lammps new style

bin/uf3_cli

@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+
+import argparse
+from cmath import log
+from fileinput import filename
+import os
+from pyexpat import features
+import sys
+import yaml
+import logging
+import uf3.util.yaml_tools as yt
+
+accepted_file_formats = ['.xyz', '.pkl']
+
+default_settings = {'verbose': 20, 'outputs_path': './outputs', 'elements': 'W', 'degree': 2, 'seed': 0, 'data': {'db_path': 'data.db', 'max_per_file': -1, 'min_diff': 0.0, 'generate_stats': True, 'progress': 'bar', 'vasp_pressure': False, 'sources': {'path': ['./w-14.xyz', './w-14.xyz'], 'pattern': '*'}, 'keys': {'atoms_key': 'geometry', 'energy_key': 'energy', 'force_key': 'force', 'size_key': 'size'}, 'pickle_path': 'data1.pkl'}, 'basis': {'r_min': 0, 'r_max': 5.5, 'resolution': 15, 'fit_offsets': True, 'trailing_trim': 3, 'leading_trim': 0, 'mask_trim': True, 'knot_strategy': 'linear', 'knots_path': 'knots.json', 'load_knots': False, 'dump_knots': False}, 'features': {
+    'db_path': 'data.db', 'features_path': 'features.h5', 'n_cores': 4, 'parallel': 'python', 'fit_forces': True, 'column_prefix': 'x', 'batch_size': 100, 'table_template': 'features_{}'}, 'model': {'model_path': 'model.json'}, 'learning': {'features_path': 'features.h5', 'splits_path': 'splits.json', 'weight': 0.5, 'model_path': 'model.json', 'batch_size': 2500, 'regularizer': {'ridge_1b': 1e-08, 'curvature_1b': 0, 'ridge_2b': 0, 'curvature_2b': 1e-08, 'ridge_3b': 1e-05, 'curvature_3b': 1e-08}}}
+
+# Find all files in the current directory
+
+
+def find_files():
+    files = []
+    for file in os.listdir(os.getcwd()):
+        if os.path.isfile(file) and os.path.splitext(file)[-1] in accepted_file_formats:
+            files.append(file)
+    return files
+
+
+def main(args):
+
+    # Argparse Setup
+    parser = argparse.ArgumentParser(prog='uf3',
+                                     usage='%(prog)s',
+                                     description='Utilities for training and testing UF3 models.')
+    subparsers = parser.add_subparsers()
+
+    # Generate starting configuration
+
+    parser_featurize = subparsers.add_parser(
+        'config', help='generate a starting config')
+    parser_featurize.set_defaults(func=yt.config)
+    parser_featurize.add_argument(
+        'degree', type=int, help='degree of n-body terms (2 or 3)', default=False)
+    parser_featurize.add_argument(
+        'atoms', type=str, help='list of atoms', nargs='+', default=False)
+
+    # Collect Data
+
+    parser_collect = subparsers.add_parser(
+        'collect', help='collect data and export to pickled file')
+    parser_collect.set_defaults(func=yt.collect)
+    group = parser_collect.add_mutually_exclusive_group()
+    group.add_argument('settings', type=str,
+                       help='settings .yaml file', nargs='?', default=False)
+    group.add_argument('-f', '--file', type=str,
+                       help='single data file to pickle to \'data.pkl\'', default=False)
+
+    # Generate features
+
+    parser_featurize = subparsers.add_parser(
+        'featurize', help='compute feature vectors')
+    parser_featurize.set_defaults(func=yt.featurize)
+    parser_featurize.add_argument(
+        'settings', type=str, help='settings .yaml file', default=False)
+
+    # Fit coefficients
+
+    parser_fit = subparsers.add_parser('fit', help='fit model to data')
+    parser_fit.set_defaults(func=yt.fit)
+    parser_fit.add_argument('settings', type=str,
+                            help='settings .yaml file', default=False)
+
+    args = parser.parse_args()
+
+    if not hasattr(args, 'func'):
+        parser.print_help()
+        sys.exit(1)
+
+    args.func(vars(args))
+
+
+if __name__ == "__main__":
+    main(sys.argv[1:])