def main():
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--mol',
action='store',
default=None,
help='Load molecule for live simulation',
metavar="FILE")
parser.add_argument('--model', action='store', default="ethanol", help='')
args = parser.parse_args()
if args.mol is None:
nuclear_charges = np.array([6, 6, 8, 1, 1, 1, 1, 1, 1])
coordinates = np.array([[0.07230959, 0.61441211, -0.03115568],
[-1.26644639, -0.27012846, -0.00720771],
[1.11516977, -0.30732869, 0.06414394],
[0.10673943, 1.44346835, -0.79573006],
[-0.02687486, 1.19350887, 0.98075343],
[-2.06614011, 0.38757505, 0.39276693],
[-1.68213881, -0.60620688, -0.97804526],
[-1.18668224, -1.07395366, 0.67075071],
[1.37492532, -0.56618891, -0.83172035]])
else:
nuclear_charges, coordinates = rmsd.get_coordinates_xyz(args.mol)
nuclear_charges = [cheminfo.convert(x) for x in nuclear_charges]
calculator = get_calculator(args.model)
constant_energy(nuclear_charges, coordinates, calculator=calculator)
return
def main(calculator):
calc = get_calculator(calculator)
if calc is None:
click.echo("Calculator `{}' not found.".format)
return
calc.start()
def main():
calculator = calculators.get_calculator("_deploy_", debug=False)
atom_labels, coordinates = rmsd.get_coordinates_xyz("examples/ethanol.xyz")
molecule = ase.Atoms(atom_labels, coordinates)
molecule.set_calculator(calculator)
dyn = BFGS(molecule)
dyn.run(fmax=0.3)
dump_xyz(molecule, "_tmp_molecule_optimize.xyz")
return
def main_md():
calculator = calculators.get_calculator("_deploy_", debug=False)
atom_labels, coordinates = rmsd.get_coordinates_xyz("examples/ethanol.xyz")
molecule = ase.Atoms(atom_labels, coordinates)
molecule.set_calculator(calculator)
energy = molecule.get_potential_energy()
print(energy)
dyn = BFGS(molecule)
dyn.run(fmax=0.5)
dump_xyz(molecule, "_tmp_molecule_optimize.xyz")
return