def generate_test_mesh_and_field():
'''We define a 1D mesh with two regions:
|<---A--->|<--B-->|
0 1 2 3 4 5 6 7 8 9
We then define a field "vec" with 3 subfields:
subfield 'vec_a' is defined in region A
subfield 'vec_b' is defined in region B
subfield 'vec_ab' is defined in both region A and B'''
dim = 1
m = nmesh.generate_1d_mesh([(0.0, 5.0), (5.0, 9.0)], 0.5)
el_a = ocaml.make_element("vec_a", [3], dim, 1)
el_b = ocaml.make_element("vec_b", [3], dim, 1)
el_ab = ocaml.make_element("vec_ab", [3], dim, 1)
els = [ocaml.empty_element,
ocaml.fuse_elements(el_ab, el_a), # region A
ocaml.fuse_elements(el_ab, el_b)] # region B
def enumerated_list(l): return zip(range(len(l)), l)
mwe = ocaml.make_mwe("vec",
m.raw_mesh,
enumerated_list(els),
[],
[(1, ['vec_ab', 'vec_a']),
(2, ['vec_ab', 'vec_b'])])
# Create the field and set it to 0 everywhere
field = ocaml.raw_make_field(mwe, [lambda x, y: 0.0], "", "")
return m, field
def make_element(name, indices, dim=None, ord=None):
"""
Create an abstract element.
"""
if dim == None:
dim = r_default_dimension[0]
if ord == None:
ord = r_default_order[0]
log.log(15, "Creating element '%s', indices=%s, ord=%s, dim=%s" % (name, str(indices), str(dim), str(ord)))
elem = ocaml.make_element(name, indices, dim, ord)
# elem.__str__=lambda (obj): "#<some element>"
# Note: we cannot do this, as elem is a PyCObject.
# If we wanted this functionality, we would have to add
# yet another level of (python-side) wrapping!
return elem
def make_element(name, indices, dim=None, ord=None):
"""
Create an abstract element.
"""
if dim == None:
dim = r_default_dimension[0]
if ord == None:
ord = r_default_order[0]
log.log(
15, "Creating element '%s', indices=%s, ord=%s, dim=%s" %
(name, str(indices), str(dim), str(ord)))
elem = ocaml.make_element(name, indices, dim, ord)
# elem.__str__=lambda (obj): "#<some element>"
# Note: we cannot do this, as elem is a PyCObject.
# If we wanted this functionality, we would have to add
# yet another level of (python-side) wrapping!
return elem
def _build_elems_on_material(self, name, shape):
# Build the 'elements' dictionary which maps an entity name to
# a corresponding element
elements = {}
for entity_name in self.regions.all_entity_names:
logger.info("Processing material '%s'" % entity_name)
elem_name = "%s_%s" % (name, entity_name)
elem = ocaml.make_element(elem_name, shape, self.dim, 1)
elements[entity_name] = elem
# Obtain a list fused_elem_by_region such that
# fused_elem_by_region[idx] is the element obtained by fusing all the
# elements corresponding to the materials defined in region idx.
# fused_elem_by_region[idx] is then the right element for that region
fused_elem_by_region = []
for entities_in_region in self.regions.entities_by_region:
# Build a list of the elements in the region
elems_in_region = map(elements.__getitem__, entities_in_region)
# Fuse all these elements
fused_elem = reduce(ocaml.fuse_elements, elems_in_region,
ocaml.empty_element)
fused_elem_by_region.append(fused_elem)
return fused_elem_by_region
def _create_field(self, field_name, subfield_name=None, row=0):
# This is the real subfield name
full_field_name = build_full_field_name(field_name, subfield_name)
# Now we get the data
f = self.open_handler()
root_data_fields = self.get_root_data_fields()
dim = self.mesh.dim
field_stuff = f.getNode(root_data_fields, field_name)
field_shape = list(field_stuff.row[full_field_name].shape)[1:]
# Get the sites where the subfield is defined (sites) and the
# corresponding coordinates (ps) and values (vs)
ps, vs, sites = self.get_field_array(field_name, subfield_name, row)
# sites now contains the dof allocation for the subfield, i.e. in
# which sites the subfield is defined.
# We now want to build a numarray of one boolean value per each site
# which says whether for that site the field is defined or not
pointsregions = self.mesh.pointsregions
num_sites = len(pointsregions)
defined = numpy.ndarray(num_sites, dtype=numpy.bool)
defined.fill(False)
for site_where_defined in sites:
defined[site_where_defined] = True
# Run over all the sites and build a list of regions where the field
# is undefined
all_regions = range(1, self.mesh.numregions)
regions_where_defined = range(1, self.mesh.numregions)
for site in range(num_sites):
if not defined[site]:
regions_owning_this_site = pointsregions[site]
for region in regions_owning_this_site:
if region in regions_where_defined:
regions_where_defined.remove(region)
# Now we know in which regions of the mesh the field is defined
logmsg("'%s' has been found in regions %s" %
(full_field_name, regions_where_defined))
# Consistency check: there musn't be a region where the field
# is partially defined!
logmsg("Now checking that there the field is always present...")
for site in range(num_sites):
field_should_be_defined_here = \
(True in [rwd in pointsregions[site]
for rwd in regions_where_defined])
# ^^^ True when this site belongs to one region which is listed
# in 'regions_where_defined'
if field_should_be_defined_here != defined[site]:
logmsg("Inconsistency while checking the field definition "
"regions: site %d belongs to region %s, but the field "
"is defined in regions %s." %
(site, pointsregions[site], regions_where_defined))
raise NmagUserError("The given file seems to be corrupt!"
