def test_centering_benzene_molecule_to_given_coordinates():
"""Tests molecule center for benzene"""
benzene = Molecule(read=benzene_xyz)
benzene.center([5, 0, -5])
assert np.allclose(benzene.get_center(), [5, 0, -5])
benzene.center()
assert np.allclose(benzene.get_center(), [0, 0, 0])
benzene.translate([0, 0, 7])
assert np.allclose(benzene.get_center(), [0, 0, 7])
benzene.rotate(([0, 0, 0], [0, 1, 0]), np.pi / 2)
assert np.allclose(benzene.get_center(), [7, 0, 0])
benzene.rotate(([0, 0, 0], [0, 1, 0]), np.pi / 2, center=True)
assert np.allclose(benzene.get_center(), [7, 0, 0])
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 build_nanocar(opts):
"""Builds Nanocar molecule."""
chassis = Molecule(read=os.path.join(chassis_dir, '%s.xyz' %
opts['chassis']))
chassis.center([opts['center-x'], opts['center-y'], opts['center-z']])
return mol2xyz(chassis)
def test_benzene_reflection_yz_plane_should_change_x_axis_position():
mol = Molecule(read=benzene_xyz)
mol.center([5, 0, 0])
mol.reflect('yz')
assert np.allclose(mol.get_center(), [-5, 0, 0])