#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
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# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, version 3.
#
# Psi4 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
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# You should have received a copy of the GNU Lesser General Public License along
# with Psi4; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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# @END LICENSE
#
import math
import itertools
import numpy as np
from psi4 import core
from psi4.driver import p4util
from psi4.driver import constants
from psi4.driver.p4util.exceptions import *
from psi4.driver import driver_nbody_helper
### Math helper functions
def nCr(n, r):
f = math.factorial
return f(n) // f(r) // f(n - r)
### Begin CBS gufunc data
def _sum_cluster_ptype_data(ptype,
ptype_dict,
compute_list,
fragment_slice_dict,
fragment_size_dict,
ret,
vmfc=False,
n=0):
"""
Sums gradient and hessian data from compute_list.
compute_list comes in as a tuple(frag, basis)
"""
if len(compute_list) == 0:
return
sign = 1
# Do ptype
if ptype == 'gradient':
for fragn, basisn in compute_list:
start = 0
grad = np.asarray(ptype_dict[(fragn, basisn)])
if vmfc:
sign = ((-1)**(n - len(fragn)))
for bas in basisn:
end = start + fragment_size_dict[bas]
ret[fragment_slice_dict[bas]] += sign * grad[start:end]
start += fragment_size_dict[bas]
elif ptype == 'hessian':
for fragn, basisn in compute_list:
hess = np.asarray(ptype_dict[(fragn, basisn)])
if vmfc:
sign = ((-1)**(n - len(fragn)))
# Build up start and end slices
abs_start, rel_start = 0, 0
abs_slices, rel_slices = [], []
for bas in basisn:
rel_end = rel_start + 3 * fragment_size_dict[bas]
rel_slices.append(slice(rel_start, rel_end))
rel_start += 3 * fragment_size_dict[bas]
tmp_slice = fragment_slice_dict[bas]
abs_slices.append(slice(tmp_slice.start * 3, tmp_slice.stop * 3))
for abs_sl1, rel_sl1 in zip(abs_slices, rel_slices):
for abs_sl2, rel_sl2 in zip(abs_slices, rel_slices):
ret[abs_sl1, abs_sl2] += hess[rel_sl1, rel_sl2]
else:
raise KeyError("ptype can only be gradient or hessian How did you end up here?")
def _print_nbody_energy(energy_body_dict, header, embedding=False):
core.print_out("""\n ==> N-Body: %s energies <==\n\n""" % header)
core.print_out(""" n-Body Total Energy [Eh] I.E. [kcal/mol] Delta [kcal/mol]\n""")
previous_e = energy_body_dict[1]
nbody_range = list(energy_body_dict)
nbody_range.sort()
for n in nbody_range:
delta_e = (energy_body_dict[n] - previous_e)
delta_e_kcal = delta_e * constants.hartree2kcalmol
int_e_kcal = (
energy_body_dict[n] - energy_body_dict[1]) * constants.hartree2kcalmol if not embedding else np.nan
core.print_out(
""" %4s %20.12f %20.12f %20.12f\n""" % (n, energy_body_dict[n], int_e_kcal, delta_e_kcal))
previous_e = energy_body_dict[n]
core.print_out("\n")
[docs]def nbody_gufunc(func, method_string, **kwargs):
"""
Computes the nbody interaction energy, gradient, or Hessian depending on input.
This is a generalized univeral function for computing interaction and total quantities.
:returns: *return type of func* |w--w| The data.
:returns: (*float*, :py:class:`~psi4.core.Wavefunction`) |w--w| data and wavefunction with energy/gradient/hessian set appropriately when **return_wfn** specified.
:type func: function
:param func: ``energy`` || etc.
Python function that accepts method_string and a molecule. Returns a
energy, gradient, or Hessian as requested.
:type method_string: string
:param method_string: ``'scf'`` || ``'mp2'`` || ``'ci5'`` || etc.
First argument, lowercase and usually unlabeled. Indicates the computational
method to be passed to func.
:type molecule: :ref:`molecule <op_py_molecule>`
:param molecule: ``h2o`` || etc.
