def V(values=None): # pylint:disable=dangerous-default-value
if hasattr(V, "counter"):
V.counter += 1
else:
V.counter = 0
substitutions = list(zip(symbolic_expressions, values))
new_zmat = zmolecule.subs(substitutions)
if isfile(input_path(V.counter)):
result = {}
while len(result.keys()) < 3:
try:
result = molpro.parse_output(output_path(V.counter))
except FileNotFoundError:
pass
sleep(0.5)
else:
result = molpro.calculate(
molecule=new_zmat, forces=True,
el_calc_input=input_path(V.counter),
start_orb=start_orb_path(V.counter - 1) if V.counter else start_orb,
hamiltonian=hamiltonian, basis=basis,
charge=charge, title=title,
multiplicity=multiplicity,
num_procs=num_procs, mem_per_proc=mem_per_proc, **kwargs)
return result['energy']
def V(C_rad=None, calculated=[]): # pylint:disable=dangerous-default-value
try:
previous_zmat = calculated[-1].copy()
except IndexError:
new_zmat = zmolecule.copy()
else:
new_zmat = get_new_zmat(C_rad, previous_zmat)
if isfile(input_path(len(calculated))):
result = {}
while len(result.keys()) < 3:
try:
result = molpro.parse_output(output_path(len(calculated)))
except FileNotFoundError:
pass
sleep(0.5)
else:
result = molpro.calculate(
molecule=new_zmat, forces=True,
el_calc_input=input_path(len(calculated)),
hamiltonian=hamiltonian, basis=basis,
charge=charge, title=title,
multiplicity=multiplicity,
num_procs=num_procs, mem_per_proc=mem_per_proc, **kwargs)
calculated.append(new_zmat)
return result['energy']
def calculate(molecule,
hamiltonian,
basis,
el_calc_input=None,
backend=None,
charge=fixed_defaults['charge'],
forces=fixed_defaults['forces'],
title=fixed_defaults['title'],
multiplicity=fixed_defaults['multiplicity'],
**kwargs):
"""Calculate the energy of a molecule.
Args:
molecule (chemcoord.Cartesian or chemcoord.Zmat or str):
If it is a string, it has to be a valid xyz-file.
hamiltonian (str): {hamiltonian}
basis (str): {basis}
el_calc_input (str): {el_calc_input}
backend (str): {backend}
charge (int): {charge}
forces (bool): {forces}
title (str): {title}
multiplicity (int): {multiplicity}
Returns:
dict: A dictionary with at least the keys
``'structure'`` and ``'energy'`` which contains the energy in Hartree.
If forces were calculated, the key ``'gradient'`` contains the
gradient in Hartree / Angstrom.
"""
if backend is None:
backend = conf_defaults['backend']
if backend == 'molpro':
return molpro.calculate(el_calc_input=el_calc_input,
molecule=molecule,
hamiltonian=hamiltonian,
basis=basis,
charge=charge,
forces=forces,
title=title,
multiplicity=multiplicity)
elif backend == 'molcas':
return molcas.calculate(el_calc_input=el_calc_input,
molecule=molecule,
hamiltonian=hamiltonian,
basis=basis,
charge=charge,
forces=forces,
title=title,
multiplicity=multiplicity)
else:
raise ValueError('Backend {} is not implemented.'.format(backend))
def grad_V(values=None, get_calculated=False,
calculated=[]): # pylint:disable=dangerous-default-value
if get_calculated:
return calculated
elif values is not None:
substitutions = list(zip(symbolic_expressions, values))
new_zmat = zmolecule.subs(substitutions)
if isfile(input_path(len(calculated))):
result = {}
while len(result.keys()) < 3:
try:
result = molpro.parse_output(output_path(len(calculated)))
except FileNotFoundError:
pass
sleep(0.5)
else:
result = molpro.calculate(
molecule=new_zmat, forces=True,
el_calc_input=input_path(len(calculated)),
hamiltonian=hamiltonian, basis=basis,
charge=charge, title=title,
multiplicity=multiplicity,
num_procs=num_procs, mem_per_proc=mem_per_proc, **kwargs)
