Geometric

Major changes:

- Minimum energy conical intersection / crossing point optimization will now work for all engines. The CLI has changed: provide a second input file to compute the second state for optimizing the crossing point.
- Optimizations that fail to converge or produce errors in the underlying QC code now raise exceptions and cause geomeTRIC to exit with error codes. yudongqiu
- Internal API for Engine objects has changed. Previously `Engine.calc()` returns the energy and gradient as a 2-tuple. Now it returns a dictionary containing a minimum of 2 key/value pairs as: `{'energy':energy, 'gradient':gradient}`.
- Custom convergence criteria are now available via the CLI and JSON API. Provide the name of a hard-coded set of criteria, and/or custom individual criteria for energy, grms, gmax, drms, dmax. Individual criteria will override the values provided by the set. The default convergence criteria come from the `GAU` set (same values compared to before). Additional criteria sets are defined in the code located here: https://github.com/leeping/geomeTRIC/blob/master/geometric/optimize.py#L799 . jthorton

Minor changes:

- Handlers no longer print newlines by default. Newline characters are added by hand to the end of each logging message where they are needed.
- Improvements to molecule.py and nifty.py imported from other packages
- Improved handling of TeraChem guess files

- More stable behavior when failed to enforce constraints.
- Some more unit tests.

Major changes:

- New feature: Second derivatives of internal coordinates w/r.t. Cartesian coordinates and transformation of Hessians from Cartesian to internal coordinates

- Improved performance and stability of constrained optimizations that set --enforce

Major changes:

- Logging now used for all output, allows more flexible control of messages and writing to files by default: bgobbi
- OpenMM is now available as a compute engine. Provide a PDB file name using the `--pdb` argument, and supply a force field or system XML file as the input file.
- `--enforce` now accepts a floating point threshold argument and will strictly enforce constraint satisfaction when the deviation from the constraint value falls below the threshold. Still an experimental feature.

Improvements and Fixes:

- Overall reorganization into a single `Optimizer` class
- Added tests and improved coverage
- QCArchive interface changes

Major changes:

- Refactor main Optimize() function into classes with the goal of separating out calcEnergyForce(): bgobbi

Improvements and Fixes:

- Fix conversion errors in QCArchive interface

Improvements and fixes:

- Improved writing of output in "scan" (for the improper dihedral project).
- PDB reader is now included (for purposes of user-defined fragments in TRIC coordinate system).
- Optimizations using Psi4 engine will make use of user-supplied PDB and/or radii.