Add Rotational Initialization

As the title describes, for presto.

Summer Updates

A few relatively minor changes, mostly centered around xtb/presto integration.

• New PointCharge class which can be added to Gaussian input files.
• fail_silently option enabled for GaussianFile.read_file(), which allows you to check in-progress jobs without a try...catch loop.
• Molecule.csearch() now allows non-GFN2 levels of theory, and can pass command-line arguments to xtb.
• Automatic SI generation with  SIFile.py now allows all .xyz files to be written to a new directory as well.
• Various minor improvements to Gaussian File parsing to handle edge cases.

Fall/Winter Updates

Collected minor updates from the last 6 months; lots of bugfixes around GaussianFile parsing and quasiclassical initialization.

Added ability to specify molecule kwarg to GaussianFile.__init__().

June Updates

Major updates:

• XYZFile now possesses an ensemble property, not a molecule property. (Calling xyzfile.molecule will give a DeprecationWarning but is permitted for now.)

Minor updates:

• Classical initialization has been added to cctk.quasiclassical, along with the ability to perform mode-specific configuration.

April Updates

Major updates:

• Added ability to Boltzmann-weight properties from conformational ensembles with ConformationalEnsemble.boltzmann_average("property", temp=450).
• Added ability to compute GFN2-xtb energies for static molecules with Molecule.compute_energy()

Minor updates:

• Fixed ReadTheDocs bug which was breaking autogen of API. Sorry!
• Caught some m/z computation bugs.
• Added Molecule.coulomb_analysis() to calculate pairwise charge–charge interactions between fragments.

Happy Easter!

March Updates

Major changes:

• A class SIFile has been added to enable automatic formatting of output files. This is a work in progress.
• cctk.Molecule.to_string() and cctk.Molecule.from_string(string) now permit storage of cctk.Molecule objects. Part of the string is yaml-formatted, but most is not very human-readable (compressed ndarray bytes).

Minor changes:

• velocities can now also be generated from cctk.quasiclassical to initialize quasiclassical MD trajectories.
• charge and multiplicity have been added to cctk.XYZFile. Thanks to Gabe Gomes for pointing out this mistake.
• A new function compute_mass_spectrum has been added to cctk.helper_functions, and the mass spec backend from cctk.Molecule has been moved there.
• A new function cctk.Molecule.equal() has been added to allow for comparison of molecules.
• A bug in cctk.optimize has been fixed. Thanks to Gabe Gomes for pointing out this mistake.

Winter Updates

Minor changes:

• MP2, MP3, MP4, CI, and CC energies can now be read from Gaussian.
• Vibrational mode intensities and dipole vectors can now be read from Gaussian.
• cctk.Molecule now has a function atoms_moving_in_imaginary which returns a list of atomic numbers moving in the imaginary.
• Miscellaneous bugfixes to cctk.GaussianFile.read_file() have been applied.
• get_avg_mass() and get_z_from_mass() have been applied to cctk.helper_functions to convert between average elemental weight and atomic number.
• cctk.Molecule limit_solvent_shell() now lets you focus the solvation on a specific solute atom.
• cctk.XYZFile now has a function write_ensemble_to_file() which generates MOLDEN-compatible .xyz trajectories.

October Updates

Fairly minor update comprised of several bug fixes. The only substantive new feature is the ability to read NMR shielding tensors from Gaussian.

August/September Updates

Major changes:

• Integration with xtb and crest has now been added in cctk/optimize.py. Calling molecule.optimize() will optimize the molecule at the GFN2-xtb level of theory, while calling molecule.csearch() will run a full conformational search and return a ConformationalEnsemble (this can be slow). These external packages must be accessible by bash, or cctk will throw an error.

Minor changes:

• A bug pertaining to reading Gaussian output files for molecules with only one atom has been fixed.
• ConformationalEnsemble.eliminate_redundant() now returns the RMSD values for each conformer.

Frequency Hotfix

Minor hotfix relating to frequency parsing.