energy, grad_energy_X = result['energy'], result['gradient']
grad_energy_C = _get_grad_energy_C(new_zmat, grad_energy_X)
zm_values_rad = zmolecule.loc[:, value_cols].values
zm_values_rad[:, [1, 2]] = sympy.rad(zm_values_rad[:, [1, 2]])
energy_symb = np.sum(zm_values_rad * grad_energy_C)
grad_energy_symb = sympy.Matrix([
energy_symb.diff(arg) for arg in symbolic_expressions])
grad_energy_symb = np.array(grad_energy_symb.subs(substitutions))
grad_energy_symb = grad_energy_symb.astype('f8').flatten()
new_zmat.metadata['energy'] = energy
new_zmat.metadata['symbols'] = substitutions
calculated.append({'energy': energy, 'structure': new_zmat,
'symbols': substitutions})
with open(md_out, 'a') as f:
f.write(_get_table_row(calculated, grad_energy_symb))
if is_converged(calculated, etol=etol):
raise ConvergenceFinished(successful=True)
elif len(calculated) >= max_iter:
raise ConvergenceFinished(successful=False)
return grad_energy_symb
else:
raise ValueError
def grad_V(C_rad=None, get_calculated=False,
calculated=[]): # pylint:disable=dangerous-default-value
if get_calculated:
return calculated
elif C_rad is not None:
try:
previous_zmat = calculated[-1]['structure'].copy()
except IndexError:
new_zmat = zmolecule.copy()
else:
new_zmat = get_new_zmat(C_rad, previous_zmat)
if isfile(input_path(len(calculated))):
result = {}
while len(result.keys()) < 3:
try:
result = molpro.parse_output(output_path(len(calculated)))
except FileNotFoundError:
pass
sleep(0.5)
else:
result = molpro.calculate(
molecule=new_zmat, forces=True,
el_calc_input=input_path(len(calculated)),
hamiltonian=hamiltonian, basis=basis,
charge=charge, title=title,
multiplicity=multiplicity,
num_procs=num_procs, mem_per_proc=mem_per_proc, **kwargs)
energy, grad_energy_X = result['energy'], result['gradient']
grad_energy_C = _get_grad_energy_C(new_zmat, grad_energy_X)
new_zmat.metadata['energy'] = energy
new_zmat.metadata['grad_energy'] = grad_energy_C
calculated.append({'energy': energy, 'grad_energy': grad_energy_C,
'structure': new_zmat})
with open(md_out, 'a') as f:
f.write(_get_table_row(calculated, grad_energy_X))
if is_converged(calculated, grad_energy_X, etol=etol, gtol=gtol):
raise ConvergenceFinished(successful=True)
elif len(calculated) >= max_iter:
raise ConvergenceFinished(successful=False)
return grad_energy_C.flatten()
else:
raise ValueError
def calculate(molecule,
hamiltonian,
basis,
el_calc_input=None,
backend=None,
charge=fixed_defaults['charge'],
calculation_type=fixed_defaults['calculation_type'],
forces=fixed_defaults['forces'],
title=fixed_defaults['title'],
multiplicity=fixed_defaults['multiplicity'],
**kwargs):
"""Calculate the energy of a molecule.
Args:
molecule (chemcoord.Cartesian or chemcoord.Zmat or str):
If it is a string, it has to be a valid xyz-file.
hamiltonian (str): {hamiltonian}
basis (str): {basis}
el_calc_input (str): {el_calc_input}
backend (str): {backend}
charge (int): {charge}
calculation_type (str): {calculation_type}
forces (bool): {forces}
title (str): {title}
multiplicity (int): {multiplicity}
Returns:
cclib.Parser : A `cclib <https://cclib.github.io/>`_
parsed data instance.
"""
if backend is None:
backend = conf_defaults['backend']
if backend == 'molpro':
return molpro.calculate(el_calc_input=el_calc_input,
molecule=molecule,
hamiltonian=hamiltonian,
basis=basis,
charge=charge,
calculation_type=calculation_type,
forces=forces,
title=title,
multiplicity=multiplicity,
**kwargs)
else:
raise ValueError('Backend {} is not implemented.'.format(backend))