# -*- coding: utf-8 -*- # # Copyright (c) 2023, the cclib development team # # This file is part of cclib (http://cclib.github.io) and is distributed under # the terms of the BSD 3-Clause License. """Tests for the cclib2ase bridge in cclib.""" import unittest import numpy as np from cclib import ccopen from cclib.bridge import cclib2ase from cclib.parser.utils import find_package if not find_package('ase'): raise ImportError('Must install ase to run this test') from ase import Atoms from ase.calculators.emt import EMT import pytest class ASETest(unittest.TestCase): """Tests for the cclib2ase bridge in cclib.""" def setUp(self): super(ASETest, self).setUp() def test_makease_allows_optimization(self): """Ensure makease works from direct input.""" h2 = cclib2ase.makease([[0, 0, 0], [0, 0, 0.7]], [1, 1]) # Check whether converting back gives the expected data, data = cclib2ase.makecclib(h2) assert np.allclose(data.atomcoords, [[[0, 0, 0], [0, 0, 0.7]]]) assert np.allclose(data.atomnos, [1, 1]) assert np.allclose(data.atommasses, [1.008, 1.008]) assert np.isclose(data.natom, 2) assert np.isclose(data.charge, 0) assert np.isclose(data.mult, 1) assert np.isclose(data.temperature, 0) def test_makecclib_retrieves_optimization(self): """Ensure makecclib works with native ASE Atoms objects.""" h2 = Atoms("H2", positions=[[0, 0, 0], [0, 0, 0.7]]) # Check whether converting back gives the expected data, data = cclib2ase.makecclib(h2) assert np.allclose(data.atomcoords, [[[0, 0, 0], [0, 0, 0.7]]]) assert np.allclose(data.atomnos, [1, 1]) assert np.allclose(data.atommasses, [1.008, 1.008]) assert np.isclose(data.natom, 2) assert np.isclose(data.charge, 0) assert np.isclose(data.mult, 1) assert np.isclose(data.temperature, 0) def test_makease_works_with_openshells(self): """Ensure makease works from parsed data for open-shell molecules.""" # Make sure we can construct an open shell molecule, data = ccopen("data/ORCA/basicORCA4.2/dvb_sp_un.out").parse() # Check we have no gradients, as they will be generated by ASE. with pytest.raises(AttributeError): data.grads dvb_sp_un = cclib2ase.makease( data.atomcoords[-1], data.atomnos, data.atomcharges["mulliken"], data.atomspins["mulliken"], data.atommasses, ) # Check whether converting back gives the expected data. ase_data = cclib2ase.makecclib(dvb_sp_un) assert np.allclose(ase_data.atomcoords, [data.atomcoords[-1]]) assert np.allclose(ase_data.atomnos, data.atomnos) assert np.allclose( ase_data.atomcharges["mulliken"], data.atomcharges["mulliken"] ) assert np.allclose( ase_data.atomspins["mulliken"], data.atomspins["mulliken"] ) assert np.allclose(ase_data.atommasses, data.atommasses) assert np.isclose(ase_data.charge, data.charge) assert np.isclose(ase_data.mult, data.mult) assert np.isclose(ase_data.natom, len(data.atomnos)) assert np.isclose(ase_data.temperature, 0) # Make sure our object is compatible with ASE API. dvb_sp_un.calc = EMT(label="dvb_sp_un") # not a serious calculator! # Converting back should give updated results. ase_data = cclib2ase.makecclib(dvb_sp_un) assert np.allclose(ase_data.atomcoords, [data.atomcoords[-1]]) assert np.allclose(ase_data.atomnos, data.atomnos) assert np.allclose(ase_data.atommasses, data.atommasses) assert np.allclose( ase_data.atomcharges["mulliken"], data.atomcharges["mulliken"] ) assert np.allclose( ase_data.atomspins["mulliken"], data.atomspins["mulliken"] ) assert np.isclose(ase_data.charge, data.charge) assert np.isclose(ase_data.mult, data.mult) assert np.isclose(ase_data.natom, len(data.atomnos)) assert np.isclose(ase_data.temperature, 0) # Both energies and gradients are from the EMT calculation. assert np.allclose(ase_data.scfenergies, [7.016800805424298]) assert np.shape(ase_data.grads) == (1, ase_data.natom, 3) def test_makease_works_with_closedshells(self): """Ensure makease works from parsed data for closed-shell molecules.""" # Make sure we can construct a closed shell molecule. data = ccopen("data/ORCA/basicORCA4.2/dvb_ir.out").parse() dvb_ir = cclib2ase.makease( data.atomcoords[-1], data.atomnos, data.atomcharges["mulliken"], None, # no atomspins data.atommasses, ) # check whether converting back gives the