def compute_nbody_components(func, method_string, metadata):
"""Computes requested N-body components.
Performs requested computations for psi4::Molecule object `molecule` according to
`compute_list` with function `func` at `method_string` level of theory.
Parameters
----------
func : {'energy', 'gradient', 'hessian'}
Function object to be called within N-Body procedure.
method_string : str
Indicates level of theory to be passed to function `func`.
metadata : dict of str
Dictionary of N-body metadata.
Required ``'key': value`` pairs:
``'compute_list'``: dict of int: set
List of computations to perform. Keys indicate body-levels, e.g,. `compute_list[2]` is the
list of all 2-body computations required.
``'kwargs'``: dict
Arbitrary keyword arguments to be passed to function `func`.
Returns
-------
dict of str: dict
Dictionary containing computed N-body components.
Contents:
``'energies'``: dict of set: float64
Dictionary containing all energy components required for given N-body procedure.
``'ptype'``: dict of set: float64 or dict of set: psi4.Matrix
Dictionary of returned quantities from calls of function `func` during N-body computations
``'intermediates'``: dict of str: float64
Dictionary of psivars for intermediate N-body computations to be set at the end of the
N-body procedure.
"""
# Get required metadata
kwargs = metadata['kwargs']
molecule = metadata['molecule']
#molecule = core.get_active_molecule()
compute_list = metadata['compute_dict']['all']
# Now compute the energies
energies_dict = {}
gradients_dict = {}
ptype_dict = {}
intermediates_dict = {}
if kwargs.get('charge_method', False) and not metadata['embedding_charges']:
metadata['embedding_charges'] = driver_nbody_helper.compute_charges(kwargs['charge_method'],
kwargs.get('charge_type', 'MULLIKEN_CHARGES').upper(), molecule)
for count, n in enumerate(compute_list.keys()):
core.print_out("\n ==> N-Body: Now computing %d-body complexes <==\n\n" % n)
total = len(compute_list[n])
for num, pair in enumerate(compute_list[n]):
core.print_out(
"\n N-Body: Computing complex (%d/%d) with fragments %s in the basis of fragments %s.\n\n" %
(num + 1, total, str(pair[0]), str(pair[1])))
ghost = list(set(pair[1]) - set(pair[0]))
current_mol = molecule.extract_subsets(list(pair[0]), ghost)
current_mol.set_name("%s_%i_%i" % (current_mol.name(), count, num))
if metadata['embedding_charges']: driver_nbody_helper.electrostatic_embedding(metadata, pair=pair)
# Save energies info
ptype_dict[pair], wfn = func(method_string, molecule=current_mol, return_wfn=True, **kwargs)
core.set_global_option_python('EXTERN', None)
energies_dict[pair] = core.variable("CURRENT ENERGY")
gradients_dict[pair] = wfn.gradient()
var_key = "N-BODY (%s)@(%s) TOTAL ENERGY" % (', '.join([str(i) for i in pair[0]]), ', '.join(
[str(i) for i in pair[1]]))
intermediates_dict[var_key] = core.variable("CURRENT ENERGY")
core.print_out("\n N-Body: Complex Energy (fragments = %s, basis = %s: %20.14f)\n" % (str(
pair[0]), str(pair[1]), energies_dict[pair]))
# Flip this off for now, needs more testing
#if 'cp' in bsse_type_list and (len(bsse_type_list) == 1):
# core.set_global_option('DF_INTS_IO', 'LOAD')
core.clean()
return {
'energies': energies_dict,
'gradients': gradients_dict,
'ptype': ptype_dict,
'intermediates': intermediates_dict
}
def compute_nbody_components(func, method_string, metadata):
"""Computes requested N-body components.
Performs requested computations for psi4::Molecule object `molecule` according to
`compute_list` with function `func` at `method_string` level of theory.
Parameters
----------
func : str
{'energy', 'gradient', 'hessian'}
Function object to be called within N-Body procedure.
method_string : str
Indicates level of theory to be passed to function `func`.
metadata : dict of str
Dictionary of N-body metadata.
Required ``'key': value`` pairs:
``'compute_list'``: dict of int: set
List of computations to perform. Keys indicate body-levels, e.g,. `compute_list[2]` is the
list of all 2-body computations required.
``'kwargs'``: dict
Arbitrary keyword arguments to be passed to function `func`.
Returns
-------
dict of str: dict
Dictionary containing computed N-body components.
Contents:
``'energies'``: dict of set: float64
Dictionary containing all energy components required for given N-body procedure.
``'ptype'``: dict of set: float64 or dict of set: psi4.Matrix
Dictionary of returned quantities from calls of function `func` during N-body computations
``'intermediates'``: dict of str: float64
Dictionary of psivars for intermediate N-body computations to be set at the end of the
N-body procedure.
"""
# Get required metadata
kwargs = metadata['kwargs']
molecule = metadata['molecule']
#molecule = core.get_active_molecule()
compute_list = metadata['compute_dict']['all']
# Now compute the energies
energies_dict = {}
gradients_dict = {}
ptype_dict = {}
intermediates_dict = {}
if kwargs.get('charge_method',
False) and not metadata['embedding_charges']:
metadata['embedding_charges'] = driver_nbody_helper.compute_charges(
kwargs['charge_method'],
kwargs.get('charge_type', 'MULLIKEN_CHARGES').upper(), molecule)
for count, n in enumerate(compute_list.keys()):
core.print_out(
"\n ==> N-Body: Now computing %d-body complexes <==\n\n" % n)
total = len(compute_list[n])
for num, pair in enumerate(compute_list[n]):
core.print_out(
"\n N-Body: Computing complex (%d/%d) with fragments %s in the basis of fragments %s.\n\n"
% (num + 1, total, str(pair[0]), str(pair[1])))
ghost = list(set(pair[1]) - set(pair[0]))
current_mol = molecule.extract_subsets(list(pair[0]), ghost)
current_mol.set_name("%s_%i_%i" % (current_mol.name(), count, num))
if metadata['embedding_charges']:
driver_nbody_helper.electrostatic_embedding(metadata,
pair=pair)
# Save energies info
ptype_dict[pair], wfn = func(method_string,
molecule=current_mol,
return_wfn=True,
**kwargs)
core.set_global_option_python('EXTERN', None)
energies_dict[pair] = core.variable("CURRENT ENERGY")
gradients_dict[pair] = wfn.gradient()
var_key = "N-BODY (%s)@(%s) TOTAL ENERGY" % (', '.join(
[str(i)
for i in pair[0]]), ', '.join([str(i) for i in pair[1]]))
intermediates_dict[var_key] = core.variable("CURRENT ENERGY")
core.print_out(
"\n N-Body: Complex Energy (fragments = %s, basis = %s: %20.14f)\n"
% (str(pair[0]), str(pair[1]), energies_dict[pair]))
# Flip this off for now, needs more testing
#if 'cp' in bsse_type_list and (len(bsse_type_list) == 1):
# core.set_global_option('DF_INTS_IO', 'LOAD')
core.clean()
return {
'energies': energies_dict,
'gradients': gradients_dict,
'ptype': ptype_dict,
'intermediates': intermediates_dict
}
