def define_facemirrors(
self, phi_s_initial, phi_e_initial
): # Facemirrors are copies of the variables solved on the axial meshes..
self.phi_s_facemirror = FaceVariable(
mesh=self.p2d_mesh, value=phi_s_initial
) # ..and applied to the upper face of the p2d mesh in each domain
self.phi_e_facemirror = FaceVariable(mesh=self.p2d_mesh,
value=phi_e_initial)
self.j0_facemirror = FaceVariable(mesh=self.p2d_mesh, value=self.j0[0])
def Cs_p2d_diffcoeff_function(self):
self.Cs_p2d_diffCoeff = FaceVariable(
mesh=self.p2d_mesh, rank=2, value=[[[0., 0.], [0., 0.]]]
) # As always with FiPy, diffusion coefficients are defined on the faces (hence facevar)
self.numerixed_Cs_p2d_diffCoeff = numerix.array(
self.Cs_p2d_diffCoeff
) # Temporarily convert to a NumPy array to edit the values
(self.numerixed_Cs_p2d_diffCoeff[1][1]) = self.Ds * (
self.radial_faces**2.0
) / self.Rs # Assign a non-zero value to the diff. coefficient in the y-axis only..
self.Cs_p2d_diffCoeff = FaceVariable(
mesh=self.p2d_mesh, rank=2, value=self.numerixed_Cs_p2d_diffCoeff
) # ..which constrains diffusion to 1D. Now recreate the facevar with the new value
def _genTorque(self):
"""Generate Torque"""
self.Lambda = FaceVariable(name='Torque at cell faces', mesh=self.mesh, rank=1)
self.LambdaCell = CellVariable(name='Torque at cell centers', mesh=self.mesh)
LambdaArr = np.zeros(self.rF.shape)
LambdaArr[1:] = self.chi*np.power(1.0/(self.rF[1:]*self.gamma-1.0), 4)
#LambdaArr[self.gap] = 0.0; LambdaArr[self.gap] = LambdaArr.max()
self.Lambda.setValue(LambdaArr)
self.LambdaCell.setValue(self.chi*np.power(1.0/(self.r*self.gamma-1.0), 4))
self.LambdaCell[np.where(self.LambdaCell > LambdaArr.max())] = LambdaArr.max()
def Battery_facevariables(self, neg_De_eff, sep_De_eff, pos_De_eff,
neg_epsilon_e, sep_epsilon_e, pos_epsilon_e,
normalised_neg_length, normalised_sep_length):
self.De_eff = FaceVariable(
mesh=self.axial_mesh
) # Define effective diffusion coefficient as a FiPy facevariable
self.De_eff.setValue(
neg_De_eff,
where=(self.axial_mesh.faceCenters[0] <= normalised_neg_length)
) # Set its value to that for the neg. diff. coefficient in the negative electrode domain
self.De_eff.setValue(
sep_De_eff,
where=((
normalised_neg_length # Set its value to the correct value in the separator
< self.axial_mesh.faceCenters[0]) &
(self.axial_mesh.faceCenters[0] <
(normalised_neg_length + normalised_sep_length))))
self.De_eff.setValue(
pos_De_eff,
where=(
self.axial_mesh.faceCenters[
0] # Set its value to the correct value in the positive electrode domain
>= (normalised_neg_length + normalised_sep_length)))
self.epsilon_e_eff_facevariable = FaceVariable(
mesh=self.axial_mesh
) # Define electrolyte phase volume fraction as a FiPy facevariable
self.epsilon_e_eff_facevariable.setValue(
neg_epsilon_e**self.
brug, # Compute eff. value for neg. domain & set it in neg. electrode domain
where=(self.axial_mesh.faceCenters[0] <= normalised_neg_length))
self.epsilon_e_eff_facevariable.setValue(
sep_epsilon_e**self.
brug, # Compute eff. value for sep. domain & set it in sep. electrode domain
where=((normalised_neg_length < self.axial_mesh.faceCenters[0]) &
(self.axial_mesh.faceCenters[0] <
(normalised_neg_length + normalised_sep_length))))
self.epsilon_e_eff_facevariable.setValue(
pos_epsilon_e**self.
