mwe_phi = nfem2.make_mwe("mwe_phi", [(1, element_phi)])
mwe_J = nfem2.make_mwe("mwe_J", [(1, element_J)])
diffop_laplace = nfem2.diffop("-<d/dxj drho_by_dt|sigma|d/dxj phi>, j:2")
diffop_J = nfem2.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 = nfem2.make_field(mwe_sigma, fun_sigma0)
# Dirichlet Boundary Conditions on our sample:
def laplace_dbc(coords):
if (abs(coords[1]) > (2.5 - 0.05)):
return 1
else:
return 0
def laplace_dbc_values(dof_name_indices, coords):
if (coords[1] > 0.0):
return 1.0
else:
if "nan" in str(magn):
#print ">>"+str(magn)+"<<<<<<<"
m[ax + "." + bx[:8] + "," + ay + "." +
by[:8]] = [0.0, 0.0, 0.0]
else:
# print ax+"."+bx[:8]+","+ay+"."+by[:8], ">>"+str(magn)+"<<"
m[ax + "." + bx[:8] + "," + ay + "." + by[:8]] = magn
# Later on, we will modify this field:
field_sigma = None
field_m = None
ocaml.sys_check_heap()
field_sigma = nfem2.make_field(mwe_sigma, fun_sigma0)
field_m = nfem2.make_field(mwe_M, fun_fill_m)
# Note the ignore_jumps parameter:
# we indeed ARE interested just in the
# surface outflow of electrical current!
for i in range(1, 5): # was: range(1,5)
update_sigma(field_sigma, i)
print "Forcing ocaml GC!"
sys.stdout.flush()
ocaml.sys_check_heap()
#print "Iteration ",i," sigma at origin: ",nfem2.probe_field(field_sigma,[0.0,0.0])
total_current = compute_total_current(field_sigma)
def constant_current(voltage):
# Dirichlet Boundary Conditions on our sample:
def laplace_dbc(coords):
# top contact bottom contact
if (coords[1] > 990.0
and coords[0] > 420.0) or (coords[1] < -40.0):
return 1
else:
return 0
def laplace_dbc_values(dof_name_indices, coords):
if (coords[1] > 500.0
): # greater or smaller than 1/2height of the sample
return voltage
else:
return 0.0
prematrix_laplace = nfem2.prematrix(diffop_laplace,
mwe_drho_by_dt,
mwe_phi,
mwe_mid=mwe_sigma)
prematrix_J = nfem2.prematrix(diffop_J,
mwe_J,
mwe_phi,
mwe_mid=mwe_sigma)
code_recompute_conductivity = """
if(have_sigma_Py)
{
double len2_J, sprod_MJ, cos2;
double len2_M=M(0)*M(0)+M(1)*M(1)+M(2)*M(2);
len2_J=J(0)*J(0)+J(1)*J(1)+J(2)*J(2);
sprod_MJ=M(0)*J(0)+M(1)*J(1)+M(2)*J(2);
cos2=(fabs(len2_J)<1e-8)?0.0:(sprod_MJ*sprod_MJ/(len2_M*len2_J));
sigma_Py = sigma0_Py /( 1. + alpha * cos2);
}
/* printf(\"cos2=%f sigma = %8.6f\\n \",cos2, sigma); */
"""
recompute_conductivity = nfem2.site_wise_applicator(
parameter_names=["sigma0_Py", "sigma0_Au", "alpha"],
# all the names of extra parameters
code=code_recompute_conductivity,
field_mwes=[mwe_sigma, mwe_J, mwe_M])
# computing the total current through the sample:
code_integrate_div_J = """
if(coords(1)>990.0 && coords(0)>420.0)
{
total_current_up+=drho_by_dt;
}
else if(coords(1)<-40.0)
{
total_current_down+=drho_by_dt;
}
else
{
double j=drho_by_dt;
if(j>0)total_bad_current_plus+=j;
else total_bad_current_minus+=j;
}
"""
accumulate_J_total = nfem2.site_wise_applicator(
parameter_names=[
"total_current_up", "total_current_down",
"total_bad_current_plus", "total_bad_current_minus"
],
code=code_integrate_div_J,
position_name="coords",
cofield_mwes=[mwe_drho_by_dt])
def update_sigma(the_field_sigma, i):
compute_J = nfem2.prematrix_applicator(
prematrix_J, field_mid=the_field_sigma)
