def _build_lam_object(self, model):
assert self.is_owned(), "Cannot build LAM object: CCode is not owned."
assert self.ccode != None
required_quantities = self.get_all_quantities()
return \
nlam.lam_local(self.get_full_name(),
aux_args=self.intensive_params,
field_mwes=required_quantities,
c_code=self.ccode)
def _build_lam_object(self, model):
assert self.is_owned(), "Cannot build LAM object: CCode is not owned."
assert self.ccode != None
required_quantities = self.get_all_quantities()
return \
nlam.lam_local(self.get_full_name(),
aux_args=self.intensive_params,
field_mwes=required_quantities,
c_code=self.ccode)
def _build_lam_object(self, model, context=None):
intensive_params = [] # For now...
if self.ocaml_to_parse:
eq_text = self.get_text(context=context)
mwes_for_eq = self.get_all_quantities()
return \
nlam.lam_local(self.get_full_name(),
aux_args=intensive_params,
field_mwes=mwes_for_eq,
equation=eq_text)
else:
ccode = self.get_ccode(context=context)
mwes_for_eq = self.get_all_quantities()
return \
nlam.lam_local(self.get_full_name(),
aux_args=intensive_params,
field_mwes=mwes_for_eq,
c_code=ccode)
def _build_lam_object(self, model, context=None):
intensive_params = [] # For now...
if self.ocaml_to_parse:
eq_text = self.get_text(context=context)
mwes_for_eq = self.get_all_quantities()
return \
nlam.lam_local(self.get_full_name(),
aux_args=intensive_params,
field_mwes=mwes_for_eq,
equation=eq_text)
else:
ccode = self.get_ccode(context=context)
mwes_for_eq = self.get_all_quantities()
return \
nlam.lam_local(self.get_full_name(),
aux_args=intensive_params,
field_mwes=mwes_for_eq,
c_code=ccode)
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)