def get_integrals(self, names=None, kind=None):
"""
Get integrals, initialized from problem configuration if available.
Parameters
----------
names : list, optional
If given, only the named integrals are returned.
kind : 'v' or 's', optional
If given, only integrals of the given kind are returned.
Returns
-------
integrals : Integrals instance
The requested integrals.
"""
conf_integrals = self.conf.get_default_attr('integrals', {})
integrals = Integrals.from_conf(conf_integrals)
if names is not None:
integrals.update([integrals[ii] for ii in names
if ii in integrals.names])
if kind is not None:
integrals.update([ii for ii in integrals
if ii.kind.startswith(kind)])
return integrals
def get_integrals(self, names=None, kind=None):
"""
Get integrals, initialized from problem configuration if available.
Parameters
----------
names : list, optional
If given, only the named integrals are returned.
kind : 'v' or 's', optional
If given, only integrals of the given kind are returned.
Returns
-------
integrals : Integrals instance
The requested integrals.
"""
conf_integrals = self.conf.get('integrals', {})
integrals = Integrals.from_conf(conf_integrals)
if names is not None:
integrals.update(
[integrals[ii] for ii in names if ii in integrals.names])
if kind is not None:
integrals.update(
[ii for ii in integrals if ii.kind.startswith(kind)])
return integrals
def get_integrals(self, names=None):
"""
Get integrals, initialized from problem configuration if available.
Parameters
----------
names : list, optional
If given, only the named integrals are returned.
Returns
-------
integrals : Integrals instance
The requested integrals.
"""
conf_integrals = self.conf.get("integrals", {})
integrals = Integrals.from_conf(conf_integrals)
if names is not None:
integrals.update([integrals[ii] for ii in names if ii in integrals.names])
return integrals
def set_equations(self, conf_equations, user=None, cache_override=None, keep_solvers=False):
equations = Equations.from_conf(conf_equations)
equations.setup_terms(self.domain.regions, self.variables, self.materials, user)
i_names = equations.get_term_integral_names()
self.integrals = Integrals.from_conf(self.conf.integrals, i_names)
self.integrals.set_quadratures(fea.collect_quadratures())
self.geometries = {}
equations.describe_geometry(self.geometries, self.variables, self.integrals)
## print self.geometries
## pause()
# Call after describe_geometry(), as it sets ap.surface_data.
self.variables.setup_dof_conns()
if cache_override is None:
cache_override = get_default_attr(self.conf.fe, "cache_override", True)
equations.set_cache_mode(cache_override)
self.equations = equations
if not keep_solvers:
self.solvers = None
#python implementation of the Hartree-Fock method
import numpy as np
import math
from basis import Basis
from integrals import Integrals
from scf import SCF
Basis = Basis()
Integrals = Integrals()
SCF = SCF()
##################################
#init main variables
#contains information user provided information about the system
system = {
#nuclear coordinates
"R":[[0.0,0.0,-1.0], [0.0,0.0,1.0]],
#atomic number
"Z":[1,1],
#number of electron
"N":[2.0]
}
#basis set
basis = Basis.buildBasis(system["Z"], system["R"])
print(basis)
def eval_term(
state,
term_desc,
conf,
domain,
variables,
materials,
ts,
funmod=None,
chunk_size=1000,
term_prefixes=None,
caches=None,
ret_caches=False,
override=True,
new_geometries=True,
dw_mode="vector",
tangent_matrix=None,
**kwargs
):
"""Evaluate a term. May not succeed!"""
if term_prefixes is None:
term_prefixes = {}
if caches is None:
caches = DataCaches()
equation = Equation.from_desc("tmp", term_desc, term_prefixes)
equation.setup_terms(domain.regions, variables, materials, caches, kwargs)
for cache in caches.itervalues():
cache.set_mode(override=override)
if new_geometries:
i_names = equation.get_term_integral_names()
integrals = Integrals.from_conf(conf.integrals, i_names)
integrals.set_quadratures(quadratures)
geometries = {}
equation.describe_geometry(geometries, variables, integrals)
variables.data_from_state(state)
if "call_mode" in kwargs:
itype = kwargs["call_mode"].split("_")[0]
else:
# itype according to the first term in term_desc!
itype = equation.terms[0].itype
if itype == "dw":
variables.setup_dof_conns()
if not variables.has_eq_map:
variables.equation_mapping(conf.ebcs, conf.epbcs, domain.regions, ts, funmod)
variables.setup_lcbc_operators(conf.lcbcs, domain.regions)
variables.setup_a_dof_conns()
if dw_mode == "vector":
residual = variables.create_stripped_state_vector()
assemble_vector(residual, equation, variables, materials, chunk_size, group_can_fail=False, **kwargs)
if variables.has_lcbc:
op_lcbc = variables.op_lcbc
residual = op_lcbc.T * residual
ret_val = residual
elif dw_mode == "matrix":
if tangent_matrix is None:
tangent_matrix = variables.create_matrix_graph()
tangent_matrix.data[:] = 0.0
assemble_matrix(tangent_matrix, equation, variables, materials, chunk_size, group_can_fail=False, **kwargs)
if variables.has_lcbc:
op_lcbc = variables.op_lcbc
tangent_matrix = op_lcbc.T * tangent_matrix * op_lcbc
tangent_matrix = tangent_matrix.tocsr()
tangent_matrix.sort_indices()
ret_val = tangent_matrix
else:
print dw_mode
raise ValueError
elif itype == "d":
kwargs.setdefault("call_mode", "d_eval")
val = 0.0
for term in equation.terms:
args = build_args(term, variables, materials, **kwargs)
for ig in term.iter_groups():
for aux, iels, status in term(chunk_size=chunk_size, **args):
val += term.sign * aux
ret_val = val
elif itype == "di":
val = None
for term in equation.terms:
args = build_args(term, variables, materials, **kwargs)
for ig in term.iter_groups():
for aux, iels, status in term(chunk_size=chunk_size, **args):
if val is None:
val = term.sign * aux
else:
val += term.sign * aux
ret_val = val
elif (itype == "de") or (itype == "dq"):
val = None
for term in equation.terms:
args = build_args(term, variables, materials, **kwargs)
for ig in term.iter_groups():
for aux, iels, status in term(chunk_size=chunk_size, **args):
if val is None:
val = term.sign * aux
else:
val = nm.concatenate((val, term.sign * aux), axis=0)
ret_val = val
else:
raise NotImplementedError, "unknown term integration type: %s" % itype
if ret_caches:
return ret_val, caches
else:
return ret_val