Gaussian-step

* Fixed a bug in the shape of the gradients array when reading from the punch
file. They are now correctly output as a [natoms][3] array.

2025.1.29: Added an option to save the structure in the standard orientation.
* Added an option to save the structure in the standard orientation, which is
the orientation used by Gaussian for the calculations. This is useful for
visualizing the structure, and is also the orientation for e.g. the calculated
orbitals.
* Fixed a bug in displaying the structure with the orbitals or density. The sructure
is now always in the standard orientation, regardless of the option above, as it
must be since the orbitals and density are calculated in the standard orientation.

* Added the atom energies for the 6-31G and 6-311G basis set families for the
PBErev (PBEhPBE), HSE06 (HSEH1PBE), PBE0 (PBE1PBE), and PBE0rev (PBEH1PBE) density
functionals for the thermodynamics step.
* Added the electronic state to the output and properties
* Added refereneces for all the methods and DFT functional in the GUI.
* Improved the output to include the full name of the method and DFT functional

* Added the method and basis set to the header of the Thermochemistry.txt report.
* Caught some cases where the system name was reported as None.

* The code was not properly handling the DFT methods in the thermodynamics step.
This has been fixed.
* Improved the reporting on why the atomization energy or enthalpy of formation could
not be calculated.

* Added the atom energies for the 6-31G and 6-311G basis sets to the thermodynamics
step for HF, B3LYP, all MP, CC, CBS-xx, and Gn composite methods
* Added detailed output of the thermochemistry calculations in Thermochemistry.txt
* Allowed composite methods to be access through the Thermodynamics Step.
* Added ability to print and/or save the basis set to a file.
* Added options for the numerical grids used in DFT calculations.

* The code checks that the gradients in the punch file are similar to those in the
output. Apparently the check was too tight, so it has been loosened. A warning is
printed if the gradients differ too much so that we can understand if it is an
issue.