"Cannot proceed!")
logmsg("Check successful: definition regions are %s" %
regions_where_defined)
logmsg("Creating a new element '%s' for the field" % full_field_name)
element = ocaml.make_element(full_field_name, field_shape, dim,
self.field_order)
logmsg("Creating MWE")
element_assoc = zip(regions_where_defined,
[element] * len(regions_where_defined))
properties = zip(regions_where_defined,
[[full_field_name]] * len(regions_where_defined))
mwe = ocaml.make_mwe(field_name, self.mesh.raw_mesh, element_assoc, [],
properties)
logmsg("Creating the field")
field = ocaml.raw_make_field(mwe, [], "", "")
# We now try to understand how to map the data from file into the
# newly created field
metadata = ocaml.mwe_subfield_metadata(field, full_field_name)
new_site_ids, new_pos, new_shape, new_site_vols = metadata
num_new_sites = len(new_site_ids)
if num_new_sites != len(sites):
raise NmagUserError("The re-created field seems inconsistent "
"with the one saved to file. Number of "
"sites is %d for saved and %d for new field. "
"Cannot proceed!" % (num_sites, num_new_sites))
# Check that the new field is binary compatible with the old one
# this is really what we expect and allows us to set the field
# by just passing a numarray as retrieved from the file
need_map = False
for i in range(num_new_sites):
if new_site_ids[i] != sites[i]:
need_map = True
if need_map:
raise NmagUserError("need_map=True, not implemented because this"
"was not expected to happen, anyway! Contact"
"Matteo ([email protected])")
self.fields[full_field_name] = field
timer1.start("x")
ff.set_fielddata_from_numpyarray(field, full_field_name, vs)
timer1.stop("x")
return field
#ocaml.init_hlib("/home/fangohr/build/HLib-1.3/Library/.libs/libhmatrix-1.3.so")
ocaml.init_hlib("/home/tf/HLib-1.3/Library/.libs/libhmatrix-1.3.so")
#raw_mesh=ocaml.mesh_readfile("periodic/periodic.nmesh",False)
mesh = nmesh.load_ascii("periodic/periodic-1d-2.nmesh")
raw_mesh = mesh.raw_mesh
print "MESH: ", raw_mesh
sys.stdout.flush()
if ocaml.petsc_is_mpi():
print "*** PARALLEL EXECUTION *** (not yet supported here!)"
sys.exit(0) # DDD add parallel support!
elem_phi = ocaml.make_element("phi", [], 1, 1) # scalar element
mwe_phi = ocaml.make_mwe("phi", raw_mesh, [(0, ocaml.empty_element),
(1, elem_phi)], [])
mwe_dphi_dt = ocaml.mwe_sibling(mwe_phi, "dphi_dt", "dphi_dt/phi",
[("phi", "dphi_dt")])
mwe_laplace_phi = ocaml.mwe_sibling(mwe_phi, "laplace_phi", "laplace_phi/phi",
[("phi", "laplace_phi")])
def fun_phi0(dof_name, dof_pos):
x = dof_pos[0] / 10.0
# sx = math.sin((x-0.4)*2*3.1415926535)
sx = math.sin((x - 0.4) * 2 * 3.1415926535)
phi = math.exp(-sx * sx)
return phi
# ocaml.init_hlib("/home/fangohr/build/HLib-1.3/Library/.libs/libhmatrix-1.3.so")
ocaml.init_hlib("/home/tf/HLib-1.3/Library/.libs/libhmatrix-1.3.so")
# raw_mesh=ocaml.mesh_readfile("periodic/periodic.nmesh",False)
mesh = nmesh.load_ascii("periodic/periodic-1d-2.nmesh")
raw_mesh = mesh.raw_mesh
print "MESH: ", raw_mesh
sys.stdout.flush()
if ocaml.petsc_is_mpi():
print "*** PARALLEL EXECUTION *** (not yet supported here!)"
sys.exit(0) # DDD add parallel support!
elem_phi = ocaml.make_element("phi", [], 1, 1) # scalar element
mwe_phi = ocaml.make_mwe("phi", raw_mesh, [(0, ocaml.empty_element), (1, elem_phi)], [])
mwe_dphi_dt = ocaml.mwe_sibling(mwe_phi, "dphi_dt", "dphi_dt/phi", [("phi", "dphi_dt")])
mwe_laplace_phi = ocaml.mwe_sibling(mwe_phi, "laplace_phi", "laplace_phi/phi", [("phi", "laplace_phi")])
def fun_phi0(dof_name, dof_pos):
x = dof_pos[0] / 10.0
# sx = math.sin((x-0.4)*2*3.1415926535)
sx = math.sin((x - 0.4) * 2 * 3.1415926535)
phi = math.exp(-sx * sx)
return phi
field_phi0 = ocaml.raw_make_field(mwe_phi, [fun_phi0], "", "")
sys.stdout.flush()
if ocaml.petsc_is_mpi():
print "*** PARALLEL EXECUTION *** (not yet supported here!)"
