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.

Bug fixes: orbital plots and output

• The plots of the HOMO and LUMO were shifted by one orbital due to some code counting from 1 and other, from 0. Sigh.
• The output to Job.out was inadvertently truncated.

Added structure file for plots of density and orbitals

Always write the current structure as 'structure.sdf' in the directory where the cube files for orbitals and densities are written. The Dashboard picks up this file to render the structure along with the surfaces.