Bugfix: errors using short names of methods and functionals

• There were bugs in the code that caused errors when using short names, e.g. "HF" or "CCD" for the method, or e.g. "B3LYP" for the density functional.

Enhancement: added sempiempirical methods

• Added the various semiempirical methods supported by Gaussian so they can be used from SEAMM.

Enhancements: added bond orders and improved transition state optimization

• Added ability to calculate the Wiberg bond order matrix and optionally use to set the bond orders of the structure.
• Enhanced the optimization for transitions states to capture the vibrational analysis if the second derivatives are calculated, and report on the stability of the structure.

Bugfix: issues when used in loop

• Fixed a bug that caused the plug-in to fail when used in a loop.
• Improved the creation of the gaussian.ini file to both work better and keep the comments in the file.

Cleaned up logging from code.

• The logging was a bit aggressive, so moved most logging down to the debug level. This will make the output of e.g. geomeTRIC more readable.

Added optimization of transition states, and...

• Corrected implementation of composite methods (Gn, CBS-x) to handle optimization.
• Added target of the optimization to allow transition states and saddle points.
• Corrected a bug in handling the maximum number of optimization steps.
• Corrected bug determining if optimization completed properly.
• Corrected bug handling the composite method results.

Added number of optimization steps to results

• Added the number of steps for the optimizations to the results that can be output to tables, variables, etc.

Added control over symmetry and gradients

• Updated to new calculation handling, with ~/SEAMM/gaussian.ini controlling access to the installed version of Gaussian on the machine.
• Added energy and gradients to results to support general use in e.g. energy scans.
• Added control over the use of symmetry

Switched to new way to run Gaussian, added option to just write input file

• Switched to using the new way to run executables, which supports containers.
• Added an option to just write the input file, without running Gaussian. This is useful for debugging, and for running Gaussian on a remote server.

Bug fixes: variable for functional, and parsing FChk file

• Fixed a problem with handling the functional if it was a variable rather than a specific functional.
• Fixed a problem parsing the FChk file. For exponents > 99 the FORTRAN format used in Gaussian drops the "E", resulting in numbers like 0.947-104 that caused a problem when trying to read them.