test_rb_min.py

import numpy as np
from autode import Molecule
from autode.atoms import Atom
from ade_rb_opt import opt_rb_coords
from autode.geom import are_coords_reasonable
from autode.bonds import get_ideal_bond_length_matrix


def rb_minimised_is_reasonable(molecule):

    r0 = get_ideal_bond_length_matrix(molecule.atoms, molecule.graph.edges())

    n_atoms = molecule.n_atoms
    coords = opt_rb_coords(py_coords=molecule.coordinates,
                           py_bonded_matrix=molecule.bond_matrix,
                           py_r0_matrix=np.asarray(r0, dtype='f8'),
                           py_k_matrix=1 * np.ones((n_atoms, n_atoms),
                                                   dtype='f8'),
                           py_c_matrix=0.01 * np.ones((n_atoms, n_atoms),
                                                      dtype='f8'),
                           py_exponent=8)

    molecule.coordinates = coords
    molecule.print_xyz_file(filename='tmp.xyz')

    assert are_coords_reasonable(coords)


def test_h2():
    """Simple 1D optimisation of H2, slightly displaced from it's minimum"""

    h2 = Molecule(atoms=[Atom('H'), Atom('H', x=1.1)])

    # Add a bond between the two H atoms
    h2.graph.add_edge(0, 1)

    rb_minimised_is_reasonable(h2)
    assert np.isclose(h2.distance(0, 1), 0.8, atol=0.1)


def test_alkanes():

    rb_minimised_is_reasonable(molecule=Molecule(smiles='C'))
    rb_minimised_is_reasonable(molecule=Molecule(smiles='CCCC'))


def _test_tmp():

    butane = Molecule(smiles='CCCCCCCC')

    from autode.conformers.conf_gen import get_simanl_conformer
    tmp = get_simanl_conformer(butane, save_xyz=False)
    tmp.print_xyz_file(filename='tmp.xyz')

    # butane.populate_conformers(n_confs=5)
    # for i, conf in enumerate(butane.conformers):
    #     conf.print_xyz_file(filename=f'tmp{i}.xyz')