Switched to fractional coordinates internally for periodic systems

There should be no effect on users; however, SEAMM by convention uses fractional coordinates for all periodic systems, converting to Cartesians as needed.

Restructured documentation and moved to new theme.

Merge pull request #27 from molssi-seamm/dev

Reorganized documentation and switched to new theme

Substantial improvements!

What's Changed

Added ability to solvate molecules and increased the options to include

• spherical regions
• cubic and rectangular regions
• cubic and rectangular unit cells for periodic systems
• input molecules from any combination of system/configurations and SMILES
• reworked GUI to be more intuitive.

Full Changelog: 2021.11.27...2022.5.31

Corrected issue with atom types

Fixed a bug with ensuring that the atom types are correctly applied to the system if they exist in the original system.

Bugfix -- problems with the new ideal gas approach fixed

Merge pull request #21 from molssi-seamm/bugfix

Bugfix for using the ideal gas approach

Multiple different molecules available with SMILES

This release adds

• the ability to directly generate multiple different molecules from SMILES, giving the stoichiometry for packing into the fluid box.
• specifying the desired cell with the temperature and pressure, along with one of the volume, length of the box side, number of molecules or number of atoms. This uses the ideal gas law, so will only be reasonable at higher temperatures and lower densities.

Additionally, internally the release adds integration tests to check whether the module works properly in the SEAMM environment.

Update for internal change in argument parsing.

2021.6.3

Updated for the seamm argument parser moving to seamm_util.

Added installer for PACKMOL executable

Add a plug-in specific installer for handling the PACKMOL executable, which is installed in the seamm-packmol conda environment by default.

Added to the documentation.

Streamlined the documentation, adding a description for the plug-in.
Also tidied up the description for PyPI, which is used by the new installer, and added keywords to help with searches.

Updated to be compatible with new system classes.

Merge pull request #18 from molssi-seamm/system2

Updated to be compatible with the new system classes.