The target molecule, if not the last molecule defined.
:type return_wfn: :ref:`boolean <op_py_boolean>`
:param return_wfn: ``'on'`` || |dl| ``'off'`` |dr|
Indicate to additionally return the :py:class:`~psi4.core.Wavefunction`
calculation result as the second element of a tuple.
:type bsse_type: string or list
:param bsse_type: ``'cp'`` || ``['nocp', 'vmfc']`` || |dl| ``None`` |dr| || etc.
Type of BSSE correction to compute: CP, NoCP, or VMFC. The first in this
list is returned by this function. By default, this function is not called.
:type max_nbody: int
:param max_nbody: ``3`` || etc.
Maximum n-body to compute, cannot exceed the number of fragments in the moleucle.
:type ptype: string
:param ptype: ``'energy'`` || ``'gradient'`` || ``'hessian'``
Type of the procedure passed in.
:type return_total_data: :ref:`boolean <op_py_boolean>`
:param return_total_data: ``'on'`` || |dl| ``'off'`` |dr|
If True returns the total data (energy/gradient/etc) of the system,
otherwise returns interaction data.
:type levels: dict
:param levels: ``{1: 'ccsd(t)', 2: 'mp2', 'supersystem': 'scf'}`` || ``{1: 2, 2: 'ccsd(t)', 3: 'mp2'}`` || etc
Dictionary of different levels of theory for different levels of expansion
Note that method_string is not used in this case.
supersystem computes all higher order n-body effects up to nfragments.
:type embedding_charges: dict
:param embedding_charges: ``{1: [-0.834, 0.417, 0.417], ..}``
Dictionary of atom-centered point charges. keys: 1-based index of fragment, values: list of charges for each fragment.
:type charge_method: string
:param charge_method: ``scf/6-31g`` || ``b3lyp/6-31g*`` || etc
Method to compute point charges for monomers. Overridden by embedding_charges if both are provided.
:type charge_type: string
:param charge_type: ``MULLIKEN_CHARGES`` || ``LOWDIN_CHARGES``
Default is ``MULLIKEN_CHARGES``
"""
# Initialize dictionaries for easy data passing
metadata, component_results, nbody_results = {}, {}, {}
# Parse some kwargs
kwargs = p4util.kwargs_lower(kwargs)
if kwargs.get('levels', False):
return driver_nbody_helper.multi_level(func, **kwargs)
metadata['ptype'] = kwargs.pop('ptype', None)
metadata['return_wfn'] = kwargs.pop('return_wfn', False)
metadata['return_total_data'] = kwargs.pop('return_total_data', False)
metadata['molecule'] = kwargs.pop('molecule', core.get_active_molecule())
metadata['molecule'].update_geometry()
metadata['molecule'].fix_com(True)
metadata['molecule'].fix_orientation(True)
metadata['embedding_charges'] = kwargs.get('embedding_charges', False)
metadata['kwargs'] = kwargs
core.clean_variables()
if metadata['ptype'] not in ['energy', 'gradient', 'hessian']:
raise ValidationError("""N-Body driver: The ptype '%s' is not regonized.""" % metadata['ptype'])
# Parse bsse_type, raise exception if not provided or unrecognized
metadata['bsse_type_list'] = kwargs.pop('bsse_type')
if metadata['bsse_type_list'] is None:
raise ValidationError("N-Body GUFunc: Must pass a bsse_type")
if not isinstance(metadata['bsse_type_list'], list):
metadata['bsse_type_list'] = [metadata['bsse_type_list']]
for num, btype in enumerate(metadata['bsse_type_list']):
metadata['bsse_type_list'][num] = btype.lower()
if btype.lower() not in ['cp', 'nocp', 'vmfc']:
raise ValidationError("N-Body GUFunc: bsse_type '%s' is not recognized" % btype.lower())
metadata['max_nbody'] = kwargs.get('max_nbody', -1)
metadata['max_frag'] = metadata['molecule'].nfragments()
if metadata['max_nbody'] == -1:
metadata['max_nbody'] = metadata['molecule'].nfragments()
else:
metadata['max_nbody'] = min(metadata['max_nbody'], metadata['max_frag'])
# Flip this off for now, needs more testing
# If we are doing CP lets save them integrals
#if 'cp' in bsse_type_list and (len(bsse_type_list) == 1):
# # Set to save RI integrals for repeated full-basis computations
# ri_ints_io = core.get_global_option('DF_INTS_IO')
# # inquire if above at all applies to dfmp2 or just scf
# core.set_global_option('DF_INTS_IO', 'SAVE')
# psioh = core.IOManager.shared_object()
# psioh.set_specific_retention(97, True)
bsse_str = metadata['bsse_type_list'][0]
if len(metadata['bsse_type_list']) > 1:
bsse_str = str(metadata['bsse_type_list'])
core.print_out("\n\n")
core.print_out(" ===> N-Body Interaction Abacus <===\n")
core.print_out(" BSSE Treatment: %s\n" % bsse_str)
# Get compute list
metadata = build_nbody_compute_list(metadata)
# Compute N-Body components
component_results = compute_nbody_components(func, method_string, metadata)
# Assemble N-Body quantities
nbody_results = assemble_nbody_components(metadata, component_results)
# Build wfn and bind variables
wfn = core.Wavefunction.build(metadata['molecule'], 'def2-svp')
dicts = [
'energies', 'ptype', 'intermediates', 'energy_body_dict', 'gradient_body_dict', 'hessian_body_dict', 'nbody',
'cp_energy_body_dict', 'nocp_energy_body_dict', 'vmfc_energy_body_dict'
]
if metadata['ptype'] == 'gradient':
wfn.set_gradient(nbody_results['ret_ptype'])
nbody_results['gradient_body_dict'] = nbody_results['ptype_body_dict']
elif metadata['ptype'] == 'hessian':
nbody_results['hessian_body_dict'] = nbody_results['ptype_body_dict']
wfn.set_hessian(nbody_results['ret_ptype'])
component_results_gradient = component_results.copy()
component_results_gradient['ptype'] = component_results_gradient['gradients']
metadata['ptype'] = 'gradient'
nbody_results_gradient = assemble_nbody_components(metadata, component_results_gradient)
wfn.set_gradient(nbody_results_gradient['ret_ptype'])
nbody_results['gradient_body_dict'] = nbody_results_gradient['ptype_body_dict']
for r in [component_results, nbody_results]:
for d in r:
if d in dicts:
for var, value in r[d].items():
try:
wfn.set_scalar_variable(str(var), value)
core.set_scalar_variable(str(var), value)
except:
wfn.set_array_variable(d.split('_')[0].upper() + ' ' + str(var), core.Matrix.from_array(value))
core.set_variable("CURRENT ENERGY", nbody_results['ret_energy'])
wfn.set_variable("CURRENT ENERGY", nbody_results['ret_energy'])
if metadata['return_wfn']:
return (nbody_results['ret_ptype'], wfn)
else:
return nbody_results['ret_ptype']
def build_nbody_compute_list(metadata):
"""Generates the list of N-Body computations to be performed for a given BSSE type.
Parameters
----------
metadata : dict of str
Dictionary containing N-body metadata.
Required ``'key': value`` pairs:
``'bsse_type_list'``: list of str
List of requested BSSE treatments. Possible values include lowercase ``'cp'``, ``'nocp'``,
and ``'vmfc'``.
``'max_nbody'``: int
Maximum number of bodies to include in the N-Body treatment.
Possible: `max_nbody` <= `max_frag`
Default: `max_nbody` = `max_frag`
``'max_frag'``: int
Number of distinct fragments comprising full molecular supersystem.
Returns
-------
metadata : dict of str
Dictionary containing N-body metadata.
New ``'key': value`` pair:
``'compute_dict'`` : dict of str: dict
Dictionary containing subdicts enumerating compute lists for each possible BSSE treatment.