laplace_solver = nfem2.laplace_solver(
prematrix_laplace,
dirichlet_bcs=[(-1, 4, laplace_dbc),
(-1, 6, laplace_dbc)],
mwe_mid=the_field_sigma)
cofield_drho_by_dt = nfem2.make_cofield(mwe_drho_by_dt)
#
field_phi = laplace_solver(cofield_drho_by_dt,
dbc_values=laplace_dbc_values)
field_J = nfem2.cofield_to_field(compute_J(field_phi))
# Next, let us compute the new condictivity by site-wise operation on
# field_J. We just overwrite field_sigma:
recompute_conductivity(
[sigma0_Py, sigma0_Au, alpha],
fields=[the_field_sigma, field_J, field_m])
return the_field_sigma
def compute_total_current(the_field_sigma):
laplace_solver = nfem2.laplace_solver(
prematrix_laplace,
# boundary conditions are defined on objects 4 and 6
dirichlet_bcs=[(-1, 4, laplace_dbc),
(-1, 6, laplace_dbc)],
mwe_mid=the_field_sigma)
compute_div_J = nfem2.prematrix_applicator(
prematrix_laplace, field_mid=the_field_sigma)
cofield_drho_by_dt = nfem2.make_cofield(mwe_drho_by_dt)
field_phi = laplace_solver(cofield_drho_by_dt,
dbc_values=laplace_dbc_values)
compute_J = nfem2.prematrix_applicator(
prematrix_J, field_mid=the_field_sigma)
field_J = nfem2.cofield_to_field(compute_J(field_phi))
cofield_div_J = compute_div_J(field_phi)
field_div_J = nfem2.cofield_to_field(cofield_div_J)
current = accumulate_J_total([0.0, 0.0, 0.0, 0.0],
cofields=[cofield_div_J])
return current, field_phi, the_field_sigma, field_J
global field_m
global field_sigma
# Later on, we will modify this fields:
field_sigma = None
field_m = None
ocaml.sys_check_heap()
field_sigma = nfem2.make_field(mwe_sigma, fun_sigma0)
## print "#######################################"
## print "## FIRST BATCH SIGMA ##"
## print "#######################################"
## nfem2.field_print_contents(field_sigma)
field_m = nfem2.make_field(mwe_M, fun_fill_m)
## print "#######################################"
## print "## FIRST BATCH M ##"
## print "#######################################"
## nfem2.field_print_contents(field_m)
# update sigma
for i in range(1, 3):
update_sigma(field_sigma, i)
print "Forcing ocaml GC!"
sys.stdout.flush()
## nfem2.field_print_contents(field_sigma)
ocaml.sys_check_heap()
total_current, field_phi, field_sigma, field_J = compute_total_current(
field_sigma)
nfem2_visual.fields2vtkfile(field_sigma,
"sigma" + str(fi) + ".vtk")
nfem2_visual.fields2vtkfile(field_phi,
"phi" + str(fi) + ".vtk")
nfem2_visual.fields2vtkfile(
field_J, "current-density" + str(fi) + ".vtk")
voltage_contact7 = nfem2.probe_field(
field_phi, [-20.0, 630.0, 40.0])[0][1]
voltage_contact8 = nfem2.probe_field(
field_phi, [-20.0, 385.0, 40.0])[0][1]
print total_current
resistance = voltage / total_current[
1] # resistance: potential / (downward current)
print "Current: ", total_current
print "Resistance: ", resistance
# ideal voltage is 150 in our units (to respect 150 microA in the experiment)
string2file = "voltage-contacts_11-9: %f\t total current: %f\t contact7: %f\t contact8: %f\n" % (
voltage, total_current[1], voltage_contact7,
voltage_contact8)
amrDataFile.write(
str(fi) + " " + str(resistance) + " " +
str(total_current) + "\n")
amrDataFile.write(string2file)
amrDataFile.flush()
return total_current[1] - 150.
ay, by = y.split(".")