brug, # Compute eff. value for pos. domain & set it in pos. electrode domain
where=(self.axial_mesh.faceCenters[0] >=
(normalised_neg_length + normalised_sep_length)))
def Battery_cellvariables(self, neg_epsilon_e, sep_epsilon_e,
pos_epsilon_e, neg_a_s, pos_a_s, nx_neg, nx_sep,
nx_pos, j_battery_value, ce_initial,
phi_e_initial, neg_L, sep_L, pos_L, neg_De_eff,
sep_De_eff, pos_De_eff):
self.Ce = CellVariable(mesh=self.axial_mesh,
value=ce_initial,
hasOld=True)
self.phi_e = CellVariable(mesh=self.axial_mesh, value=phi_e_initial)
self.epsilon_e_value = numerix.zeros(nx_neg + nx_sep + nx_pos)
self.epsilon_e_value[0:nx_neg], self.epsilon_e_value[
nx_neg:nx_neg + nx_sep] = neg_epsilon_e, sep_epsilon_e
self.epsilon_e_value[nx_neg + nx_sep:] = pos_epsilon_e
self.epsilon_e = CellVariable(mesh=self.axial_mesh,
value=self.epsilon_e_value)
self.epsilon_e_eff_value = numerix.zeros(nx_neg + nx_sep + nx_pos)
self.epsilon_e_eff_value[0:nx_neg] = neg_epsilon_e**self.brug
self.epsilon_e_eff_value[nx_neg:nx_neg +
nx_sep] = sep_epsilon_e**self.brug
self.epsilon_e_eff_value[nx_neg + nx_sep:] = pos_epsilon_e**self.brug
self.epsilon_e_eff = CellVariable(mesh=self.axial_mesh,
value=self.epsilon_e_eff_value)
self.a_s_value = numerix.zeros(nx_neg + nx_pos + nx_sep)
self.a_s_value[0:nx_neg] = neg_a_s
self.a_s_value[nx_neg:nx_neg + nx_sep] = 0.0
self.a_s_value[nx_neg + nx_sep:] = pos_a_s
self.a_s = CellVariable(mesh=self.axial_mesh, value=self.a_s_value)
self.L_value = numerix.zeros(nx_neg + nx_pos + nx_sep)
self.L_value[0:nx_neg], self.L_value[nx_neg:nx_neg +
nx_sep] = neg_L, sep_L
self.L_value[nx_neg + nx_sep:] = pos_L
self.L = CellVariable(mesh=self.axial_mesh, value=self.L_value)
self.De_eff_value = numerix.zeros(nx_neg + nx_pos + nx_sep)
self.De_eff_value[0:nx_neg], self.De_eff_value[
nx_neg:nx_neg + nx_sep], self.De_eff_value[
nx_neg + nx_sep:] = neg_De_eff, sep_De_eff, pos_De_eff
self.De_eff = CellVariable(mesh=self.axial_mesh,
value=self.De_eff_value)
self.j_battery = CellVariable(mesh=self.axial_mesh,
value=j_battery_value)
def initializeDiagnostic(self,
variable,
funpointer,
default=0.0,
face_variable=False,
output_variable=True):
if not face_variable:
self.variables[variable] = CellVariable(name=variable,
mesh=self.mesh.mesh,
value=default)
else:
self.variables[variable] = FaceVariable(name=variable,
mesh=self.mesh.mesh,
value=default)
self.diagnostic_modules[variable] = DiagnosticModule(funpointer, self)
if output_variable:
self.variables_store.append(variable)
self.diagnostic_update_order.append(variable)
class Battery():
def __init__(
self, cell_temperature_celcius, capacity_Ah, bruggeman_coefficient,
charge_transfer_coefficient, current_collector_cross_section_area,
electrolyte_diffusivity,
transference_number): # Initialises physical properties of cell
########################################## Compute & Assign Constants ##################################################
self.T = 273.0 + cell_temperature_celcius # Could move into electrode-level later
self.Q = capacity_Ah * 3600.0
self.brug = bruggeman_coefficient # Could move into electrode-level later when electrodes may have unique brug. values
self.alpha = charge_transfer_coefficient # Could move into electrode-level later when electrodes may have unique alpha values
self.A = current_collector_cross_section_area
self.De = electrolyte_diffusivity
self.t_plus = transference_number
def Battery_scale_quantities(self, overall_thickness, kappa_string):
# self.L = overall_thickness
self.kappa = lambdify(
Ce, sympify(kappa_string), "numpy"
) # Function to return electrolyte electrical conductivity, given a species concentration
# NOTE: Consider changing this function's name since it's only the kappa definition now
######################################## Battery-level Mesh Generation #################################################
def define_global_mesh(self, node_spacing, normalised_domain_thickness
): # Only Ce & phi_e are solved on this mesh
self.dx = node_spacing # node_spacing vector passed can be either uniformly or non-uniformly spaced points
self.L_normalised = normalised_domain_thickness
self.axial_mesh = Grid1D(Lx=self.L_normalised, dx=self.dx)
def Battery_cellvariables(self, neg_epsilon_e, sep_epsilon_e,
pos_epsilon_e, neg_a_s, pos_a_s, nx_neg, nx_sep,
nx_pos, j_battery_value, ce_initial,
phi_e_initial, neg_L, sep_L, pos_L, neg_De_eff,
sep_De_eff, pos_De_eff):