sys.exit(0) # DDD add parallel support!
nr_nodes=ocaml.petsc_mpi_nr_nodes()
nr_points=ocaml.mesh_nr_points(raw_mesh)
z=nr_points/nr_nodes
distrib = [int(round(z*(i+1)))-int(round(z*i)) for i in range(0,nr_nodes)]
slack=nr_points-reduce(lambda x,y:x+y,distrib)
distrib[0] = distrib[0] + slack
print "*** RAW MESH %s *** DISTRIB %s ***" %(repr(raw_mesh),repr(distrib))
ocaml.mesh_set_vertex_distribution(raw_mesh,distrib)
elem_V=ocaml.make_element("V",[3],2,1) # vector
elem_S=ocaml.make_element("S",[],2,1) # scalar element
mwe_V=ocaml.make_mwe("V",raw_mesh,[(0,ocaml.empty_element),(1,elem_V)],[])
mwe_S=ocaml.make_mwe("S",raw_mesh,[(0,ocaml.empty_element),(1,elem_S)],[])
mwe_M=ocaml.mwe_sibling(mwe_V,"M","M/V",[("V","M")])
mwe_dM=ocaml.mwe_sibling(mwe_V,"dM","dM/V",[("V","dM")])
mwe_H_exch=ocaml.mwe_sibling(mwe_V,"H_exch","H_exch/V",[("V","H_exch")])
mwe_H_total=ocaml.mwe_sibling(mwe_V,"H_total","H_total/V",[("V","H_total")])
mwe_rho=ocaml.mwe_sibling(mwe_S,"rho","rho/S",[("S","rho")])
mwe_phi=ocaml.mwe_sibling(mwe_S,"phi","phi/S",[("S","phi")])
def fun_M0(dof_name,dof_pos):
def jT_lam(
name="jT",
sigma_el=1.0, # electrical conductivity
sigma_th=0.1, # thermal conductivity
c_heat=1.0 / 10., # heat capacity
T_initial=300.0,
mesh=None,
ksp_tolerances={}):
print "Debug: c_heat = %f, sigma_el=%f, sigma_th=%f" % (c_heat, sigma_el,
sigma_th)
#sys.exit(0)
intensive_params = ["TIME", "Phi_ext"]
raw_mesh = mesh.raw_mesh
dim = ocaml.mesh_dim(raw_mesh)
def get_tol(name):
if ksp_tolerances.has_key(name):
ksp_tolerances[name]
else:
None
elem_V = ocaml.make_element("V", [dim], dim, 1)
elem_S = ocaml.make_element("S", [], dim, 1)
def fun_outer_region(coords):
if coords[0] < -499.9 or coords[0] > 499.9:
return -2
else:
return -1
def fun_T_initial(field, pos):
#print ("SAMPLING field %s AT: %s" % (field,pos))
return T_initial
def fun_T_initial_debug(field, pos):
print("SAMPLING field %s AT: %s" % (field, pos))
# return T_initial
x, y, z = pos
if x < 0:
return 300
else:
return 100
return 0.0 #should not occur
mwe_V = ocaml.make_mwe("V", raw_mesh, [(0, ocaml.empty_element),
(1, elem_V)], [fun_outer_region])
mwe_S = ocaml.make_mwe("S", raw_mesh, [(0, ocaml.empty_element),
(1, elem_S)], [fun_outer_region])
mwe_j = ocaml.mwe_sibling(mwe_V, "j", "j/V", [("V", "j")])
mwe_phi = ocaml.mwe_sibling(mwe_S, "phi", "phi/S", [("S", "phi")])
mwe_rho = ocaml.mwe_sibling(mwe_S, "rho", "rho/S", [("S", "rho")])
mwe_T = ocaml.mwe_sibling(mwe_S, "T", "T/S", [("S", "T")])
mwe_Laplace_T = ocaml.mwe_sibling(mwe_S, "Laplace_T", "Laplace_T/S",
[("S", "Laplace_T")])
mwe_dTdt = ocaml.mwe_sibling(mwe_S, "dTdt", "dTdt/S", [("S", "dTdt")])
master_mwes_and_fields_by_name = {}
master_mwes_and_fields_by_name["T"] = (mwe_T,
ocaml.raw_make_field(
mwe_T, [fun_T_initial], "", ""))
master_mwes_and_fields_by_name["Laplace_T"] = (mwe_j,
ocaml.raw_make_field(
mwe_Laplace_T, [], "",
""))
master_mwes_and_fields_by_name["j"] = (mwe_j,
ocaml.raw_make_field(
mwe_j, [], "", ""))
master_mwes_and_fields_by_name["phi"] = (mwe_phi,
ocaml.raw_make_field(
mwe_phi, [], "", ""))
master_mwes_and_fields_by_name["rho"] = (mwe_rho,
ocaml.raw_make_field(
mwe_rho, [], "", ""))
# Note that at present, SITE_WISE does not work properly with restricted vectors,
# so we will have to set the heating voltage throughout the sample, and throw away
# the values inside the bulk then.
ccode_heating = """
if(have_phi) {
if(COORDS(0)<0) {phi= 0.5*Phi_ext;}
else {phi= -0.5*Phi_ext;}
}
"""