Contents:
``'all'``: dict of int: set
Set containing full list of computations required
``'cp'``: dict of int: set
Set containing list of computations required for CP procedure
``'nocp'``: dict of int: set
Set containing list of computations required for non-CP procedure
``'vmfc_compute'``: dict of int: set
Set containing list of computations required for VMFC procedure
``'vmfc_levels'``: dict of int: set
Set containing list of levels required for VMFC procedure
"""
# What levels do we need?
nbody_range = range(1, metadata['max_nbody'] + 1)
fragment_range = range(1, metadata['max_frag'] + 1)
cp_compute_list = {x: set() for x in nbody_range}
nocp_compute_list = {x: set() for x in nbody_range}
vmfc_compute_list = {x: set() for x in nbody_range}
vmfc_level_list = {x: set() for x in nbody_range} # Need to sum something slightly different
# Verify proper passing of bsse_type_list
bsse_type_remainder = set(metadata['bsse_type_list']) - {'cp', 'nocp', 'vmfc'}
if bsse_type_remainder:
raise ValidationError("""Unrecognized BSSE type(s): %s
Possible values are 'cp', 'nocp', and 'vmfc'.""" % ', '.join(str(i) for i in bsse_type_remainder))
# Build up compute sets
if 'cp' in metadata['bsse_type_list']:
# Everything is in dimer basis
basis_tuple = tuple(fragment_range)
for nbody in nbody_range:
for x in itertools.combinations(fragment_range, nbody):
if metadata['max_nbody'] == 1: break
cp_compute_list[nbody].add((x, basis_tuple))
# Add monomers in monomer basis
for x in fragment_range:
cp_compute_list[1].add(((x, ), (x, )))
if 'nocp' in metadata['bsse_type_list']:
# Everything in monomer basis
for nbody in nbody_range:
for x in itertools.combinations(fragment_range, nbody):
nocp_compute_list[nbody].add((x, x))
if 'vmfc' in metadata['bsse_type_list']:
# Like a CP for all combinations of pairs or greater
for nbody in nbody_range:
for cp_combos in itertools.combinations(fragment_range, nbody):
basis_tuple = tuple(cp_combos)
for interior_nbody in nbody_range:
for x in itertools.combinations(cp_combos, interior_nbody):
combo_tuple = (x, basis_tuple)
vmfc_compute_list[interior_nbody].add(combo_tuple)
vmfc_level_list[len(basis_tuple)].add(combo_tuple)
# Build a comprehensive compute_range
compute_list = {x: set() for x in nbody_range}
for n in nbody_range:
compute_list[n] |= cp_compute_list[n]
compute_list[n] |= nocp_compute_list[n]
compute_list[n] |= vmfc_compute_list[n]
core.print_out(" Number of %d-body computations: %d\n" % (n, len(compute_list[n])))
metadata['compute_dict'] = {
'all': compute_list,
'cp': cp_compute_list,
'nocp': nocp_compute_list,
'vmfc_compute': vmfc_compute_list,
'vmfc_levels': vmfc_level_list
}
return metadata
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 assemble_nbody_components(metadata, component_results):
"""Assembles N-body components into interaction quantities according to requested BSSE procedure(s).
Parameters
-----------
metadata : dict of str
Dictionary of N-body metadata.
Required ``'key': value`` pairs:
``'ptype'``: {'energy', 'gradient', 'hessian'}
Procedure which has generated the N-body components to be combined.
``'bsse_type_list'``: list of str
List of requested BSSE treatments. Possible values include lowercase ``'cp'``, ``'nocp'``,
and ``'vmfc'``.
``'max_nbody'``: int
Maximum number of bodies to include in the N-Body treatment.
Possible: `max_nbody` <= `max_frag`
Default: `max_nbody` = `max_frag`
``'max_frag'``: int
Number of distinct fragments comprising full molecular supersystem.
``'energies_dict'``: dict of set: float64
Dictionary containing all energy components required for given N-body procedure.
``'ptype_dict'``: dict of set: float64 or dict of set: psi4.Matrix
Dictionary of returned quantities from calls of function `func` during N-body computations
``'compute_dict'``: dict of str: dict
Dictionary containing {int: set} subdicts enumerating compute lists for each possible
BSSE treatment.
