cf. issue #8

Extended the code to incorporate two-particle bonds.

clog() only logs on the root rank.

Probably add ArgumentParser for --verbose to control logging output.

1. echos the conf key value pairs
2. add --destdir, --profile, --verbose
3. reformat output files to standard 5 digit beam shard names:
   https://beam.apache.org/releases/javadoc/2.2.0/org/apache/beam/sdk/io/ShardNameTemplate.html
   (assuming we will run to 1M ranks)

This is buggy but at least allows me to run the code.

Logging exchange cost and use new pmesh exchange routines.

Use the standard python package directory layout. Add utils/ directory
for auxiliary scripts. Add a placeholder docs/ directory for future
sphinx autodoc deployment.

Adds a requirements.txt file to manage python package dependencies.

Also update the README with how to build for different use cases.

Also update build instructions in README

Ensure that github-linguist does not incorrectly classify any OCCAM
input/output files as ROFF text-formatting files

Revert commit 29a56a4940d71db8ca25450d868ed769ccef88c4. Turns out it is
necessary that test/ is a python module in order to test without
installing the main source as a package with `pip install -e .` first.
Need to add setup.py, clean up main.py, and make a proper package
before this file can be removed.

This way we avoid opening/closing the file an extra time when reading
the data in main.py.

Remove all the (2.479 / 298) approximations in different places,
absorbing the definition of the constant into Config. Also change all
instances of (3 / 2) to 1.5.

Implement separate thermostat coupling groups

Splits molecules after the charmm-gui Martini equilibration makes
everything one giant molecule with all the particles.

Add split_gro_molecules.py

Instead of only removing the linear center of mass momentum at the
beginning of the simulation if cancel_com_momentum is True, we remove
the linear momentum at the start *and* every cancel_com_momentum steps
if an integer value is specified.

Add option to remove linear center of mass momentum every N steps

* Move to tomli, drop nested lists in config.toml

* Update test

* Update requirements

* Update conftest

* Update nesting for bonds, angles and chi

…tead of range

…n the topology