Various TS check improvements

[alongd]

This PR contains various commit from the infamous ts2 branch. Also, added an option for users to specify skip_nmd: True in the input file to skip the TS normal mode displacement check if it is problematic.

[codecov[bot]]

Codecov Report

Attention: 18 lines in your changes are missing coverage. Please review.

Comparison is base (976fde1) 73.75% compared to head (e7aea63) 73.72%.

Files	Patch %	Lines
arc/main.py	25.00%	4 Missing and 2 partials :warning:
arc/checks/ts.py	70.58%	5 Missing :warning:
arc/mapping/engine.py	60.00%	2 Missing :warning:
arc/species/converter.py	0.00%	1 Missing and 1 partial :warning:
arc/scheduler.py	50.00%	1 Missing :warning:
arc/statmech/arkane.py	66.66%	1 Missing :warning:
arc/utils/scale.py	0.00%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #715 +/- ## ========================================== - Coverage 73.75% 73.72% -0.03% ========================================== Files 99 99 Lines 26940 26964 +24 Branches 5605 5610 +5 ========================================== + Hits 19869 19880 +11 - Misses 5677 5688 +11 - Partials 1394 1396 +2 ``` | [Flag](https://app.codecov.io/gh/ReactionMechanismGenerator/ARC/pull/715/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReactionMechanismGenerator) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/ReactionMechanismGenerator/ARC/pull/715/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReactionMechanismGenerator) | `73.72% <73.52%> (-0.03%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReactionMechanismGenerator#carryforward-flags-in-the-pull-request-comment) to find out more.

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[JintaoWu98]

Looks great!