``'kwargs'``: dict
Arbitrary keyword arguments.
component_results : dict of str: dict
Dictionary containing computed N-body components.
Required ``'key': value`` pairs:
``'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.
Returns
-------
results : dict of str
Dictionary of all N-body results.
Contents:
``'ret_energy'``: float64
Interaction data requested. If multiple BSSE types requested in `bsse_type_list`, the
interaction data associated with the *first* BSSE type in the list is returned.
``'nbody_dict'``: dict of str: float64
Dictionary of relevant N-body psivars to be set
``'energy_body_dict'``: dict of int: float64
Dictionary of total energies at each N-body level, i.e., ``results['energy_body_dict'][2]``
is the sum of all 2-body total energies for the supersystem.
``'ptype_body_dict'``: dict or dict of int: array_like
Empty dictionary if `ptype is ``'energy'``, or dictionary of total ptype arrays at each
N-body level; i.e., ``results['ptype_body_dict'][2]`` for `ptype` ``'gradient'``is the
total 2-body gradient.
"""
# Unpack metadata
kwargs = metadata['kwargs']
nbody_range = range(1, metadata['max_nbody'] + 1)
# Unpack compute list metadata
compute_list = metadata['compute_dict']['all']
cp_compute_list = metadata['compute_dict']['cp']
nocp_compute_list = metadata['compute_dict']['nocp']
vmfc_compute_list = metadata['compute_dict']['vmfc_compute']
vmfc_level_list = metadata['compute_dict']['vmfc_levels']
# Build size and slices dictionaries
fragment_size_dict = {
frag: metadata['molecule'].extract_subsets(frag).natom()
for frag in range(1, metadata['max_frag'] + 1)
}
start = 0
fragment_slice_dict = {}
for k, v in fragment_size_dict.items():
fragment_slice_dict[k] = slice(start, start + v)
start += v
molecule_total_atoms = sum(fragment_size_dict.values())
# Final dictionaries
cp_energy_by_level = {n: 0.0 for n in nbody_range}
nocp_energy_by_level = {n: 0.0 for n in nbody_range}
cp_energy_body_dict = {n: 0.0 for n in nbody_range}
nocp_energy_body_dict = {n: 0.0 for n in nbody_range}
vmfc_energy_body_dict = {n: 0.0 for n in nbody_range}
# Build out ptype dictionaries if needed
if metadata['ptype'] != 'energy':
if metadata['ptype'] == 'gradient':
arr_shape = (molecule_total_atoms, 3)
elif metadata['ptype'] == 'hessian':
arr_shape = (molecule_total_atoms * 3, molecule_total_atoms * 3)
else:
raise KeyError("N-Body: ptype '%s' not recognized" % ptype)
cp_ptype_by_level = {n: np.zeros(arr_shape) for n in nbody_range}
nocp_ptype_by_level = {n: np.zeros(arr_shape) for n in nbody_range}
vmfc_ptype_by_level = {n: np.zeros(arr_shape) for n in nbody_range}
cp_ptype_body_dict = {n: np.zeros(arr_shape) for n in nbody_range}
nocp_ptype_body_dict = {n: np.zeros(arr_shape) for n in nbody_range}
vmfc_ptype_body_dict = {n: np.zeros(arr_shape) for n in nbody_range}
else:
cp_ptype_by_level, cp_ptype_body_dict = {}, {}
nocp_ptype_by_level, nocp_ptype_body_dict = {}, {}
vmfc_ptype_body_dict = {}
# Sum up all of the levels
nbody_dict = {}
for n in nbody_range:
# Energy
# Extract energies for monomers in monomer basis for CP total data
if n == 1:
cp_monomers_in_monomer_basis = [v for v in cp_compute_list[1] if len(v[1]) == 1]
cp_monomer_energies = 0.0
cp_monomer_energy_list = []
for i in cp_monomers_in_monomer_basis:
cp_monomer_energy_list.append(component_results['energies'][i])
cp_monomer_energies += component_results['energies'][i]
cp_compute_list[1].remove(i)
cp_energy_by_level[n] = sum(component_results['energies'][v] for v in cp_compute_list[n])
nocp_energy_by_level[n] = sum(component_results['energies'][v] for v in nocp_compute_list[n])
# Special vmfc case
if n > 1:
vmfc_energy_body_dict[n] = vmfc_energy_body_dict[n - 1]
for tup in vmfc_level_list[n]:
vmfc_energy_body_dict[n] += ((-1)**(n - len(tup[0]))) * component_results['energies'][tup]
# Do ptype
if metadata['ptype'] != 'energy':
_sum_cluster_ptype_data(metadata['ptype'], component_results['ptype'], cp_compute_list[n],
fragment_slice_dict, fragment_size_dict, cp_ptype_by_level[n])
_sum_cluster_ptype_data(metadata['ptype'], component_results['ptype'], nocp_compute_list[n],
fragment_slice_dict, fragment_size_dict, nocp_ptype_by_level[n])
_sum_cluster_ptype_data(
metadata['ptype'],
component_results['ptype'],
vmfc_level_list[n],
fragment_slice_dict,
fragment_size_dict,
vmfc_ptype_by_level[n],
vmfc=True,
n=n)