self.Ce = CellVariable(mesh=self.axial_mesh,
value=ce_initial,
hasOld=True)
self.phi_e = CellVariable(mesh=self.axial_mesh, value=phi_e_initial)
self.epsilon_e_value = numerix.zeros(nx_neg + nx_sep + nx_pos)
self.epsilon_e_value[0:nx_neg], self.epsilon_e_value[
nx_neg:nx_neg + nx_sep] = neg_epsilon_e, sep_epsilon_e
self.epsilon_e_value[nx_neg + nx_sep:] = pos_epsilon_e
self.epsilon_e = CellVariable(mesh=self.axial_mesh,
value=self.epsilon_e_value)
self.epsilon_e_eff_value = numerix.zeros(nx_neg + nx_sep + nx_pos)
self.epsilon_e_eff_value[0:nx_neg] = neg_epsilon_e**self.brug
self.epsilon_e_eff_value[nx_neg:nx_neg +
nx_sep] = sep_epsilon_e**self.brug
self.epsilon_e_eff_value[nx_neg + nx_sep:] = pos_epsilon_e**self.brug
self.epsilon_e_eff = CellVariable(mesh=self.axial_mesh,
value=self.epsilon_e_eff_value)
self.a_s_value = numerix.zeros(nx_neg + nx_pos + nx_sep)
self.a_s_value[0:nx_neg] = neg_a_s
self.a_s_value[nx_neg:nx_neg + nx_sep] = 0.0
self.a_s_value[nx_neg + nx_sep:] = pos_a_s
self.a_s = CellVariable(mesh=self.axial_mesh, value=self.a_s_value)
self.L_value = numerix.zeros(nx_neg + nx_pos + nx_sep)
self.L_value[0:nx_neg], self.L_value[nx_neg:nx_neg +
nx_sep] = neg_L, sep_L
self.L_value[nx_neg + nx_sep:] = pos_L
self.L = CellVariable(mesh=self.axial_mesh, value=self.L_value)
self.De_eff_value = numerix.zeros(nx_neg + nx_pos + nx_sep)
self.De_eff_value[0:nx_neg], self.De_eff_value[
nx_neg:nx_neg + nx_sep], self.De_eff_value[
nx_neg + nx_sep:] = neg_De_eff, sep_De_eff, pos_De_eff
self.De_eff = CellVariable(mesh=self.axial_mesh,
value=self.De_eff_value)
self.j_battery = CellVariable(mesh=self.axial_mesh,
value=j_battery_value)
############################# Define Eff. Diff. Coefficients & Volume Fractions ########################################
def Battery_facevariables(self, neg_De_eff, sep_De_eff, pos_De_eff,
neg_epsilon_e, sep_epsilon_e, pos_epsilon_e,
normalised_neg_length, normalised_sep_length):
self.De_eff = FaceVariable(
mesh=self.axial_mesh
) # Define effective diffusion coefficient as a FiPy facevariable
self.De_eff.setValue(
neg_De_eff,
where=(self.axial_mesh.faceCenters[0] <= normalised_neg_length)
) # Set its value to that for the neg. diff. coefficient in the negative electrode domain
self.De_eff.setValue(
sep_De_eff,
where=((
normalised_neg_length # Set its value to the correct value in the separator
< self.axial_mesh.faceCenters[0]) &
(self.axial_mesh.faceCenters[0] <
(normalised_neg_length + normalised_sep_length))))
self.De_eff.setValue(
pos_De_eff,
where=(
self.axial_mesh.faceCenters[
0] # Set its value to the correct value in the positive electrode domain
>= (normalised_neg_length + normalised_sep_length)))
self.epsilon_e_eff_facevariable = FaceVariable(
mesh=self.axial_mesh
) # Define electrolyte phase volume fraction as a FiPy facevariable
self.epsilon_e_eff_facevariable.setValue(
neg_epsilon_e**self.
brug, # Compute eff. value for neg. domain & set it in neg. electrode domain
where=(self.axial_mesh.faceCenters[0] <= normalised_neg_length))
self.epsilon_e_eff_facevariable.setValue(
sep_epsilon_e**self.
brug, # Compute eff. value for sep. domain & set it in sep. electrode domain
where=((normalised_neg_length < self.axial_mesh.faceCenters[0]) &
(self.axial_mesh.faceCenters[0] <
(normalised_neg_length + normalised_sep_length))))
self.epsilon_e_eff_facevariable.setValue(
pos_epsilon_e**self.
brug, # Compute eff. value for pos. domain & set it in pos. electrode domain
where=(self.axial_mesh.faceCenters[0] >=
(normalised_neg_length + normalised_sep_length)))
#run gmsh gui to produce this mesh (.msh file)
#gmsh infiniteCylinder01.geo
filename = 'infiniteCylinder01.msh'
mesh = Gmsh2D(filename, communicator=serialComm)
del filename
T_initial = 425.08 #deg K
var = CellVariable(mesh=mesh, value=T_initial)
rho = 6980. #kg/m^3
cp = 227. #J/kg/K
k = 59.6 #W/m/K
D_thermal = k / rho / cp
D = FaceVariable(mesh=mesh, value=D_thermal)
eq = TransientTerm() == DiffusionTerm(coeff=D)
X_faces, Y_faces = mesh.faceCenters
surfaceFaces = (Y_faces > 0) & (
(X_faces**2 + Y_faces**2)**.5 > R_outer - cellSize / 10.)
#convectionCoeff=200. #W/m^2/K
Bi_desired = 10.
convectionCoeff = Bi_desired * k / R_inner
logging.info('convection coefficient is %.2E' % convectionCoeff)
Bi = convectionCoeff * R_inner / k #Biot number
logging.info('Biot number is %.2E' % Bi)
nx = 10
ny = 1
valueLeft = 0.
fluxRight = 1.
timeStepDuration = 1.
