energy of a fine opt job since it attempts to parse the fine opt before it is completed

Here is an input file that I have seen the issue occur

project: "rmg_rxn_1216"
level_of_theory: "wb97xd/def2tzvp"
job_types:
  rotors: False
  irc: False
  fine: True
  sp: True
compute_thermo: False
allow_nonisomorphic_2d: False
species:
  - label: "rmg_rxn_1216_r1_ON=O"
    smiles: "ON=O"
  - label: "rmg_rxn_1216_r2_sbr-C-sbr#N"
    smiles: "[C]#N"
  - label: "rmg_rxn_1216_p1_sbr-O--sbrsbr-N+-sbr=O"
    smiles: "[O-][N+]=O"
  - label: "rmg_rxn_1216_p2_C#N"
    smiles: "C#N"
reactions:
  - label: "rmg_rxn_1216_r1_ON=O + rmg_rxn_1216_r2_sbr-C-sbr#N <=> rmg_rxn_1216_p1_sbr-O--sbrsbr-N+-sbr=O + rmg_rxn_1216_p2_C#N"

The exception:

Exception has occurred: InputError       (note: full exception trace is shown but execution is paused at: _run_module_as_main)
Could not find file /home/calvin.p/runs/ARC/rmg_rxn_1216/calcs/Species/rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O/opt_a2957/output.out
  File "/home/calvin.p/Code/ARC/arc/parser.py", line 325, in parse_e_elect
    raise InputError(f'Could not find file {path}')
  File "/home/calvin.p/Code/ARC/arc/scheduler.py", line 2733, in post_sp_actions
    zpe_scale_factor=zpe_scale_factor)
  File "/home/calvin.p/Code/ARC/arc/scheduler.py", line 1306, in run_sp_job
    level=level,
  File "/home/calvin.p/Code/ARC/arc/scheduler.py", line 1544, in spawn_post_opt_jobs
    self.run_sp_job(label)
  File "/home/calvin.p/Code/ARC/arc/scheduler.py", line 622, in schedule_jobs
    self.spawn_post_opt_jobs(label=label, job_name=job_name)
  File "/home/calvin.p/Code/ARC/arc/scheduler.py", line 519, in __init__
    self.schedule_jobs()
  File "/home/calvin.p/Code/ARC/arc/main.py", line 646, in execute
    output=self.output,
  File "/home/calvin.p/Code/ARC/ARC.py", line 65, in main
    arc_object.execute()
  File "/home/calvin.p/Code/ARC/ARC.py", line 69, in <module>
    main()
  File "/home/calvin.p/mambaforge/envs/arc_env/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/calvin.p/mambaforge/envs/arc_env/lib/python3.7/runpy.py", line 193, in _run_module_as_main (Current frame)
    "__main__", mod_spec)
arc.exceptions.InputError: Could not find file /home/calvin.p/runs/ARC/rmg_rxn_1216/calcs/Species/rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O/opt_a2957/output.out

And when looking at arc.log we see it has spawned job opt_2957 but it has yet to end

Running local queue job **opt_a2957** using gaussian for rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O (fine opt)
  Ending job conf_opt_4 for TS0 (run time: 0:13:12)
Warning: Conformer 4 for TS0 did not converge.


Warning: Troubleshooting TS0 job conf_opt_4 which failed with status: "errored,"
with keywords: ['MaxOptCycles', 'GL9999'] in gaussian. The error "Maximum optimization cycles reached." was derived from the following line in the log file:
"Number of steps exceeded".
Troubleshooting conf_opt job in gaussian for TS0 using int=(Acc2E=14), using nosymm, using opt=(cartesian), opt=(maxcycle=200), opt=(RFO)
Running local queue job conf_opt_4 (a2958) using gaussian for TS0
  Ending job opt_a2955 for rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O (run time: 0:00:46)

Optimized geometry for rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O at wb97xd/def2tzvp:
O       0.00000000    1.15416400   -0.25380800
N       0.00000000    0.00000000    0.58013300
O       0.00000000   -1.15416400   -0.25380800

Running local queue job freq_a2959 using gaussian for rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O
Not running an sp job for rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O at wb97xd/def2tzvp, software: gaussian since the optimization was done at the same level of theory. Using the optimization output to parse the sp energy.

I think it is also important to point out that ARC is running opt and fine opt for a species twice in parallel.
Refer to opt_a2951 and opt_a2953 for the opt
Refer to opt_a2955 and opt_a2957 for the fine opt

Running local queue job **opt_a2951** using gaussian for **rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O**
  Ending job conf_opt_3 for TS0 (run time: 0:08:50)
Warning: Conformer 3 for TS0 did not converge.


Warning: Troubleshooting TS0 job conf_opt_3 which failed with status: "errored,"
with keywords: ['MaxOptCycles', 'GL9999'] in gaussian. The error "Maximum optimization cycles reached." was derived from the following line in the log file:
"Number of steps exceeded".
Troubleshooting conf_opt job in gaussian for TS0 using int=(Acc2E=14), using scf=(qc), using nosymm, using opt=(cartesian), opt=(maxcycle=200)
Running local queue job conf_opt_3 (a2952) using gaussian for TS0
  Ending job conf_opt_0 for rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O (run time: 0:01:28)

Conformer jobs for rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O successfully terminated.

Most stable conformer for species rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O was found to be isomorphic with the 2D graph representation [O]N=O

Conformer number 0 for species rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O is used for geometry optimization.
Running local queue job **opt_a2953** using gaussian for **rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O**
  Ending job conf_opt_3 for TS0 (run time: 0:04:37)
Warning: Conformer 3 for TS0 did not converge.


Warning: Troubleshooting TS0 job conf_opt_3 which failed with status: "errored,"
with keywords: ['MaxOptCycles', 'GL9999'] in gaussian. The error "Maximum optimization cycles reached." was derived from the following line in the log file:
"Number of steps exceeded".
Troubleshooting conf_opt job in gaussian for TS0 using int=(Acc2E=14), using scf=(qc), using nosymm, using opt=(cartesian), opt=(maxcycle=200), opt=(RFO)
Running local queue job conf_opt_3 (a2954) using gaussian for TS0
  Ending job opt_a2951 for rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O (run time: 0:01:27)
**Running local queue job opt_a2955 using gaussian for rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O (fine opt)**
  Ending job opt_a2953 for rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O (run time: 0:01:27)
**Running local queue job opt_a2957 using gaussian for rmg_rxn_1216_p1_sbr-O--sbrsbr-Np-sbr=O (fine opt)**
  Ending job conf_opt_4 for TS0 (run time: 0:13:12)
Warning: Conformer 4 for TS0 did not converge.