expected data. ase_data = cclib2ase.makecclib(dvb_ir) assert np.allclose(ase_data.atomcoords, [data.atomcoords[-1]]) assert np.allclose(ase_data.atomnos, data.atomnos) assert np.allclose( ase_data.atomcharges["mulliken"], data.atomcharges["mulliken"] ) assert np.allclose(ase_data.atomspins["mulliken"], 0) assert np.allclose(ase_data.atommasses, data.atommasses) assert np.isclose(ase_data.charge, data.charge, atol=1e-5) assert np.isclose(ase_data.mult, data.mult) assert np.isclose(ase_data.natom, len(data.atomnos)) assert np.isclose(ase_data.temperature, 0) def test_write_and_read_trivial_trajectories(self): """Ensure write and read trajectory files with single structures.""" # An open-shell single point calculation. data = ccopen("data/ORCA/basicORCA4.2/dvb_sp_un.out").parse() cclib2ase.write_trajectory("dvb_sp_un.traj", data) trajdata = cclib2ase.read_trajectory("dvb_sp_un.traj") assert np.allclose(trajdata.atomcoords, data.atomcoords) assert np.allclose(trajdata.scfenergies, data.scfenergies) # No grads here. assert np.allclose(trajdata.atomnos, data.atomnos) assert np.allclose(trajdata.atommasses, data.atommasses) assert np.allclose(trajdata.natom, data.natom) assert np.allclose(trajdata.charge, data.charge) assert np.allclose(trajdata.mult, data.mult) assert np.allclose(trajdata.moments, data.moments) # No temperature here. # No freeenergy here. assert np.allclose( trajdata.atomcharges["mulliken"], data.atomcharges["mulliken"] ) assert np.allclose( trajdata.atomspins["mulliken"], data.atomspins["mulliken"] ) # A closed-shell single structure frequency calculation. data = ccopen("data/ORCA/basicORCA4.2/dvb_ir.out").parse() cclib2ase.write_trajectory("dvb_ir.traj", data) trajdata = cclib2ase.read_trajectory("dvb_ir.traj") assert np.allclose(trajdata.atomcoords, data.atomcoords) assert np.allclose(trajdata.scfenergies, data.scfenergies) # No grads here. assert np.allclose(trajdata.atomnos, data.atomnos) assert np.allclose(trajdata.atommasses, data.atommasses) assert np.allclose(trajdata.natom, data.natom) assert np.allclose(trajdata.charge, data.charge, atol=1e-5) assert np.allclose(trajdata.mult, data.mult) assert np.allclose(trajdata.moments, data.moments) # No temperature here. # No freeenergy here. assert np.allclose( trajdata.atomcharges["mulliken"], data.atomcharges["mulliken"] ) # No atomspins here. def test_write_and_read_opt_trajectories(self): """Ensure write and read trajectory files with optimizations.""" # Geometry optimization. data = ccopen("data/ORCA/basicORCA4.2/dvb_gopt.out").parse() cclib2ase.write_trajectory("dvb_gopt.traj", data) trajdata = cclib2ase.read_trajectory("dvb_gopt.traj") assert np.allclose(trajdata.atomcoords, data.atomcoords) assert np.allclose(trajdata.scfenergies, data.scfenergies) assert np.allclose(trajdata.grads, data.grads) assert np.allclose(trajdata.atomnos, data.atomnos) assert np.allclose(trajdata.atommasses, data.atommasses) assert np.allclose(trajdata.natom, data.natom) assert np.allclose(trajdata.charge, data.charge) assert np.allclose(trajdata.mult, data.mult) assert np.allclose(trajdata.moments, data.moments, atol=1e-5) # No temperature here. # No freeenergy here. assert np.allclose( trajdata.atomcharges["mulliken"], data.atomcharges["mulliken"] ) # No atomspins here. def test_read_ase_native_trajectory(self): """Ensure we can read ASE native trajectory files.""" trajdata = cclib2ase.read_trajectory("test/bridge/h2o.traj") assert np.allclose(len(trajdata.atomcoords), 7) assert np.allclose( # initial structure trajdata.atomcoords[0], [[0, 0, 0], [1, 0, 0], [0, 1, 0]] ) assert np.allclose(trajdata.scfenergies[0], -324.61300863874163) assert np.allclose( # final structure trajdata.atomcoords[-1], [ [0.06884815, 0.06884815, -0.00000000], [1.00852115, -0.07736930, 0.00000000], [-0.07736930, 1.00852115, 0.00000000], ], ) assert np.allclose(trajdata.scfenergies[-1], -324.9073873170798) assert np.allclose(trajdata.atomnos, [8, 1, 1]) assert np.allclose(trajdata.atommasses, [15.999, 1.008, 1.008]) assert np.allclose(trajdata.natom, 3) assert np.allclose(trajdata.charge, 0) assert np.allclose(trajdata.mult, 1) if __name__ == "__main__": unittest.main()