if "nan" in str(magn):
# print ">>"+str(magn)+"<<<<<<<"
m[ax + "." + bx[:8] + "," + ay + "." + by[:8]] = [0.0, 0.0, 0.0]
else:
# print ax+"."+bx[:8]+","+ay+"."+by[:8], ">>"+str(magn)+"<<"
m[ax + "." + bx[:8] + "," + ay + "." + by[:8]] = magn
# Later on, we will modify this field:
field_sigma = None
field_m = None
ocaml.sys_check_heap()
field_sigma = nfem2.make_field(mwe_sigma, fun_sigma0)
field_m = nfem2.make_field(mwe_M, fun_fill_m)
# Note the ignore_jumps parameter:
# we indeed ARE interested just in the
# surface outflow of electrical current!
for i in range(1, 5): # was: range(1,5)
update_sigma(field_sigma, i)
print "Forcing ocaml GC!"
sys.stdout.flush()
ocaml.sys_check_heap()
# print "Iteration ",i," sigma at origin: ",nfem2.probe_field(field_sigma,[0.0,0.0])
total_current = compute_total_current(field_sigma)
def constant_current( voltage ):
# Dirichlet Boundary Conditions on our sample:
def laplace_dbc(coords):
# top contact bottom contact
if (coords[1] > 990.0 and coords[0] > 420.0) or (coords[1] < -40.0) :
return 1
else:
return 0
def laplace_dbc_values(dof_name_indices,coords):
if(coords[1] > 500.0): # greater or smaller than 1/2height of the sample
return voltage
else:
return 0.0
prematrix_laplace=nfem2.prematrix(diffop_laplace,
mwe_drho_by_dt,mwe_phi,
mwe_mid=mwe_sigma)
prematrix_J=nfem2.prematrix(diffop_J,
mwe_J,mwe_phi,
mwe_mid=mwe_sigma)
code_recompute_conductivity="""
if(have_sigma_Py)
{
double len2_J, sprod_MJ, cos2;
double len2_M=M(0)*M(0)+M(1)*M(1)+M(2)*M(2);
len2_J=J(0)*J(0)+J(1)*J(1)+J(2)*J(2);
sprod_MJ=M(0)*J(0)+M(1)*J(1)+M(2)*J(2);
cos2=(fabs(len2_J)<1e-8)?0.0:(sprod_MJ*sprod_MJ/(len2_M*len2_J));
sigma_Py = sigma0_Py /( 1. + alpha * cos2);
}
/* printf(\"cos2=%f sigma = %8.6f\\n \",cos2, sigma); */
"""
recompute_conductivity=nfem2.site_wise_applicator(parameter_names=["sigma0_Py","sigma0_Au","alpha"],
# all the names of extra parameters
code=code_recompute_conductivity,
field_mwes=[mwe_sigma,mwe_J,mwe_M]
)
# computing the total current through the sample:
code_integrate_div_J="""
if(coords(1)>990.0 && coords(0)>420.0)
{
total_current_up+=drho_by_dt;
}
else if(coords(1)<-40.0)
{
total_current_down+=drho_by_dt;
}
else
{
double j=drho_by_dt;
if(j>0)total_bad_current_plus+=j;
else total_bad_current_minus+=j;
}
"""
accumulate_J_total=nfem2.site_wise_applicator(parameter_names=["total_current_up",
"total_current_down",
"total_bad_current_plus",
"total_bad_current_minus"
],
code=code_integrate_div_J,
position_name="coords",
cofield_mwes=[mwe_drho_by_dt])
def update_sigma(the_field_sigma,i):
compute_J=nfem2.prematrix_applicator(prematrix_J,
field_mid=the_field_sigma)
laplace_solver=nfem2.laplace_solver(prematrix_laplace,
dirichlet_bcs=[(-1,4,laplace_dbc),(-1,6,laplace_dbc)],
mwe_mid=the_field_sigma)
cofield_drho_by_dt=nfem2.make_cofield(mwe_drho_by_dt)
#
field_phi = laplace_solver(cofield_drho_by_dt,
dbc_values=laplace_dbc_values)
field_J = nfem2.cofield_to_field(compute_J(field_phi))
# Next, let us compute the new condictivity by site-wise operation on
# field_J. We just overwrite field_sigma:
recompute_conductivity([sigma0_Py,sigma0_Au,alpha],fields=[the_field_sigma,field_J,field_m])
return the_field_sigma
