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 get_master(self):
if self._master != None:
return self._master
else:
assert self.vivified, "Cannot get master before vivification of field(%s)" % self.name
self._master = field = ocaml.raw_make_field(self.mwe, [], "", "")
return field
def get_master(self):
if self._master != None:
return self._master
else:
assert self.vivified, \
"Cannot get master before vivification of field(%s)" % self.name
self._master = field = ocaml.raw_make_field(self.mwe, [], "", "")
return field
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], "", "")
field_phi = ocaml.raw_make_field(mwe_phi, [], "", "")
eq_rhs = "dphi_dt <- laplace_phi;"
lam = make_linalg_machine(
"lam_phi",
mwes=[mwe_phi, mwe_dphi_dt, mwe_laplace_phi],
vectors=[
lam_vector(name="v_phi", mwe_name="phi"),
lam_vector(name="v_dphi_dt", mwe_name="dphi_dt"),
lam_vector(name="v_laplace_phi", mwe_name="laplace_phi"),
],
operators=[
lam_operator(
"op_laplace",
xpos = dof_pos[0]
ypos = dof_pos[1]
#xspos=math.sin(2*3.141592653589793*(2.0+xpos+5.0)/10.0)
#yspos=math.cos(2*3.141592653589793*(3.0+ypos+5.0)/10.0)
#r2=xspos-0.5*yspos
#alpha=math.exp(-r2*r2)
alpha=2*3.141592653589793*(2.0+xpos+5.0)/10.0
alpha=3.141592653589793/4.0
if ix==0:
return 0.0
elif ix==1:
return math.sin(alpha)
else:
return -math.cos(alpha)
field_M0=ocaml.raw_make_field(mwe_M,[fun_M0],"","")
field_M=ocaml.raw_make_field(mwe_M,[],"","")
field_H_exch=ocaml.raw_make_field(mwe_H_exch,[],"","")
eq_rhs="""
%range i:3, j:3, k:3, p:3, q:3;
dM(i) <-
1.2*eps(i,j,k)*M(j)*H_total(k)
+ (-0.03)*eps(i,j,k)*M(j)*eps(k,p,q)*M(p)*H_total(q)
+ (-1.0)*(M(j)*M(j)+(-1.0))*M(i);
""";
eq_H_total="""
%range j:3;
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)
max_order = 2
krylov_max = 100
max_it = 1000000
my_mesh = nmesh.load(mesh_filename)
(lam, master_mwes_and_fields_by_name) = jT_lam(
mesh=my_mesh,
sigma_el=su.of(sigma), # electrical conductivity
sigma_th=su.of(k), # thermal conductivity
c_heat=su.of(c_heat), # heat capacity
T_initial=su.of(T_initial),
)
(mwe_T, field_T) = master_mwes_and_fields_by_name['T']
sundialsbuffer_initial = ocaml.raw_make_field(mwe_T, [], "",
"sundials_initial")
sundialsbuffer_final = ocaml.raw_make_field(mwe_T, [], "", "sundials_final")
sundialsbuffer_starting = ocaml.raw_make_field(mwe_T, [], "", "sundials_work")
ocaml.field_copy_into(field_T, sundialsbuffer_initial)
ocaml.field_copy_into(field_T, sundialsbuffer_starting)
(cvode,fun_timings)=ocaml.raw_make_linalg_machine_cvode(\
lam, sundialsbuffer_starting,
"jacobian","execute_jplan",
"rhs",
jacobi_same_nonzero_pattern,
max_order,
krylov_max,
)
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)
jacobi_same_nonzero_pattern=False
max_order=2
krylov_max=100
max_it=1000000
my_mesh=nmesh.load(mesh_filename)
(lam,master_mwes_and_fields_by_name) = jT_lam(mesh=my_mesh,
sigma_el=su.of(sigma), # electrical conductivity
sigma_th=su.of(k), # thermal conductivity
c_heat=su.of(c_heat),# heat capacity
T_initial=su.of(T_initial),
)
(mwe_T,field_T) = master_mwes_and_fields_by_name['T']
sundialsbuffer_initial = ocaml.raw_make_field(mwe_T,[],"","sundials_initial")
sundialsbuffer_final = ocaml.raw_make_field(mwe_T,[],"","sundials_final")
sundialsbuffer_starting = ocaml.raw_make_field(mwe_T,[],"","sundials_work")
ocaml.field_copy_into(field_T, sundialsbuffer_initial)
ocaml.field_copy_into(field_T, sundialsbuffer_starting)
(cvode,fun_timings)=ocaml.raw_make_linalg_machine_cvode(\
lam, sundialsbuffer_starting,
"jacobian","execute_jplan",
"rhs",
jacobi_same_nonzero_pattern,
max_order,
krylov_max,
)
def make_field(mwe, initial_values=None, petsc_name="", restriction=""):
log.log(15, "About to create field from mwe XXX")
iv = []
if initial_values:
iv = [initial_values]
return ocaml.raw_make_field(mwe, iv, restriction, petsc_name)
# Our differential operators:
diffop_laplace = ocaml.make_diffop("-<d/dxj drho_by_dt|sigma|d/dxj phi>, j:2")
diffop_grad_phi = ocaml.make_diffop("<J(k)|sigma|d/dxk phi>, k:2")
# Initial conductivity is spatially constant:
def fun_sigma0(dof_name_indices, position):
return sigma0
# Later on, we will modify this field:
field_sigma = ocaml.raw_make_field(mwe_sigma, [fun_sigma0], "") # petsc name - auto-generated if "".
print "field_sigma: ", field_sigma
print "Sigma at origin: ", ocaml.probe_field(field_sigma, "sigma", [0.0, 0.0])
sys.stdout.flush()
# Dirichlet Boundary Conditions on our sample:
def laplace_dbc(coords):
if abs(coords[1]) > (2.5 - 0.05):
return 1
else:
return 0
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
sys.exit()
def make_field(mwe, initial_values=None, petsc_name="", restriction=""):
log.log(15, "About to create field from mwe XXX")
iv = []
if initial_values:
iv = [initial_values]
return ocaml.raw_make_field(mwe, iv, restriction, petsc_name)
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
sys.exit()
(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], "", "")
field_phi = ocaml.raw_make_field(mwe_phi, [], "", "")
eq_rhs = "dphi_dt <- laplace_phi;"
lam = make_linalg_machine(
"lam_phi",
mwes=[mwe_phi, mwe_dphi_dt, mwe_laplace_phi],
vectors=[
lam_vector(name="v_phi", mwe_name="phi"),
lam_vector(name="v_dphi_dt", mwe_name="dphi_dt"),
lam_vector(name="v_laplace_phi", mwe_name="laplace_phi"),
],
operators=[
lam_operator("op_laplace",
"laplace_phi",
diffop_laplace = ocaml.make_diffop("-<d/dxj drho_by_dt|sigma|d/dxj phi>, j:2")
diffop_grad_phi = ocaml.make_diffop("<J(k)|sigma|d/dxk phi>, k:2")
# Initial conductivity is spatially constant:
def fun_sigma0(dof_name_indices, position):
return sigma0
# Later on, we will modify this field:
field_sigma = ocaml.raw_make_field(
mwe_sigma,
[fun_sigma0],
"" # petsc name - auto-generated if "".
)
print "field_sigma: ", field_sigma
print "Sigma at origin: ", ocaml.probe_field(field_sigma, "sigma", [0.0, 0.0])
sys.stdout.flush()
# Dirichlet Boundary Conditions on our sample:
def laplace_dbc(coords):
if (abs(coords[1]) > (2.5 - 0.05)):
return 1
else:
return 0
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
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