def type_mof(filename, output_dir, ff="uff", output_files=True):
obconversion = OBConversion()
obconversion.SetInAndOutFormats("cif", "xyz")
obmol = OBMol()
# Read MOF file and unit cell and write xyz file
obconversion.ReadFile(obmol, filename)
unitcell = openbabel.toUnitCell(obmol.GetData(openbabel.UnitCell))
uc = [
unitcell.GetA(),
unitcell.GetB(),
unitcell.GetC(),
unitcell.GetAlpha(),
unitcell.GetBeta(),
unitcell.GetGamma()
]
obconversion.WriteFile(obmol, 'mof_tmp.xyz')
# Replicate unit cell using angstrom
mol = Molecule(read='mof_tmp.xyz')
mol.set_cell(uc)
n_atoms = len(mol.atoms)
mol333 = mol.replicate([3, 3, 3], center=True)
print(mol333.cell)
mol333.write('mof333.cif', cell=mol333.cell.to_list())
# Type FF
obconversion.ReadFile(obmol, 'mof333.cif')
ff = OBForceField.FindForceField("UFF")
if not ff.Setup(obmol):
print("Error: could not setup force field")
ff.GetAtomTypes(obmol)
# Get atom types for the middle cell
types = []
for atom_idx, obatom in enumerate(OBMolAtomIter(obmol)):
if atom_idx >= n_atoms * 13 and atom_idx < n_atoms * 14:
ff_atom_type = obatom.GetData("FFAtomType").GetValue()
types.append(ff_atom_type)
if output_files:
mof_name = os.path.splitext(os.path.basename(filename))[0]
with open(os.path.join(output_dir, mof_name + "-obabel.log"),
'w') as f:
f.write("NOTE: types order is the same as the CIF input file.\n")
f.write("types= %s" % str(types))
uniq_types = sorted(set(types))
return [str(i) for i in uniq_types]
def test_piyzaz_replication_4_4_4_without_centering():
"""Tests replicating PIYZAZ (CCDC) 4x4x4 without centering.
Reference structure is generated using Mercury software."""
piyzaz = Molecule(read=piyzaz111_xyz)
piyzaz.set_cell(piyzaz_cell_parameters)
piyzaz444 = piyzaz.replicate([4, 4, 4], center=False)
piyzaz444_ref = Molecule(read=piyzaz444_xyz)
assert np.allclose(piyzaz444.coordinates, piyzaz444_ref.coordinates)
assert set(piyzaz444.atoms) == set(piyzaz444_ref.atoms)
assert piyzaz444.cell.a == piyzaz.cell.a * 4
assert piyzaz444.cell.b == piyzaz.cell.b * 4
assert piyzaz444.cell.c == piyzaz.cell.c * 4
assert piyzaz444.cell.alpha == piyzaz.cell.alpha
assert piyzaz444.cell.beta == piyzaz.cell.beta
assert piyzaz444.cell.gamma == piyzaz.cell.gamma
def test_piyzaz_replication_2_3_1_without_centering():
"""Tests replicating PIYZAZ (CCDC) 2x3x1 without centering.
Reference structure is generated using Mercury software."""
piyzaz = Molecule(read=piyzaz111_xyz)
piyzaz.set_cell(piyzaz_cell_parameters)
piyzaz231 = piyzaz.replicate([2, 3, 1], center=False)
piyzaz231_ref = Molecule(read=piyzaz231_xyz)
assert np.allclose(piyzaz231.coordinates, piyzaz231_ref.coordinates)
assert set(piyzaz231.atoms) == set(piyzaz231_ref.atoms)
assert piyzaz231.cell.a == piyzaz.cell.a * 2
assert piyzaz231.cell.b == piyzaz.cell.b * 3
assert piyzaz231.cell.c == piyzaz.cell.c * 1
assert piyzaz231.cell.alpha == piyzaz.cell.alpha
assert piyzaz231.cell.beta == piyzaz.cell.beta
assert piyzaz231.cell.gamma == piyzaz.cell.gamma
def setup_lammps(opts):
"""Write LAMMPS simulation files."""
# Read structure information
coords = np.array(opts['cjson']['atoms']['coords']['3d'])
atoms = [
periodictable.elements[i].symbol
for i in opts['cjson']['atoms']['elements']['number']
]
nanocar = Molecule(atoms=atoms,
coordinates=np.array(coords).reshape(
(int(len(coords) / 3)), 3))
opts['box_x'], opts['box_y'], opts[
'box_z'] = opts['box_x'] * 10, opts['box_y'] * 10, opts['box_z'] * 10
nanocar.set_cell([opts['box_x'], opts['box_y'], opts['box_z'], 90, 90, 90])
nanocar.center([opts['box_x'] / 2, opts['box_y'] / 2, opts['box_z'] / 2])
if not os.path.isdir(opts['dir']):
# try removing the last part of the path (a file)
parent = (Path(opts['dir']).parent.absolute())
if not os.path.isdir(parent):
opts['dir'] = PLUGIN_DIR
print('Directory not found! Using plug-in directory -> %s' %
PLUGIN_DIR)
else:
opts['dir'] = parent
data_file = os.path.join(opts['dir'], 'data.nanocar')
write_data_file(data_file, nanocar)
# Write input file
surface_info = read_surface_info()
surface_ids = surface_info['id']
surface_atoms = surface_ids[1] - surface_ids[0]
num_atoms = len(nanocar.atoms)
if surface_ids[0] == 1:
mol_ids = [num_atoms - surface_atoms, num_atoms]
else:
mol_ids = [1, num_atoms - surface_atoms - 1]
input_file = os.path.join(opts['dir'], 'in.nanocar')
inp_parameters = {
'sim_length': opts['sim_length'],
'ts': opts['timestep'],
'mol_ids': mol_ids,
'surface_ids': surface_ids,
'T': 300
}
write_input_file(input_file, nanocar, inp_parameters)
def test_piyzaz_replication_2_2_2_with_centering():
"""Tests replicating PIYZAZ (CCDC) 2x2x2 with centering.
Reference structure is generated using Mercury software."""
piyzaz = Molecule(read=piyzaz111_xyz)
piyzaz.set_cell(piyzaz_cell_parameters)
piyzaz222 = piyzaz.replicate([2, 2, 2], center=True)
# Move the reference structure so that it's centered to original cell position
piyzaz222_ref = Molecule(read=piyzaz222_xyz)
transvec = np.sum(piyzaz.cell.vectors, axis=0) * -1 / 2
piyzaz222_ref.translate(transvec)
assert np.allclose(piyzaz222.coordinates, piyzaz222_ref.coordinates)
assert set(piyzaz222.atoms) == set(piyzaz222_ref.atoms)
assert piyzaz222.cell.a == piyzaz.cell.a * 2
assert piyzaz222.cell.b == piyzaz.cell.b * 2
assert piyzaz222.cell.c == piyzaz.cell.c * 2
assert piyzaz222.cell.alpha == piyzaz.cell.alpha
assert piyzaz222.cell.beta == piyzaz.cell.beta
assert piyzaz222.cell.gamma == piyzaz.cell.gamma