L = 10.
dx = L / nx
dy = 1.
mesh = Tri2D(dx, dy, nx, ny)
var = CellVariable(name="solution variable", mesh=mesh, value=valueLeft)
diffCoeff = FaceVariable(mesh=mesh, value=1.0)
x = mesh.faceCenters[0]
diffCoeff.setValue(0.1, where=(L / 4. <= x) & (x < 3. * L / 4.))
var.faceGrad.constrain([[1.], [0.]], mesh.facesRight)
var.constrain(valueLeft, mesh.facesLeft)
if __name__ == '__main__':
import fipy.tests.doctestPlus
exec(fipy.tests.doctestPlus._getScript())
input('finished')
c0[20:50] = 1.0
# mobile domain concentration
cm = CellVariable(name="$c_m$", mesh=m, value=c0)
# immobile domain concentration
cim = CellVariable(name="$c_{im}$", mesh=m, value=0.0)
cm.constrain(0, m.facesLeft)
cm.constrain(0, m.facesRight)
cim.constrain(0, m.facesLeft)
cim.constrain(0, m.facesRight)
# advective flow velocity
u = FaceVariable(mesh=m, value=(0.0,), rank=1)
# 1D convection diffusion equation (mobile domain)
# version with \frac{\partial c_{im}}{\partial t}
eqM = (TransientTerm(1.0,var=cm) + TransientTerm(betaT,var=cim) ==
DiffusionTerm(DR,var=cm) - ExponentialConvectionTerm(u/(Rm*phim),var=cm))
# immobile domain (lumped approach)
eqIM = TransientTerm(Rim*phiim,var=cim) == beta/Rim*(cm - ImplicitSourceTerm(1.0,var=cim))
# couple equations
eqn = eqM & eqIM
viewer = Viewer(vars=(cm,cim), datamin=0.0, datamax=1.0)
viewer.plot()
time = 0.0
nx = 800
cfl = 0.1
K = 4.
rho = 1.
dx = L / nx
m = Grid1D(nx=nx, dx=dx) + X0
x, = m.cellCenters
q = CellVariable(mesh=m, rank=1, elementshape=(2, ))
q[0, :] = numerix.exp(-50 * (x - 0.3)**2) * numerix.cos(20 * (x - 0.3))
q[0, x > 0.3] = 0.
Ax = FaceVariable(mesh=m,
rank=3,
value=[((0, K), (1 / rho, 0))],
elementshape=(1, 2, 2))
eqn = TransientTerm() + CentralDifferenceConvectionTerm(Ax) == 0
if __name__ == '__main__':
from fipy import MatplotlibViewer as Viewer
vi = Viewer((q[0], q[1]))
vi.plot()
for step in range(500):
eqn.solve(q, dt=cfl * dx)
if step % 10 == 0 and __name__ == '__main__':
vi.plot()
if __name__ == '__main__':
'''.format(cellSize, l1, l2,
math.tan(beta) * (l2 - l1), l3,
math.tan(alpha) * l3)
mesh = Gmsh3D(geometryTemplate)
phi = CellVariable(name="Pressure", mesh=mesh, value=P0)
# Berechnete Werte ------------------------------------------------------------
Dx = material["k_x"] * fluid["dichte"]
Dy = material["k_y"] * fluid["dichte"]
Dz = material["k_y"] * fluid["dichte"]
# D ist eine Face Variable, da der Koeffizient für jede Flaeche einzelnd berechenet wird
D = FaceVariable(mesh=mesh, value=((Dx, 0, 0), (0, Dy, 0), (0, 0, Dz)))
# boundry conditions ----------------------------------------------------------
phi.constrain(Pres, where=mesh.physicalFaces["inner"])
phi.constrain(Pamb, where=mesh.physicalFaces["outer"])
# Solving ---------------------------------------------------------------------
eq = DiffusionTerm(coeff=D)
sweep = 0
phi_old = phi.copy()
max_diff = 10e10
class Circumbinary(object):
def __init__(self, rmax=1.0e4, ncell=300, dt=1.0e-6, delta=1.0e-100,
fudge=1.0e-3, q=1.0, gamma=100, mdisk=0.1, odir='output',
bellLin=True, emptydt=0.001, **kargs):
self.rmax = rmax
self.ncell = ncell
self.dt = dt
self.delta = delta
self.mDisk = mdisk
Omega0 = (G*M/(gamma*a)**3)**0.5
nu0 = alpha*cs**2/Omega0
self.chi = 2*fudge*q**2*np.sqrt(G*M)/nu0/a*(gamma*a)**1.5
self.T0 = mu*Omega0/alpha/k*nu0
self.gamma = gamma
self.fudge = fudge
self.q = q
self.nu0 = nu0
self.t = 0.0
self.odir = odir
self.bellLin = bellLin
self.emptydt = emptydt
self._genGrid()
self.r = self.mesh.cellCenters.value[0]
self.rF = self.mesh.faceCenters.value[0]
if self.q > 0.0:
self.gap = np.where(self.rF < 1.7/gamma)
else:
self.gap = np.where(self.rF < 1.0/gamma)
self._genSigma()
self._genTorque()
self._genT(bellLin=self.bellLin, **kargs)
self._genVr()
self._buildEq()
