"""Tools for simulations with sGDML."""
import os
from os.path import exists
import numpy as np
from ase.io import read
from sgdml import __version__
from sgdml.utils import io
[docs]def db_to_sgdml(db_file, dataset_file, name=None):
"""Convert an ASE DB to a sGDML dataset.
Note:
Licensed under MIT license.
Copyright (c) 2018-2020 Stefan Chmiela
Args:
db_file (:obj:`Path`): database filename.
dataset_file (:obj:`Path`): sGDML dataset file.
name (:obj:`str`): name of the new dataset.
"""
# MIT License
#
# Copyright (c) 2018-2020 Stefan Chmiela
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
# File checks
if not exists(db_file):
raise FileNotFoundError(db_file + " is not in this directory!")
if exists(dataset_file):
print(dataset_file + " already exists. Overwriting...")
basename = os.path.splitext(os.path.basename(db_file))[0]
mols = read(db_file, index=':')
# filter incomplete outputs from trajectory
mols = [mol for mol in mols if mol.get_calculator() is not None]
R, z, E, F = None, None, None, None
calc = mols[0].get_calculator()
if 'forces' not in calc.results:
raise ValueError("Forces are missing in the database file!")
Z = np.array([mol.get_atomic_numbers() for mol in mols])
if not (Z == Z[0]).all():
raise ValueError('Order of atoms changes accross database!')
R = np.array([mol.get_positions() for mol in mols])
z = Z[0]
E = np.array([mol.get_potential_energy() for mol in mols])
F = np.array([mol.get_forces() for mol in mols])
if name is None:
name = basename
# Base variables contained in every model file.
base_vars = {
'type': 'd',
'code_version': __version__,
'name': name,
'theory': 'QMC',
'R': R,
'z': z,
'F': F,
}
base_vars['F_min'], base_vars['F_max'] = np.min(F.ravel()), np.max(F.ravel())
base_vars['F_mean'], base_vars['F_var'] = np.mean(F.ravel()), np.var(F.ravel())
base_vars['r_unit'] = 'Ang'
base_vars['e_unit'] = 'eV'
if E is not None:
base_vars['E'] = E
base_vars['E_min'], base_vars['E_max'] = np.min(E), np.max(E)
base_vars['E_mean'], base_vars['E_var'] = np.mean(E), np.var(E)
base_vars['md5'] = io.dataset_md5(base_vars)
np.savez_compressed(dataset_file, **base_vars)