# Add extracted monomers back.
for i, j in enumerate(cp_monomers_in_monomer_basis):
cp_compute_list[1].add(j)
if metadata['ptype'] != 'energy':
# Extract ptype data for monomers in monomer basis for CP total data
cp_monomer_ptype = np.zeros(arr_shape)
_sum_cluster_ptype_data(metadata['ptype'], component_results['ptype'], cp_monomers_in_monomer_basis,
fragment_slice_dict, fragment_size_dict, cp_monomer_ptype)
# Compute cp energy and ptype
if 'cp' in metadata['bsse_type_list']:
for n in nbody_range:
if n == metadata['max_frag']:
cp_energy_body_dict[n] = cp_energy_by_level[n] - bsse
if metadata['ptype'] != 'energy':
cp_ptype_body_dict[n][:] = cp_ptype_by_level[n] - bsse_ptype
continue
for k in range(1, n + 1):
take_nk = nCr(metadata['max_frag'] - k - 1, n - k)
sign = ((-1)**(n - k))
value = cp_energy_by_level[k]
cp_energy_body_dict[n] += take_nk * sign * value
if metadata['ptype'] != 'energy':
value = cp_ptype_by_level[k]
cp_ptype_body_dict[n] += take_nk * sign * value
if n == 1:
bsse = cp_energy_body_dict[n] - cp_monomer_energies
cp_energy_body_dict[n] = cp_monomer_energies
if metadata['ptype'] != 'energy':
bsse_ptype = cp_ptype_body_dict[n] - cp_monomer_ptype
cp_ptype_body_dict[n] = cp_monomer_ptype.copy()
else:
cp_energy_body_dict[n] -= bsse
if metadata['ptype'] != 'energy':
cp_ptype_body_dict[n] -= bsse_ptype
cp_interaction_energy = cp_energy_body_dict[metadata['max_nbody']] - cp_energy_body_dict[1]
nbody_dict['Counterpoise Corrected Interaction Energy'] = cp_interaction_energy
for n in nbody_range[1:]:
var_key = 'CP-CORRECTED %d-BODY INTERACTION ENERGY' % n
nbody_dict[var_key] = cp_energy_body_dict[n] - cp_energy_body_dict[1]
_print_nbody_energy(cp_energy_body_dict, "Counterpoise Corrected (CP)", metadata['embedding_charges'])
cp_interaction_energy = cp_energy_body_dict[metadata['max_nbody']] - cp_energy_body_dict[1]
nbody_dict['Counterpoise Corrected Total Energy'] = cp_energy_body_dict[metadata['max_nbody']]
nbody_dict['Counterpoise Corrected Interaction Energy'] = cp_interaction_energy
# Compute nocp energy and ptype
if 'nocp' in metadata['bsse_type_list']:
for n in nbody_range:
if n == metadata['max_frag']:
nocp_energy_body_dict[n] = nocp_energy_by_level[n]
if metadata['ptype'] != 'energy':
nocp_ptype_body_dict[n][:] = nocp_ptype_by_level[n]
continue
for k in range(1, n + 1):
take_nk = nCr(metadata['max_frag'] - k - 1, n - k)
sign = ((-1)**(n - k))
value = nocp_energy_by_level[k]
nocp_energy_body_dict[n] += take_nk * sign * value
if metadata['ptype'] != 'energy':
value = nocp_ptype_by_level[k]
nocp_ptype_body_dict[n] += take_nk * sign * value
_print_nbody_energy(nocp_energy_body_dict, "Non-Counterpoise Corrected (NoCP)", metadata['embedding_charges'])