# Note ad resistive heating: integrated power generation = U*I.
# Local power generation = E*j. As j = sigma*E, we get p = j^2/sigma,
# so the contribution to dT/dt is j^2/sigma.
eq_dTdt = """%%range k:%d;
dTdt <- (%.8f)*Laplace_T + (%.8f)*j(k)*j(k);
""" % (dim, sigma_th / c_heat, 1.0 / (c_heat * sigma_el))
print "DDD eq_dTdt: ", eq_dTdt
lam_mwes = {
"j": mwe_j,
"phi": mwe_phi,
"rho": mwe_rho,
"T": mwe_T,
"Laplace_T": mwe_Laplace_T,
"dTdt": mwe_dTdt,
}
lam_vectors = {
"v_j":
nlam.lam_vector(name="v_j", mwe_name="j"),
"v_phi":
nlam.lam_vector(name="v_phi", mwe_name="phi"),
"v_phi_boundary":
nlam.lam_vector(name="v_phi_boundary",
mwe_name="phi",
restriction="phi[boundary=-2/*]"),
"v_rho":
nlam.lam_vector(name="v_rho", mwe_name="rho"),
"v_T":
nlam.lam_vector(name="v_T", mwe_name="T"),
"v_Laplace_T":
nlam.lam_vector(name="v_Laplace_T", mwe_name="Laplace_T"),
"v_dTdt":
nlam.lam_vector(name="v_dTdt", mwe_name="dTdt"),
}
lam_operators={\
"op_j_phi":nlam.lam_operator("op_j_phi","j","phi",
"%g*<j(k) || d/dxk phi>, k:%d" % (sigma_el,dim)),
"op_Laplace_T":nlam.lam_operator("op_Laplace_T","Laplace_T","T",
"-<d/dxk Laplace_T || d/dxk T>, k:%d" % dim
),
# Tricky issue: we have DBC along the contacts and NBC everywhere else.
# XXX REPAIR: LHS field should be named "rho".
# XXX Can our "left field equals right field" syntax already cope with that?
"op_laplace_DNBC":nlam.lam_operator("op_laplace_DNBC","phi","phi",
""" -<d/dxk phi[vol] || d/dxk phi[vol]>
-<d/dxk phi[boundary=-1/1] || d/dxk phi[vol]>
-<d/dxk phi[boundary=-1/1] || d/dxk phi[boundary=-1/1]>
-<d/dxk phi[vol] || d/dxk phi[boundary=-1/1]>
;phi[boundary=-2/*]=phi[boundary=-2/*], k:%d""" %dim),
#"op_laplace_DNBC":nlam.lam_operator("op_laplace_DNBC","phi","phi",
# """ -<d/dxk phi || d/dxk phi>
# ;phi[boundary=-2/*]=phi[boundary=-2/*], k:%d""" %dim),
"op_load_DBC":nlam.lam_operator("op_load_DBC","rho","phi",
"<d/dxk rho || d/dxk phi[boundary=-2/*]>;(L||R)=(*||phi[boundary=-2/*]), k:%d" %dim),
}
lam_ksps = {
"solve_laplace_DNBC":
nlam.lam_ksp(
name="solve_laplace_DNBC",
matrix_name="op_laplace_DNBC",
ksp_type="gmres",
pc_type="ilu",
initial_guess_nonzero=True,
rtol=get_tol("DNBC.rtol"),
atol=get_tol("DNBC.atol"),
dtol=get_tol("DNBC.dtol"),
maxits=get_tol("DNBC.maxits"),
)
}
lam_local = {
"local_dTdt":
nlam.lam_local("local_dTdt",
field_mwes=["dTdt", "Laplace_T", "j"],
equation=eq_dTdt),
"local_set_phi_heating":
nlam.lam_local("local_set_phi_heating",
aux_args=intensive_params,
field_mwes=["phi"],
c_code=ccode_heating)
}
lam_jacobi = {
"jacobian":
nlam.lam_jplan(
"jacobian",
"dTdt",
["T", "Laplace_T", "j"],
[
[],
[ # all contributions to d Laplace_T/dT
("operator", "op_Laplace_T")
],
[ # all contributions to dj/dT - none in this model.
]
],
eq_dTdt)
}
lam_programs = {
"update_dTdt":
nlam.lam_program(
"update_dTdt",
commands=[
["TSTART", "update_dTdt"],
["GOSUB", "set_Laplace_T"],
["GOSUB", "set_j"],
[
"SITE-WISE-IPARAMS", "local_dTdt",
["v_dTdt", "v_Laplace_T", "v_j"], []