def compute_total_current(the_field_sigma):
laplace_solver=nfem2.laplace_solver(prematrix_laplace,
# boundary conditions are defined on objects 4 and 6
dirichlet_bcs=[(-1,4,laplace_dbc),(-1,6,laplace_dbc)],
mwe_mid=the_field_sigma)
compute_div_J=nfem2.prematrix_applicator(prematrix_laplace,
field_mid=the_field_sigma)
cofield_drho_by_dt=nfem2.make_cofield(mwe_drho_by_dt)
field_phi=laplace_solver(cofield_drho_by_dt,
dbc_values=laplace_dbc_values)
compute_J=nfem2.prematrix_applicator(prematrix_J,
field_mid=the_field_sigma)
field_J = nfem2.cofield_to_field(compute_J(field_phi))
cofield_div_J=compute_div_J(field_phi)
field_div_J = nfem2.cofield_to_field(cofield_div_J)
current = accumulate_J_total([0.0,0.0,0.0,0.0],cofields=[cofield_div_J])
return current, field_phi, the_field_sigma, field_J
global field_m
global field_sigma
# Later on, we will modify this fields:
field_sigma = None
field_m = None
ocaml.sys_check_heap()
field_sigma=nfem2.make_field(mwe_sigma,fun_sigma0)
## print "#######################################"
## print "## FIRST BATCH SIGMA ##"
## print "#######################################"
## nfem2.field_print_contents(field_sigma)
field_m=nfem2.make_field(mwe_M, fun_fill_m)
## print "#######################################"
## print "## FIRST BATCH M ##"
## print "#######################################"
## nfem2.field_print_contents(field_m)
# update sigma
for i in range(1,3):
update_sigma(field_sigma,i)
print "Forcing ocaml GC!"
sys.stdout.flush()
## nfem2.field_print_contents(field_sigma)
ocaml.sys_check_heap()
total_current, field_phi, field_sigma, field_J = compute_total_current(field_sigma)
nfem2_visual.fields2vtkfile( field_sigma, "sigma"+str(fi)+".vtk")
nfem2_visual.fields2vtkfile( field_phi, "phi"+str(fi)+".vtk")
nfem2_visual.fields2vtkfile( field_J, "current-density"+str(fi)+".vtk")
voltage_contact7 = nfem2.probe_field(field_phi,[-20.0,630.0, 40.0])[0][1]
voltage_contact8 = nfem2.probe_field(field_phi,[-20.0,385.0, 40.0])[0][1]
print total_current
resistance = voltage/total_current[1] # resistance: potential / (downward current)
print "Current: ",total_current
print "Resistance: ",resistance
# ideal voltage is 150 in our units (to respect 150 microA in the experiment)
string2file = "voltage-contacts_11-9: %f\t total current: %f\t contact7: %f\t contact8: %f\n" % (voltage, total_current[1], voltage_contact7, voltage_contact8)
amrDataFile.write(str(fi)+" "+str(resistance)+" "+str(total_current)+"\n")
amrDataFile.write(string2file)
amrDataFile.flush()
return total_current[1]-150.
mwe_sigma = nfem2.make_mwe("mwe_sigma", [(1,element_sigma)])
mwe_drho_by_dt = nfem2.make_mwe("mwe_drho_by_dt",[(1,element_drho_by_dt)])
mwe_phi = nfem2.make_mwe("mwe_phi", [(1,element_phi)])
mwe_J = nfem2.make_mwe("mwe_J", [(1,element_J)])
diffop_laplace=nfem2.diffop("-<d/dxj drho_by_dt|sigma|d/dxj phi>, j:2")
diffop_J=nfem2.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=nfem2.make_field(mwe_sigma,fun_sigma0)
# Dirichlet Boundary Conditions on our sample:
def laplace_dbc(coords):
if(abs(coords[1]) > (2.5-0.05)):
return 1
else:
return 0
def laplace_dbc_values(dof_name_indices,coords):
if(coords[1] > 0.0):
return 1.0
else:
return -1.0