Feature/nwchem

[hjjvandam]

This pull request wants to add NWChem support to DeepDriveMD.

For this purpose a new directory DeepDriveMD-pipeline/deepdrivemd/sim/nwchem has been added. Initially this directory was a copy of DeepDriveMD-pipeline/deepdrivemd/sim/openmm.

This pull requests adds the following files:

• nwchem.py - contains input generators for the various NWChem calculations needed for what DeepDriveMD tries to accomplish
• nwchem_test.py - contains a Python script that executes the functionality of nwchem.py on the 1FME example.

TO DO:

[V] create run_nwchem.py from run_openmm.py [V] adapt run_nwchem.py to executing NWChem instead of OpenMM [V] adapt config.py to NWChem [ ] other

[hjjvandam]

The run_nwchem.py component seems to be working now. The aggregation step that follows still fails. The reason the aggregation fails is that in aggregate.py the python code tries to create an HDF5 file at output_path. output_path is the name of an existing directory and therefore not a valid file name. As the file names will have to be consistent between different workflow components there has to be a convention for how these files are named. Any tips?