],
# ["DEBUG","v_dTdt","v_dTdt",0], # seems okay!
["TSTOP", "update_dTdt"],
]),
"set_Laplace_T":
nlam.lam_program(
"set_Laplace_T",
commands=[
["TSTART", "Laplace_T"],
["SM*V", "op_Laplace_T", "v_T", "v_Laplace_T"],
["CFBOX", "Laplace_T", "v_Laplace_T"],
# ["DEBUG","v_Laplace_T","v_Laplace_T",0],
["TSTOP", "Laplace_T"]
]),
"set_j":
nlam.lam_program(
"set_j",
commands=[
["TSTART", "j"],
["SITE-WISE-IPARAMS", "local_set_phi_heating", ["v_phi"], []],
[
"PULL-FEM", "phi", "phi[boundary=-2/*]", "v_phi",
"v_phi_boundary"
],
# ["DEBUG","v_phi_boundary","v_phi_boundary",0],
["SM*V", "op_load_DBC", "v_phi_boundary", "v_rho"],
# ["DEBUG","v_rho","v_rho",0],
["SCALE", "v_phi", 0.0],
["SOLVE", "solve_laplace_DNBC", "v_rho", "v_phi"],
[
"PUSH-FEM", "phi", "phi[boundary=-2/*]", "v_phi_boundary",
"v_phi"
],
# ^ This is to add proper boundary values!
["SM*V", "op_j_phi", "v_phi", "v_j"],
# ["DEBUG","v_phi","v_phi",0],
# ["DEBUG","v_j","v_j",0],
["CFBOX", "j", "v_j"],
["TSTOP", "j"]
]),
"execute_jplan":
nlam.lam_program(
"execute_jplan",
commands=[["TSTART", "execute_jplan"], ["GOSUB", "set_Laplace_T"],
["GOSUB", "set_j"],
["JPLAN", "jacobian", ["v_T", "v_Laplace_T", "v_j"]],
["TSTOP", "execute_jplan"]]),
"rhs":
nlam.lam_program(
"rhs",
args_fields=[["arg_dTdt", "dTdt"], ["arg_T",
"T"]], # [arg_name,mwe_name]
commands=[
["TSTART", "rhs"],
["DISTRIB", "arg_T", "v_T"],
# ["DEBUG","v_T","v_T",0],
["GOSUB", "update_dTdt"],
["COLLECT", "arg_dTdt", "v_dTdt"],
# ["DEBUG","v_dTdt","v_dTdt",0],
["TSTOP", "rhs"]
]),
}
lam = nlam.make_linalg_machine(name,
intensive_params=intensive_params,
mwes=lam_mwes.values(),
vectors=lam_vectors.values(),
operators=lam_operators.values(),
ksps=lam_ksps.values(),
local_operations=lam_local.values(),
jacobi_plans=lam_jacobi.values(),
programs=lam_programs.values())
return (lam, master_mwes_and_fields_by_name)
def jT_lam(name="jT",
sigma_el=1.0, # electrical conductivity
sigma_th=0.1, # thermal conductivity
c_heat=1.0/10.,# heat capacity
T_initial=300.0,
mesh=None,
ksp_tolerances={}
):
print "Debug: c_heat = %f, sigma_el=%f, sigma_th=%f" % (c_heat,sigma_el,sigma_th)
#sys.exit(0)
intensive_params=["TIME","Phi_ext"]
raw_mesh=mesh.raw_mesh
dim = ocaml.mesh_dim(raw_mesh)
def get_tol(name):
if ksp_tolerances.has_key(name):
ksp_tolerances[name]
else:
None
elem_V = ocaml.make_element("V", [dim], dim, 1)
elem_S = ocaml.make_element("S", [], dim, 1)
def fun_outer_region(coords):
if coords[0]<-499.9 or coords[0]>499.9:
return -2
else:
return -1
def fun_T_initial(field,pos):
#print ("SAMPLING field %s AT: %s" % (field,pos))
return T_initial
def fun_T_initial_debug(field,pos):
print ("SAMPLING field %s AT: %s" % (field,pos))
# return T_initial
x,y,z=pos
if x < 0:
return 300
else:
return 100
return 0.0 #should not occur
mwe_V=ocaml.make_mwe("V",raw_mesh,[(0,ocaml.empty_element),(1,elem_V)],[fun_outer_region])
mwe_S=ocaml.make_mwe("S",raw_mesh,[(0,ocaml.empty_element),(1,elem_S)],[fun_outer_region])
mwe_j=ocaml.mwe_sibling(mwe_V,"j","j/V",[("V","j")])
mwe_phi=ocaml.mwe_sibling(mwe_S,"phi","phi/S",[("S","phi")])
mwe_rho=ocaml.mwe_sibling(mwe_S,"rho","rho/S",[("S","rho")])
mwe_T=ocaml.mwe_sibling(mwe_S,"T","T/S",[("S","T")])
mwe_Laplace_T=ocaml.mwe_sibling(mwe_S,"Laplace_T","Laplace_T/S",[("S","Laplace_T")])
mwe_dTdt=ocaml.mwe_sibling(mwe_S,"dTdt","dTdt/S",[("S","dTdt")])
master_mwes_and_fields_by_name={}
master_mwes_and_fields_by_name["T"]=(mwe_T,ocaml.raw_make_field(mwe_T,[fun_T_initial],"",""))
master_mwes_and_fields_by_name["Laplace_T"]=(mwe_j,ocaml.raw_make_field(mwe_Laplace_T,[],"",""))
master_mwes_and_fields_by_name["j"]=(mwe_j,ocaml.raw_make_field(mwe_j,[],"",""))
master_mwes_and_fields_by_name["phi"]=(mwe_phi,ocaml.raw_make_field(mwe_phi,[],"",""))
master_mwes_and_fields_by_name["rho"]=(mwe_rho,ocaml.raw_make_field(mwe_rho,[],"",""))
# Note that at present, SITE_WISE does not work properly with restricted vectors,
# so we will have to set the heating voltage throughout the sample, and throw away
# the values inside the bulk then.
ccode_heating= """
if(have_phi) {
if(COORDS(0)<0) {phi= 0.5*Phi_ext;}
else {phi= -0.5*Phi_ext;}
}
"""