nocp_interaction_energy = nocp_energy_body_dict[metadata['max_nbody']] - nocp_energy_body_dict[1]
nbody_dict['Non-Counterpoise Corrected Total Energy'] = nocp_energy_body_dict[metadata['max_nbody']]
nbody_dict['Non-Counterpoise Corrected Interaction Energy'] = nocp_interaction_energy
for n in nbody_range[1:]:
var_key = 'NOCP-CORRECTED %d-BODY INTERACTION ENERGY' % n
nbody_dict[var_key] = nocp_energy_body_dict[n] - nocp_energy_body_dict[1]
# Compute vmfc ptype
if 'vmfc' in metadata['bsse_type_list']:
if metadata['ptype'] != 'energy':
for n in nbody_range:
if n > 1:
vmfc_ptype_body_dict[n] = vmfc_ptype_by_level[n-1]
vmfc_ptype_body_dict[n] += vmfc_ptype_by_level[n]
_print_nbody_energy(vmfc_energy_body_dict, "Valiron-Mayer Function Couterpoise (VMFC)",
metadata['embedding_charges'])
vmfc_interaction_energy = vmfc_energy_body_dict[metadata['max_nbody']] - vmfc_energy_body_dict[1]
nbody_dict['Valiron-Mayer Function Couterpoise Total Energy'] = vmfc_energy_body_dict[metadata['max_nbody']]
nbody_dict['Valiron-Mayer Function Couterpoise Interaction Energy'] = vmfc_interaction_energy
for n in nbody_range[1:]:
var_key = 'VMFC-CORRECTED %d-BODY INTERACTION ENERGY' % n
nbody_dict[var_key] = vmfc_energy_body_dict[n] - vmfc_energy_body_dict[1]
# Returns
results = {}
results['nbody'] = nbody_dict
for b in ['cp', 'nocp', 'vmfc']:
results['%s_energy_body_dict' % b] = eval('%s_energy_body_dict' % b)
results['%s_energy_body_dict' % b] = {str(i) + b: j for i, j in results['%s_energy_body_dict' % b].items()}
# Figure out and build return types
return_method = metadata['bsse_type_list'][0]
if return_method == 'cp':
results['ptype_body_dict'] = cp_ptype_body_dict
results['energy_body_dict'] = cp_energy_body_dict
elif return_method == 'nocp':
results['ptype_body_dict'] = nocp_ptype_body_dict
results['energy_body_dict'] = nocp_energy_body_dict
elif return_method == 'vmfc':
results['ptype_body_dict'] = vmfc_ptype_body_dict
results['energy_body_dict'] = vmfc_energy_body_dict
else:
raise ValidationError(
"N-Body Wrapper: Invalid return type. Should never be here, please post this error on github.")
if metadata['return_total_data']:
results['ret_energy'] = results['energy_body_dict'][metadata['max_nbody']]
else:
results['ret_energy'] = results['energy_body_dict'][metadata['max_nbody']]
results['ret_energy'] -= results['energy_body_dict'][1]
if metadata['ptype'] != 'energy':
if metadata['return_total_data']:
np_final_ptype = results['ptype_body_dict'][metadata['max_nbody']].copy()
else:
np_final_ptype = results['ptype_body_dict'][metadata['max_nbody']].copy()
np_final_ptype -= results['ptype_body_dict'][1]
results['ret_ptype'] = core.Matrix.from_array(np_final_ptype)
else:
results['ret_ptype'] = results['ret_energy']
return results
