ORCA 6.1.1 ethanol isotope vibrations, IR files and mode animations

Run lightweight postprocessing on CPU, one process/thread per program:
  bash run.sh
  bash analyze.sh work
  /public/toolkit/miniconda3/envs/ase-3.29.0/bin/python plot_results.py
The workflow uses the existing vendor precompiled ORCA 6.1.1 tools, with the
existing GCC13.3-built OpenMPI4.1.8 dependency. No new program compilation,
SCF, force, geometry optimization or quantum Hessian calculation is done.
The original B97-3c ethanol Hessian is an actual prior cluster calculation.
Use a new extraction directory for a complete repeat.

Nine analyses: original average masses, pure light isotopes, OH-site D,
all H replaced by D, O18, methyl C13, alpha C13, scale0.96 and -noproj.
Settings are in inputs/settings.json. NIST isotope masses are used for the
pure light/substituted profiles; average masses are a separate baseline.
Atom indices in the settings are zero-based. The OH hydrogen is index3,
the fourth atom; oxygen index2, methyl carbon0, alpha carbon1.

orca_vib overwrites its supplied HESS, updating frequencies, normal modes
and IR data. It retains the raw Cartesian Hessian and dipole derivatives,
translates coordinates uniformly and rounds its output masses to five
decimals. Each directory retains before-native.hess with the exact input
masses. Start from the supplied original/precise copies when repeating;
do not use a rounded rewritten file as the high-precision mass master.

Native spectra use orca_mapspc on the UPDATED case.hess. In this pinned
format its stick weights are transition dipole square T2, not main-ORCA
eps or integrated Int. The display has a 1000 offset, not transmittance.
The parser converts independently validated quantum transition strengths
to integrated IR km/mol for the separate CSV and relative-IR plots.
The preserved source compatibility note records that using standalone
orca_vib stdout with mapspc drops its first real mode. That unsupported
route is not executed or advertised by this customer workflow.

All21 physical modes are checked against an independent mass-weighted
Hessian, rigid-body projection and dipole-derivative reconstruction. Mode
mapping uses Cartesian-pattern overlap; OH reference mode26 becomes OD
mode21. Crossings/mixing mean equal indices need not identify the same mode.
The raw -noproj case is a numerical option example. Its first six residual
modes are not interpreted as internal vibrations or physical IR transitions.
Scale0.96 is illustrative, not a recommended experimental calibration.

Two actual20-frame XYZ animations for OD modes21 and26 are generated by
orca_pltvib. These are mode visualizations, not MD or a temperature model.
The -1000 energy comment is a tool placeholder, not an electronic energy.

Tables are generated in tables/: frequencies-ir.csv, matched-isotope-modes.csv,
input-and-written-masses.csv. Reference native text and figures are included.
Check the reference without rerunning the tools:
  bash analyze.sh
Plotting defaults to reference data; change its input to visualize other data.
ORCA binaries and private runtime/credentials are not included.

Primary references:
https://orca-manual.mpi-muelheim.mpg.de/contents/spectroscopyproperties/vibrations.html#isotope-shifts
https://www.faccts.de/docs/orca/6.1/manual/contents/structurereactivity/frequencies.html
https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=1&isotype=all
https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=6&isotype=all
https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=8&isotype=all