# Note ad resistive heating: integrated power generation = U*I.
# Local power generation = E*j. As j = sigma*E, we get p = j^2/sigma,
# so the contribution to dT/dt is j^2/sigma.
eq_dTdt="""%%range k:%d;
dTdt <- (%.8f)*Laplace_T + (%.8f)*j(k)*j(k);
""" % (dim,
sigma_th/c_heat,
1.0/(c_heat*sigma_el))
print "DDD eq_dTdt: ",eq_dTdt
lam_mwes={"j":mwe_j, "phi":mwe_phi, "rho":mwe_rho,
"T":mwe_T, "Laplace_T":mwe_Laplace_T,
"dTdt":mwe_dTdt,
}
lam_vectors={"v_j":nlam.lam_vector(name="v_j",mwe_name="j"),
"v_phi":nlam.lam_vector(name="v_phi",mwe_name="phi"),
"v_phi_boundary":nlam.lam_vector(name="v_phi_boundary",
mwe_name="phi",
restriction="phi[boundary=-2/*]"),
"v_rho":nlam.lam_vector(name="v_rho",mwe_name="rho"),
"v_T":nlam.lam_vector(name="v_T",mwe_name="T"),
"v_Laplace_T":nlam.lam_vector(name="v_Laplace_T",mwe_name="Laplace_T"),
"v_dTdt":nlam.lam_vector(name="v_dTdt",mwe_name="dTdt"),
}
lam_operators={\
"op_j_phi":nlam.lam_operator("op_j_phi","j","phi",
"%g*<j(k) || d/dxk phi>, k:%d" % (sigma_el,dim)),
"op_Laplace_T":nlam.lam_operator("op_Laplace_T","Laplace_T","T",
"-<d/dxk Laplace_T || d/dxk T>, k:%d" % dim
),
# Tricky issue: we have DBC along the contacts and NBC everywhere else.
# XXX REPAIR: LHS field should be named "rho".
# XXX Can our "left field equals right field" syntax already cope with that?
"op_laplace_DNBC":nlam.lam_operator("op_laplace_DNBC","phi","phi",
""" -<d/dxk phi[vol] || d/dxk phi[vol]>
-<d/dxk phi[boundary=-1/1] || d/dxk phi[vol]>
-<d/dxk phi[boundary=-1/1] || d/dxk phi[boundary=-1/1]>
-<d/dxk phi[vol] || d/dxk phi[boundary=-1/1]>
;phi[boundary=-2/*]=phi[boundary=-2/*], k:%d""" %dim),
#"op_laplace_DNBC":nlam.lam_operator("op_laplace_DNBC","phi","phi",
# """ -<d/dxk phi || d/dxk phi>
# ;phi[boundary=-2/*]=phi[boundary=-2/*], k:%d""" %dim),
"op_load_DBC":nlam.lam_operator("op_load_DBC","rho","phi",
"<d/dxk rho || d/dxk phi[boundary=-2/*]>;(L||R)=(*||phi[boundary=-2/*]), k:%d" %dim),
}
lam_ksps={"solve_laplace_DNBC":nlam.lam_ksp(name="solve_laplace_DNBC",
matrix_name="op_laplace_DNBC",
ksp_type="gmres", pc_type="ilu",
initial_guess_nonzero=True,
rtol=get_tol("DNBC.rtol"),
atol=get_tol("DNBC.atol"),
dtol=get_tol("DNBC.dtol"),
maxits=get_tol("DNBC.maxits"),
)
}
lam_local={"local_dTdt":nlam.lam_local("local_dTdt",
field_mwes=["dTdt","Laplace_T","j"],
equation=eq_dTdt),
"local_set_phi_heating":nlam.lam_local("local_set_phi_heating",
aux_args=intensive_params,
field_mwes=["phi"],
c_code=ccode_heating)
}
lam_jacobi={"jacobian":nlam.lam_jplan("jacobian","dTdt",
["T","Laplace_T","j"],
[[],
[# all contributions to d Laplace_T/dT
("operator","op_Laplace_T")],
[# all contributions to dj/dT - none in this model.