def _genGrid(self, inB=1.0):
"""Generate a logarithmically spaced grid"""
logFaces = np.linspace(-np.log(self.gamma/inB), np.log(self.rmax), num=self.ncell+1)
logFacesLeft = logFaces[:-1]
logFacesRight = logFaces[1:]
dr = tuple(np.exp(logFacesRight) - np.exp(logFacesLeft))
self.mesh = CylindricalGrid1D(dr=dr, origin=(inB/self.gamma,))
def _genSigma(self, width=0.1):
"""Create dependent variable Sigma"""
# Gaussian initial condition
value = self.mDisk*M/np.sqrt(2*np.pi)/(self.gamma*a*width)*\
np.exp(-0.5*np.square(self.r-1.0)/width**2)/(2*np.pi*self.gamma*self.r*a)
# Make it dimensionless
value /= self.mDisk*M/(self.gamma*a)**2
idxs = np.where(self.r < 0.1)
value[idxs] = 0.0
value = tuple(value)
# Create the dependent variable and set the boundary conditions
# to zero
self.Sigma = CellVariable(name='Surface density',
mesh=self.mesh, hasOld=True, value=value)
#self.Sigma.constrain(0, self.mesh.facesLeft)
#self.Sigma.constrain(0, self.mesh.facesRight)
def _genTorque(self):
"""Generate Torque"""
self.Lambda = FaceVariable(name='Torque at cell faces', mesh=self.mesh, rank=1)
self.LambdaCell = CellVariable(name='Torque at cell centers', mesh=self.mesh)
LambdaArr = np.zeros(self.rF.shape)
LambdaArr[1:] = self.chi*np.power(1.0/(self.rF[1:]*self.gamma-1.0), 4)
#LambdaArr[self.gap] = 0.0; LambdaArr[self.gap] = LambdaArr.max()
self.Lambda.setValue(LambdaArr)
self.LambdaCell.setValue(self.chi*np.power(1.0/(self.r*self.gamma-1.0), 4))
self.LambdaCell[np.where(self.LambdaCell > LambdaArr.max())] = LambdaArr.max()
def _interpT(self):
"""
Get an initial guess for T using an interpolation of the solutions for T
in the various thermodynamic limits.
"""
Lambda = self.Lambda/self.chi*self.fudge*self.q**2*G*M/a
LambdaCell = self.LambdaCell/self.chi*self.fudge*self.q**2*G*M/a
Sigma = self.Sigma*M/(self.gamma*a)**2
r = self.r*a*self.gamma #In physical units (cgs)
self.Omega = np.sqrt(G*M/r**3)
self.TvThin = np.power(9.0/4*alpha*k/sigma/mu/kappa0*self.Omega, 1.0/(3.0+beta))
self.TtiThin = np.power(1/sigma/kappa0*(OmegaIn-self.Omega)*LambdaCell, 1.0/(4.0+beta))
self.Ti = np.power(np.square(eta/7*L/4/np.pi/sigma)*k/mu/G/M*r**(-3), 1.0/7)
self.TvThick = np.power(27.0/64*kappa0*alpha*k/sigma/mu*self.Omega*Sigma**2, 1.0/(3.0-beta))
self.TtiThick = np.power(3*kappa0/16/sigma*Sigma**2*(OmegaIn-self.Omega)*LambdaCell, 1.0/(4.0-beta))
#return np.power(self.TvThin**4 + self.TvThick**4 + self.TtiThin**4 + self.TtiThick**4 + self.Ti**4, 1.0/4)/self.T0
return np.power(self.TvThin**4 + self.TvThick**4 + self.Ti**4, 1.0/4)/self.T0
def _genT(self, bellLin=True, **kargs):
"""Create a cell variable for temperature"""
if bellLin:
@pickle_results(os.path.join(self.odir, "interpolator.pkl"))
def buildInterpolator(r, gamma, q, fudge, mDisk, **kargs):
# Keep in mind that buildTemopTable() returns the log10's of the values
rGrid, SigmaGrid, temp = thermopy.buildTempTable(r*a*gamma, q=q, f=fudge, **kargs)
# Go back to dimensionless units
rGrid -= np.log10(a*gamma)
SigmaGrid -= np.log10(mDisk*M/gamma**2/a**2)
# Get the range of values for Sigma in the table
rangeSigma = (np.power(10.0, SigmaGrid.min()), np.power(10.0, SigmaGrid.max()))
# Interpolate in the log of dimensionless units
return rangeSigma, RectBivariateSpline(rGrid, SigmaGrid, temp)
# Pass the radial grid in phsyical units
# Get back interpolator in logarithmic space
rangeSigma, log10Interp = buildInterpolator(self.r, self.gamma, self.q, self.fudge, self.mDisk, **kargs)
rGrid = np.log10(self.r)
SigmaMin = np.ones(rGrid.shape)*rangeSigma[0]
SigmaMax = np.ones(rGrid.shape)*rangeSigma[1]
r = self.r*a*self.gamma #In physical units (cgs)
self.Omega = np.sqrt(G*M/r**3)
Ti = np.power(np.square(eta/7*L/4/np.pi/sigma)*k/mu/G/M*r**(-3), 1.0/7)
T = np.zeros(Ti.shape)
