def assemble_matrix(mtx, equation, variables, materials, chunk_size=1000, group_can_fail=True, **kwargs):
"""Assemble tangent matrix. Supports backward time difference of state
variables."""
if not sp.isspmatrix_csr(mtx):
raise TypeError, "must be CSR matrix!"
tmd = (mtx.data, mtx.indptr, mtx.indices)
get_a_dof_conn = variables.get_a_dof_conn
for term in equation.terms:
# print '>>>>>>', term.name, term.sign
var_names = term.get_variable_names()
args = build_args(term, variables, materials, **kwargs)
vn = term.get_virtual_name(variables=variables)
sns = term.get_state_names(variables=variables)
dc_type = term.get_dof_conn_type()
for ig in term.iter_groups():
rdc = get_a_dof_conn(vn, True, dc_type, ig)
# print vn, rdc.shape
for sn in sns:
cdc = get_a_dof_conn(sn, False, dc_type, ig)
# print sn, cdc.shape
# pause()
for mtx_in_els, iels, status in term(diff_var=sn, chunk_size=chunk_size, **args):
if status != 0:
raise StopIteration(status, term, equation, var_name_col)
assert_(mtx_in_els.shape[2:] == (rdc.shape[1], cdc.shape[1]))
sign = term.sign
if term.arg_derivatives[sn]:
sign *= 1.0 / term.dt
if mtx.dtype == nm.float64:
fem.assemble_matrix(tmd[0], tmd[1], tmd[2], mtx_in_els, iels, sign, rdc, cdc)
else:
assert_(mtx.dtype == nm.complex128)
sign = nm.array(term.sign, dtype=nm.complex128)
fem.assemble_matrix_complex(
tmd[0].real,
tmd[0].imag,
tmd[1],
tmd[2],
mtx_in_els.real,
mtx_in_els.imag,
iels,
float(sign.real),
float(sign.imag),
rdc,
cdc,
)
def assemble_vector(vec, equation, variables, materials, chunk_size=1000, **kwargs):
get_a_dof_conn = variables.get_a_dof_conn
for term in equation.terms:
## print '>>>>>>', term.name, term.sign
var_names = term.get_variable_names()
args = build_args(term, variables, materials, **kwargs)
vn = term.get_virtual_name(variables=variables)
dc_type = term.get_dof_conn_type()
## print args
## print vn
## print dc_type
for ig in term.iter_groups():
dc = get_a_dof_conn(vn, True, dc_type, ig)
## print vn, dc.shape
# pause()
for vec_in_els, iels, status in term(chunk_size=chunk_size, **args):
if status != 0:
raise StopIteration(status, term, equation)
check_finitness = False
if check_finitness and (not nm.isfinite(vec_in_els).all()):
print term.name, term.sign, ig
debug()
assert_(vec_in_els.shape[2] == dc.shape[1])
if vec.dtype == nm.float64:
fem.assemble_vector(vec, vec_in_els, iels, term.sign, dc)
else:
assert_(vec.dtype == nm.complex128)
sign = nm.array(term.sign, dtype=nm.complex128)
fem.assemble_vector_complex(
vec.real,
vec.imag,
vec_in_els.real,
vec_in_els.imag,
iels,
float(sign.real),
float(sign.imag),
dc,
)
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