]],
eq_dTdt
)}
lam_programs={"update_dTdt":nlam.lam_program("update_dTdt",
commands=[["TSTART","update_dTdt"],
["GOSUB", "set_Laplace_T"],
["GOSUB", "set_j"],
["SITE-WISE-IPARAMS", "local_dTdt",["v_dTdt","v_Laplace_T","v_j"],[]],
# ["DEBUG","v_dTdt","v_dTdt",0], # seems okay!
["TSTOP", "update_dTdt"],
]),
"set_Laplace_T":nlam.lam_program("set_Laplace_T",
commands=[["TSTART","Laplace_T"],
["SM*V","op_Laplace_T","v_T","v_Laplace_T"],
["CFBOX","Laplace_T","v_Laplace_T"],
# ["DEBUG","v_Laplace_T","v_Laplace_T",0],
["TSTOP","Laplace_T"]]),
"set_j":nlam.lam_program("set_j",
commands=[["TSTART","j"],
["SITE-WISE-IPARAMS","local_set_phi_heating",["v_phi"],[]],
["PULL-FEM","phi","phi[boundary=-2/*]","v_phi","v_phi_boundary"],
# ["DEBUG","v_phi_boundary","v_phi_boundary",0],
["SM*V","op_load_DBC","v_phi_boundary","v_rho"],
# ["DEBUG","v_rho","v_rho",0],
["SCALE","v_phi",0.0],
["SOLVE","solve_laplace_DNBC","v_rho","v_phi"],
["PUSH-FEM","phi","phi[boundary=-2/*]","v_phi_boundary","v_phi"],
# ^ This is to add proper boundary values!
["SM*V","op_j_phi","v_phi","v_j"],
# ["DEBUG","v_phi","v_phi",0],
# ["DEBUG","v_j","v_j",0],
["CFBOX","j","v_j"],
["TSTOP","j"]]),
"execute_jplan":nlam.lam_program("execute_jplan",
commands=[["TSTART","execute_jplan"],
["GOSUB", "set_Laplace_T"],
["GOSUB", "set_j"],
["JPLAN","jacobian",["v_T","v_Laplace_T","v_j"]],
["TSTOP","execute_jplan"]]),
"rhs":nlam.lam_program("rhs",
args_fields=[["arg_dTdt","dTdt"],["arg_T","T"]], # [arg_name,mwe_name]
commands=[["TSTART","rhs"],
["DISTRIB","arg_T","v_T"],
# ["DEBUG","v_T","v_T",0],
["GOSUB", "update_dTdt"],
["COLLECT","arg_dTdt","v_dTdt"],
# ["DEBUG","v_dTdt","v_dTdt",0],
["TSTOP","rhs"]
]),
}
lam=nlam.make_linalg_machine(
name,
intensive_params=intensive_params,
mwes=lam_mwes.values(),
vectors=lam_vectors.values(),
operators=lam_operators.values(),
ksps=lam_ksps.values(),
local_operations=lam_local.values(),
jacobi_plans=lam_jacobi.values(),
programs=lam_programs.values()
)
return (lam,master_mwes_and_fields_by_name)
density=density,
initial_settling_steps=50,
max_relaxation=4,
# callback=(my_function, N),
# max_steps=677
max_steps=400)
print "Mesh: ", the_mesh
sys.stdout.flush()
##### Making the elements... #####
empty_element = ocaml.empty_element
# conductivity (scalar)
element_sigma = ocaml.make_element("sigma", [], 2, element_order)
# name, max indices, dim, order
# d rho/dt charge density, will serve as a Laplace equation RHS, zero
element_drho_by_dt = ocaml.make_element("drho_by_dt", [], 2, element_order)
# Electrical potential
element_phi = ocaml.make_element("phi", [], 2, element_order)
# Electrical current - a 2d vector
element_J = ocaml.make_element("J", [2], 2, element_order)
print "element_J: ", element_J
sys.stdout.flush()
mwe_sigma = ocaml.make_mwe("mwe_sigma", the_mesh.raw_mesh,
initial_settling_steps=50,
max_relaxation=4,
# callback=(my_function, N),
# max_steps=677
max_steps=400,
)
print "Mesh: ", the_mesh
sys.stdout.flush()
##### Making the elements... #####
empty_element = ocaml.empty_element
# conductivity (scalar)
element_sigma = ocaml.make_element("sigma", [], 2, element_order)
# name, max indices, dim, order
# d rho/dt charge density, will serve as a Laplace equation RHS, zero
element_drho_by_dt = ocaml.make_element("drho_by_dt", [], 2, element_order)
# Electrical potential
element_phi = ocaml.make_element("phi", [], 2, element_order)
# Electrical current - a 2d vector
element_J = ocaml.make_element("J", [2], 2, element_order)
print "element_J: ", element_J
sys.stdout.flush()
#
# (C) 2006 Dr. Thomas Fischbacher
# Checking bulk and surface contribs for a homogeneously magnetized octahedron.
import nfem
import sys,math,time
import ocaml #need this as long as we use ocaml.probe_field
mesh = ocaml.mesh_readfile("./debug-octa.mesh")
print "MESH: ",mesh
elem_m=ocaml.make_element("m_X",[3],3,1)
elem_H_demag=ocaml.make_element("H_demag",[3],3,1)
mwe_m=ocaml.make_mwe("mwe_m",mesh,[(1,elem_m)])
mwe_h=ocaml.make_mwe("mwe_h",mesh,[(1,elem_H_demag)])
def initial_m(dof,pos): # radially outward, zero at center
ix=dof[1][0]
return pos[ix]
field_m=ocaml.raw_make_field(mwe_m,[initial_m],"")
make_field_h=ocaml.ddd_demag_fun_3d("<S||d/dxj m_X(j)>, j:3",mwe_h,mwe_m)
field_h=make_field_h(field_m)
print field_h
def _build_elems_everywhere(self, name, shape):
elem = ocaml.make_element(name, shape, self.dim, 1)
return map(lambda region: elem, self.region_materials)