# Define wrapper function that uses the interpolator and stores the results
# in an array given as a second argument. It can handle zero or negative
# Sigma values.
def func(Sigma):
good = np.logical_and(Sigma > rangeSigma[0], Sigma < rangeSigma[1])
badMin = np.logical_and(True, Sigma < rangeSigma[0])
badMax = np.logical_and(True, Sigma > rangeSigma[1])
if np.sum(good) > 0:
T[good] = np.power(10.0, log10Interp.ev(rGrid[good], np.log10(Sigma[good])))
if np.sum(badMin) > 0:
T[badMin] = np.power(10.0, log10Interp.ev(rGrid[badMin], np.log10(SigmaMin[badMin])))
if np.sum(badMax) > 0:
raise ValueError("Extrapolation to large values of Sigma is not allowed, build a table with a larger Sigmax")
T[badMax] = np.power(10.0, log10Interp.ev(rGrid[badMax], np.log10(SigmaMax[badMax])))
return T
# Store interpolator as an instance method
self._bellLinT = func
# Save the temperature as an operator variable
self.T = self.Sigma._UnaryOperatorVariable(lambda x: self._bellLinT(x))
# Initialize T with the interpolation of the various thermodynamic limits
else:
self.T = self._interpT()
def _genVr(self):
"""Generate the face variable that stores the velocity values"""
r = self.r #In dimensionless units (cgs)
# viscosity at cell centers in cgs
self.nu = alpha*k/mu/self.Omega/self.nu0*self.T
self.visc = r**0.5*self.nu*self.Sigma
#self.visc.grad.constrain([self.visc/2/self.r[0]], self.mesh.facesLeft)
#self.Sigma.constrain(self.visc.grad/self.nu*2*self.r**0.5, where=self.mesh.facesLeft)
# I add the delta to avoid divisions by zero
self.vrVisc = -3/self.rF**(0.5)/(self.Sigma.faceValue + self.delta)*self.visc.faceGrad
if self.q > 0.0:
self.vrTid = self.Lambda*np.sqrt(self.rF)
def _buildEq(self):
"""
Build the equation to solve, we can change this method to impelement other
schemes, e.g. Crank-Nicholson.
"""
# The current scheme is an implicit-upwind
if self.q > 0.0:
self.vr = self.vrVisc + self.vrTid
self.eq = TransientTerm(var=self.Sigma) == - ExplicitUpwindConvectionTerm(coeff=self.vr, var=self.Sigma)
else:
self.vr = self.vrVisc
mask_coeff = (self.mesh.facesLeft * self.mesh.faceNormals).getDivergence()
self.eq = TransientTerm(var=self.Sigma) == - ExplicitUpwindConvectionTerm(coeff=self.vr, var=self.Sigma)\
- mask_coeff*3.0/2*self.nu/self.mesh.x*self.Sigma.old
def dimensionalSigma(self):
"""
Return Sigma in dimensional form (cgs)
"""
return self.Sigma.value*self.mDisk*M/(self.gamma*a)**2
def dimensionalFJ(self):
"""
Return the viscous torque in dimensional units (cgs)
"""
return 3*np.pi*self.nu.value*self.nu0*self.dimensionalSigma()*np.sqrt(G*M*self.r*a*self.gamma)
def dimensionalTime(self, t=None, mode='yr'):
"""
Return current time in dimensional units (years or seconds)
"""
if t == None:
t = self.t
if mode == 'yr' or mode == 'years' or mode == 'year':
return t*(a*self.gamma)**2/self.nu0/(365*24*60*60)
else:
return t*(a*self.gamma)**2/self.nu0
def dimensionlessTime(self, t, mode='yr'):
"""
Returns the dimensionless value of the time given as an argument
"""
if mode == 'yr' or mode == 'years' or mode == 'year':
return t/(a*self.gamma)**2*self.nu0*(365*24*60*60)
else:
return t/(a*self.gamma)**2*self.nu0
def singleTimestep(self, dtMax=0.001, dt=None, update=True, emptyDt=False):
"""
Evolve the system for a single timestep of size `dt`
"""
if dt:
self.dt = dt
if emptyDt:
vr = self.vr.value[0]
if self.q == 0.0:
vr[0] = -3.0/2*self.nu.faceValue.value[0]/self.rF[0]
#vr[np.where(self.Sigma.value)] = self.delta
self.flux = self.rF[1:]*vr[1:]-self.rF[:-1]*vr[:-1]
self.flux = np.maximum(self.flux, self.delta)
self.dts = self.mesh.cellVolumes/(self.flux)
self.dts[np.where(self.Sigma.value == 0.0)] = np.inf
self.dts[self.gap] = np.inf
self.dt = self.emptydt*np.amin(self.dts)
self.dt = min(dtMax, self.dt)
try:
self.eq.sweep(dt=self.dt)
if np.any(self.Sigma.value < 0.0):
self.singleTimestep(dt=self.dt/2)
if update:
self.Sigma.updateOld()
self.t += self.dt
except FloatingPointError:
import ipdb; ipdb.set_trace()
def evolve(self, deltaTime, **kargs):
"""
Evolve the system using the singleTimestep method
"""
tEv = self.t + deltaTime
while self.t < tEv:
dtMax = tEv - self.t
self.singleTimestep(dtMax=dtMax, **kargs)
def revert(self):
"""
Revert evolve method if update=False was used, otherwise
it has no effect.
