[WIP] Command line interface

[henk789]

This PR addresses #4 and adds a functional CLI.

Added Features

The following functionalities are implemented:

Generating initial config with specified atoms

• Create initial config with degree and atoms

Collecting DFT data

• Collecting DFT data from single '.xyz' file/list of '.xyz' files
• Automatically searching working directory for '.xyz' files
• Converting '.xyz' files to data frame and storing as pickled file
• Loading different DFT files
• Split into train-test-validation
• Adjusting column prefix

Featurization

• Loading pickled files
• Loading '.xyz' files
• Automatic core count detection
• Specifying r_min/r_max/res_map as dict
• Specifying r_min/r_max/res_map as int/float and apply to all interactions
• Exporting features to file
• Exporting features to data frame
• Knot strategies
• Loading and dumping knots
• Only training on energies

Fitting

• Same parameters as with Python featurization
• Exporting model to json file
• Predict with fitted model
• Test errors (RMSE and MAE)
• Train on subset of featurized data
• Predict on subset of featurized data

Misc

• Automatic installation for easy use
• Default settings file
• Settings file from bspline_config

YAML parameters not yet used:

• seed
• data
  • db_path
  • max_per_file
  • min_diff
  • generate_stats
  • vasp_pressure
  • sources
    • pattern
• basis
  • fit_offsets
  • mask_trim
  • knot_strategy
  • knots_path
  • load_knots
  • dump_knots
• features
  • db_path
  • fit_forces
  • column_prefix
• learning
  • splits_path

YAML parameters added:

• verbose
• data
  • pickle_path
  • train_pickle
  • test_pickle
• features
  • batch_size
  • table_template
• learning
  • batch_size

Usage

The CLI enables quick generation of models. The tungsten example can be executed in three lines:

> uf3_cli config 3 W
> uf3_cli collect options.yaml
> uf3_cli featurize options.yaml
> uf3_cli fit options.yaml

with the required file names and training settings specified in options.yaml

The code is robust towards errors and performs type conversion where possible.