#
# (C) 2006 Dr. Thomas Fischbacher
# Checking bulk and surface contribs for a homogeneously magnetized octahedron.
import nfem
import sys, math, time
import ocaml #need this as long as we use ocaml.probe_field
mesh = ocaml.mesh_readfile("./debug-octa.mesh")
print "MESH: ", mesh
elem_m = ocaml.make_element("m_X", [3], 3, 1)
elem_H_demag = ocaml.make_element("H_demag", [3], 3, 1)
mwe_m = ocaml.make_mwe("mwe_m", mesh, [(1, elem_m)])
mwe_h = ocaml.make_mwe("mwe_h", mesh, [(1, elem_H_demag)])
def initial_m(dof, pos): # radially outward, zero at center
ix = dof[1][0]
return pos[ix]
field_m = ocaml.raw_make_field(mwe_m, [initial_m], "")
make_field_h = ocaml.ddd_demag_fun_3d("<S||d/dxj m_X(j)>, j:3", mwe_h, mwe_m)
field_h = make_field_h(field_m)
print field_h
def _create_field(self, field_name, subfield_name=None, row=0):
# This is the real subfield name
full_field_name = build_full_field_name(field_name, subfield_name)
# Now we get the data
f = self.open_handler()
root_data_fields = self.get_root_data_fields()
dim = self.mesh.dim
field_stuff = f.getNode(root_data_fields, field_name)
field_shape = list(field_stuff.row[full_field_name].shape)[1:]
# Get the sites where the subfield is defined (sites) and the
# corresponding coordinates (ps) and values (vs)
ps, vs, sites = self.get_field_array(field_name, subfield_name, row)
# sites now contains the dof allocation for the subfield, i.e. in
# which sites the subfield is defined.
# We now want to build a numarray of one boolean value per each site
# which says whether for that site the field is defined or not
pointsregions = self.mesh.pointsregions
num_sites = len(pointsregions)
defined = numpy.ndarray(num_sites, dtype=numpy.bool)
defined.fill(False)
for site_where_defined in sites:
defined[site_where_defined] = True
# Run over all the sites and build a list of regions where the field
# is undefined
all_regions = range(1, self.mesh.numregions)
regions_where_defined = range(1, self.mesh.numregions)
for site in range(num_sites):
if not defined[site]:
regions_owning_this_site = pointsregions[site]
for region in regions_owning_this_site:
if region in regions_where_defined:
regions_where_defined.remove(region)
# Now we know in which regions of the mesh the field is defined
logmsg("'%s' has been found in regions %s"
% (full_field_name, regions_where_defined))
# Consistency check: there musn't be a region where the field
# is partially defined!
logmsg("Now checking that there the field is always present...")
for site in range(num_sites):
field_should_be_defined_here = \
(True in [rwd in pointsregions[site]
for rwd in regions_where_defined])
# ^^^ True when this site belongs to one region which is listed
# in 'regions_where_defined'
if field_should_be_defined_here != defined[site]:
logmsg("Inconsistency while checking the field definition "
"regions: site %d belongs to region %s, but the field "
"is defined in regions %s."
% (site, pointsregions[site], regions_where_defined))
raise NmagUserError("The given file seems to be corrupt!"
"Cannot proceed!")
logmsg("Check successful: definition regions are %s"
% regions_where_defined)
logmsg("Creating a new element '%s' for the field" % full_field_name)
element = ocaml.make_element(full_field_name, field_shape, dim,
self.field_order)
logmsg("Creating MWE")
element_assoc = zip(regions_where_defined,
[element]*len(regions_where_defined))
properties = zip(regions_where_defined,
[[full_field_name]]*len(regions_where_defined))
mwe = ocaml.make_mwe(field_name,
self.mesh.raw_mesh,
element_assoc,
[],
properties)
logmsg("Creating the field")
field = ocaml.raw_make_field(mwe, [], "", "")
# We now try to understand how to map the data from file into the
# newly created field
metadata = ocaml.mwe_subfield_metadata(field, full_field_name)
new_site_ids, new_pos, new_shape, new_site_vols = metadata
num_new_sites = len(new_site_ids)
if num_new_sites != len(sites):
raise NmagUserError("The re-created field seems inconsistent "
"with the one saved to file. Number of "
"sites is %d for saved and %d for new field. "
"Cannot proceed!" % (num_sites,num_new_sites))
# Check that the new field is binary compatible with the old one
# this is really what we expect and allows us to set the field
# by just passing a numarray as retrieved from the file
need_map = False
for i in range(num_new_sites):
if new_site_ids[i] != sites[i]:
need_map = True
if need_map:
raise NmagUserError("need_map=True, not implemented because this"
"was not expected to happen, anyway! Contact"
"Matteo ([email protected])")
self.fields[full_field_name] = field
timer1.start("x")
ff.set_fielddata_from_numpyarray(field, full_field_name, vs)
timer1.stop("x")
return field
