ORCA 6.1.1: file exports, orbital/density cubes and point electrostatic potentials

Run in allocated CPU resources with the existing cluster modules:
  bash run.sh
  bash analyze.sh work

Run individual steps in a fresh extraction directory:
  bash run.sh prepare
  bash run.sh json
  bash run.sh plot
  bash run.sh basis
  bash run.sh potential
  bash analyze.sh work

The preparation step makes TWO fresh, one-process CPU single-point calculations:
water HF/def2-SVP and CF3Cl PBE/def2-SVP. Both complete input files are in inputs/.
ORCA is the vendor Linux precompiled 6.1.1 package, paired with OpenMPI 4.1.8
built using GCC 13.3; no ORCA source recompilation or GPU is required here.
Only launch the main ORCA driver once by its full path. Do not wrap it in mpirun.

The work directory is created once. Use a new extraction directory to repeat
all calculations. The script refuses to overwrite an existing work directory.
Reference text wavefunctions, exported matrices, native cube files and potentials
are provided under reference/work; no ORCA binaries, GBW, PAW or license files
are distributed. Check the supplied data without another SCF using:
  bash analyze.sh

JSON: case.json.conf requests basis, MO coefficients, S/H/T/V and density. The
portable checker verifies C.T S C, trace(P S)=10, P=C occ C.T, H=T+V, charges,
and the JSON -> GBW -> JSON round trip. ORCA writes original_copy.gbw in the
reverse conversion, not original.gbw. No SCF is performed by this conversion.

Plots: ORCA's orbital indices start at zero. Water has 10 electrons and five
doubly occupied orbitals, so HOMO=4 and LUMO=5. Generated 40^3 cubes are raw
native grid data. Opposite orbital colors denote the sign of the wavefunction,
not positive/negative electron density or atomic charge. The overall sign of
one orbital can be reversed without changing its physical state. Forty grid
points are an illustration setting, not a convergence result for integration.
The checker independently evaluates the Cartesian primitive-Gaussian WFN and
real-spherical s/p/d basis functions; cube values are compared at their actual
grid locations, accounting for the six-decimal grid-header precision.

Basis: NewGTO and GAMESS-US coefficients can have different raw contraction
scales. The checker compares exponents and analytically normalized contractions,
rather than asserting the printed coefficients must be identical. Water has
14 oxygen functions and five functions per hydrogen: 24 functions in total.

Potential: inputs/points.xyz begins with a point count, followed by coordinates
in BOHR, without element symbols or an XYZ comment line. This is the point
format required by orca_vpot. The nine CF3Cl points and independent Multiwfn
values are in inputs/independent-potential.json. The native call uses case.scfp
as the density name even though ORCA 6 stores densities in a container. Keep
case.gbw, case.densities and case.densitiesinfo together with the same basename.

To regenerate the three figures from reference data:
  /public/toolkit/miniconda3/envs/ase-3.29.0/bin/python plot_results.py
The program uses NumPy and Matplotlib from the existing analysis environment.
It plots actual cube slices, matrices, orbital energies and point potentials.

Official documentation:
https://www.faccts.de/docs/orca/6.1/manual/contents/utilitiesvisualization/orca_2json.html
https://orca-manual.mpi-muelheim.mpg.de/contents/utilitiesvisualization/utilities.html
https://www.faccts.de/docs/orca/6.1/manual/contents/utilitiesvisualization/plots.html