"""
self.Sigma.setValue(self.Sigma.old.value)
def writeToFile(self):
fName = self.odir + '/t{0}.pkl'.format(self.t)
with open(fName, 'wb') as f:
pickle.dump((self.t, self.Sigma.getValue()), f)
def readFromFile(self, fName):
with open(fName, 'rb') as f:
t, Sigma = pickle.load(f)
self.t = t
self.Sigma.setValue(Sigma)
def loadTimesList(self):
path = self.odir
files = os.listdir(path)
if '.DS_Store' in files:
files.remove('.DS_Store')
if 'interpolator.pkl' in files:
files.remove('interpolator.pkl')
if 'init.pkl' in files:
files.remove('init.pkl')
self.times = np.zeros((len(files),))
for i, f in enumerate(files):
match = re.match(r"^t((\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?)\.pkl", f)
if match == None:
print "WARNING: File {0} has an unexepected name".format(f)
files.remove(f)
continue
self.times[i] = float(match.group(1))
self.times.sort()
self.files = files
def loadTime(self, t):
"""
Load the file with the time closest to `t`
"""
idx = (np.abs(self.times-t)).argmin()
fName = self.odir + '/t'+str(self.times[idx]) + '.pkl'
self.readFromFile(fName)
The diffusion coefficient in the first half of the slab is double that in the second half """ from fipy import Variable, FaceVariable, CellVariable, Grid1D, TransientTerm, DiffusionTerm, Viewer from fipy.tools import numerix # Setting up a mesh nx = 50 dx = 0.02 L = nx * dx mesh = Grid1D(nx=nx, dx=dx) c = CellVariable(mesh=mesh, name=r"$c$", value=0.0) # Setting up the spatially varying diffusion coefficient # Due to the mechanics of the solver, the diffusion coefficient variable must be defined on the mesh face D = FaceVariable(mesh=mesh, value=2.0) x = mesh.faceCenters[0] D.setValue(1.0, where=(x > L / 2.0)) # Boundary conditions valueLeft = 1.0 valueRight = 0.0 c.constrain(valueLeft, mesh.facesLeft) c.constrain(valueRight, mesh.facesRight) #Equation eq = (TransientTerm() == DiffusionTerm(coeff=D)) dt = 0.001 t = Variable(0.0) time_stride = 20
// create remaining 7/8 inner shells
t1[] = Rotate {{0,0,1},{0,0,0},Pi/2} {Duplicata{Surface{1};}};
t2[] = Rotate {{0,0,1},{0,0,0},Pi} {Duplicata{Surface{1};}};
t3[] = Rotate {{0,0,1},{0,0,0},Pi*3/2} {Duplicata{Surface{1};}};
t4[] = Rotate {{0,1,0},{0,0,0},-Pi/2} {Duplicata{Surface{1};}};
t5[] = Rotate {{0,0,1},{0,0,0},Pi/2} {Duplicata{Surface{t4[0]};}};
t6[] = Rotate {{0,0,1},{0,0,0},Pi} {Duplicata{Surface{t4[0]};}};
t7[] = Rotate {{0,0,1},{0,0,0},Pi*3/2} {Duplicata{Surface{t4[0]};}};
// create entire inner and outer shell
Surface Loop(100)={1,t1[0],t2[0],t3[0],t7[0],t4[0],t5[0],t6[0]};
''', order=2).extrude(extrudeFunc=lambda r: 1.05 * r) # doctest: +GMSH
#
mmag = FaceVariable(name=r"$mmag$", mesh=mesh) # doctest: +GMSH
gridCoor = mesh.cellCenters
print("mesh created")
## Constants
kBoltzmann = 1.38064852e-23
mu0 = numerix.pi * 4.0e-7
## LLG parameters
##gamFac = 1.7608e11 * pi * 4.0e-7
gamFac = 2.2128e5
alphaDamping = 0.01
Temperature = 300
Msat = 500e3
magVolume = 2.0e-9 * (25e-9 * 25e-9) * numerix.pi
D = alphaDamping * gamFac * kBoltzmann * Temperature / ((1 + alphaDamping) * Msat * magVolume)
filename = 'infiniteCylinder01_solve_dimensionless.msh'
mesh = Gmsh2D(filename, communicator=serialComm)
del filename
#T_initial=425.08 #deg K
T_initial = 0.
var = CellVariable(mesh=mesh, value=T_initial, hasOld=True)
# rho=6980. #kg/m^3
# cp=227. #J/kg/K
# k=59.6 #W/m/K
# D_thermal=k/rho/cp
#D=FaceVariable(mesh=mesh,value=D_thermal)
D = FaceVariable(mesh=mesh, value=1.)
eq = TransientTerm() == DiffusionTerm(coeff=D)
X_faces, Y_faces = mesh.faceCenters
surfaceFaces = (Y_faces > 0) & (
(X_faces**2 + Y_faces**2)**.5 > R_outer - cellSize / 10.)
