'--overwrite', dest='overwrite', action='store_true', help='overwrite existing files', ) args = parser.parse_args() model_path, model = args.model dataset_path, dataset = args.dataset for s in ['train', 'valid']: if dataset['md5'] != model['md5_' + s]: sys.exit( ui.fail_str('[FAIL]') + ' Dataset fingerprint does not match the one referenced in model for \'%s\'.' % s ) idxs = model['idxs_' + s] R = dataset['R'][idxs, :, :] E = dataset['E'][idxs] F = dataset['F'][idxs, :, :] base_vars = { 'type': 'd', 'name': dataset['name'].astype(str), 'theory': dataset['theory'].astype(str), 'z': dataset['z'], 'R': R,
def raw_input_float(prompt): while True: try: return float(raw_input(prompt)) except ValueError: print ui.fail_str('[FAIL]') + ' That is not a valid float.'
) args = parser.parse_args() dataset_path, dataset = args.dataset name = os.path.splitext(os.path.basename(dataset_path))[0] dataset_file_name = name + '.xyz' xyz_exists = os.path.isfile(dataset_file_name) if xyz_exists and args.overwrite: print(ui.info_str('[INFO]') + ' Overwriting existing xyz dataset file.') if not xyz_exists or args.overwrite: print('Writing dataset to \'%s\'...' % dataset_file_name) else: sys.exit( ui.fail_str('[FAIL]') + ' Dataset \'%s\' already exists.' % dataset_file_name ) z = dataset['z'] R = dataset['R'] F = dataset['F'] E = dataset['E'] n = R.shape[0] try: with open(dataset_file_name, 'w') as f: for i, r in enumerate(R): f.write(str(len(r)) + '\n' + str(np.squeeze(E[i]))) for j, atom in enumerate(r): f.write('\n' + io._z_to_z_str_dict[z[j]] + '\t')
help='overwrite existing dataset file', ) args = parser.parse_args() dataset = args.dataset name = os.path.splitext(os.path.basename(dataset.name))[0] dataset_file_name = name + '.npz' dataset_exists = os.path.isfile(dataset_file_name) if dataset_exists and args.overwrite: print(ui.info_str('[INFO]') + ' Overwriting existing dataset file.') if not dataset_exists or args.overwrite: print('Writing dataset to \'%s\'...' % dataset_file_name) else: sys.exit( ui.fail_str('[FAIL]') + ' Dataset \'%s\' already exists.' % dataset_file_name) mols = read(dataset, index=':') print("\rNumber geometries found: {:>7d}\n".format(len(mols))) #cell = np.array(mols[0].get_cell()) #print(cell) Z = np.array([mol.get_atomic_numbers() for mol in mols]) all_z_the_same = (Z == Z[0]).all() if not all_z_the_same: sys.exit(ui.fail_str('[FAIL]') + ' Order of atoms changes within dataset.') # Base variables contained in every model file. base_vars = {