#convectionCoeff=200. #W/m^2/K
# Bi_desired=10.
# convectionCoeff=Bi_desired*k/R_inner
# logging.info('convection coefficient is %.2E' % convectionCoeff)
# Bi=convectionCoeff*R_inner/k #Biot number
X_faces, Y_faces = mesh.faceCenters
surfaceFaces = (Y_faces > 0) & (
(X_faces**2 + Y_faces**2)**.5 > R_outer - cellSize / 10.)
#convectionCoeff=200. #W/m^2/K
Bi_desired = 10. #SETTING
#Bi_desired=1e5
convectionCoeff = Bi_desired * k / R_inner
logging.info('convection coefficient is %.2E' % convectionCoeff)
Bi = convectionCoeff * R_inner / k #Biot number
logging.info('Biot number is %.2E' % Bi)
Gamma0 = D_thermal
Gamma = FaceVariable(mesh=mesh, value=Gamma0)
mask = surfaceFaces
Gamma.setValue(0., where=mask)
dPf = FaceVariable(mesh=mesh,
value=mesh._faceToCellDistanceRatio *
mesh.cellDistanceVectors)
Af = FaceVariable(mesh=mesh, value=mesh._faceAreas)
b = k
#RobinCoeff = (mask * Gamma0 * Af * mesh.faceNormals / (-dPf.dot(a) + b)).divergence #I changed a sign in the denominator since I suspect a sign error
#a is convectionCoeff times n_hat
#20181211: I am getting same result whichever sign in the denominator I go with; solution is stuck at initial condition
RobinCoeff = (
mask * Gamma0 * Af * mesh.faceNormals /
(-convectionCoeff * dPf.dot(mesh.faceNormals) + b)
).divergence #I changed a sign in the denominator since I suspect a sign error
g = convectionCoeff * T_infinity
surfaceFaces = (Y_faces > 0) & (
(X_faces**2 + Y_faces**2)**.5 > R_outer - cellSize / 10.)
#convectionCoeff=200. #W/m^2/K
Bi_desired = 10. #SETTING
convectionCoeff = Bi_desired * k / R_inner
logging.info('convection coefficient is %.2E' % convectionCoeff)
Bi = convectionCoeff * R_inner / k #Biot number
logging.info('Biot number is %.2E' % Bi)
#ref: https://github.com/usnistgov/fipy/blob/develop/documentation/USAGE.rst#applying-robin-boundary-conditions
#warning: avoid confusion between convectionCoeff in that fipy documentation, which refers to terms involving "a", and convectionCoeff here, which refers to a heat transfer convection coefficient at a boundary
Gamma0 = D_thermal
Gamma = FaceVariable(mesh=mesh, value=Gamma0)
mask = surfaceFaces
Gamma.setValue(0., where=mask)
dPf = FaceVariable(mesh=mesh,
value=mesh._faceToCellDistanceRatio *
mesh.cellDistanceVectors)
Af = FaceVariable(mesh=mesh, value=mesh._faceAreas)
#RobinCoeff = (mask * Gamma0 * Af / (dPf.dot(a) + b)).divergence #a is zero in our case
b = 1.
RobinCoeff = (mask * Gamma0 * Af / b).divergence #a is zero in our case
#eq = (TransientTerm() == DiffusionTerm(coeff=Gamma) + RobinCoeff * g - ImplicitSourceTerm(coeff=RobinCoeff * mesh.faceNormals.dot(a))) #a is zero in our case
# g in this formulation is -convectionCoeff/k*var, where var=T-T_infinity
eq = (TransientTerm() == DiffusionTerm(coeff=Gamma) +
ImplicitSourceTerm(RobinCoeff * -convectionCoeff / k))
# embed()
valueLeft = 0.
fluxRight = 1.
timeStepDuration = 1.
L = 10.
dx = L / nx
dy = 1.
mesh = Tri2D(dx, dy, nx, ny)
var = CellVariable(
name = "solution variable",
mesh = mesh,
value = valueLeft)
diffCoeff = FaceVariable(mesh = mesh, value = 1.0)
x = mesh.faceCenters[0]
diffCoeff.setValue(0.1, where=(L/4. <= x) & (x < 3. * L / 4.))
var.faceGrad.constrain([[1.], [0.]], mesh.facesRight)
var.constrain(valueLeft, mesh.facesLeft)
if __name__ == '__main__':
import fipy.tests.doctestPlus
exec(fipy.tests.doctestPlus._getScript())
input('finished')
