def GetAz(Bx, By, Jz, Nc, dl):
mesh = Grid2D(dx=dl[0], dy=dl[1], nx=Nc[0], ny=Nc[1])
_Az = CellVariable(mesh=mesh, value=0.0)
_Bx = CellVariable(mesh=mesh)
_Bx.value = np.reshape(Bx, Nc[0] * Nc[1], order='F')
_By = CellVariable(mesh=mesh)
_By.value = np.reshape(By, Nc[0] * Nc[1], order='F')
_Jz = CellVariable(mesh=mesh)
_Jz.value = np.reshape(Jz, Nc[0] * Nc[1], order='F')
_Az.equation = (DiffusionTerm(coeff=1.0) + _Jz == 0)
# beware of the sign of the flux : always consider outward direction
BCs = [
FixedFlux(value=_By.getFaceValue(), faces=mesh.getFacesLeft()),
FixedFlux(value=-_By.getFaceValue(), faces=mesh.getFacesRight()),
FixedFlux(value=-_Bx.getFaceValue(), faces=mesh.getFacesBottom()),
FixedFlux(value=_Bx.getFaceValue(), faces=mesh.getFacesTop())
]
_Az.equation.solve(var=_Az, boundaryConditions=BCs)
Az = np.reshape(_Az.value, Nc, order='F')
return Az
def icir_rect(self):
# step 1: Mesh
mesh = Grid2D(dx=self.gsize, dy=self.gsize, nx=self.xy_n[0], ny=self.xy_n[1])
# step 2: Equation
phi = CellVariable(mesh=mesh, name='potential phi', value=0.)
eqn = (DiffusionTerm(coeff = 1.) == 0.)
# step 3: Boundary conditions
# compute flow of 4 vertexes
# one vertex has 2 components of wind vector, (x, y)
vertexWindVec = np.array([ [0.0 for i in range(2)] for i in range(4)])
for i in range(4): # 4 vertexes
for j in range(2): # 2 components
vertexWindVec[i, j] = self.mean_flow[j] \
+ self.colored_noise(self.vertexWindVecRanInc[i][j])
# interpolate flow vector on sim area edges, and set neumann boundary
# conditions, because /grad /phi = V(x,y)
# get all points which lie on the center of edges of cells
X, Y = mesh.faceCenters
# /grad /phi array, of points of mesh face centers
# grad_phi_bc[0, :] /grad/phi_x
# grad_phi_bc[1, :] /grad/phi_y
grad_phi_bc = np.zeros_like(mesh.faceCenters())
# p: points on one edge to interpolate, 1 dimension
# vx, vy: x&y components of interpolated wind vectors of points list p
# vertex index, for interpolate bc on 4 edges
# vertexIndex[0] = [1,2], down boundary, 0<x<nx*dx, y=0
# vertexIndex[1] = [1,0], left boundary, x=0, 0<y<ny*dy
# vertexIndex[2] = [0,3], up boundary, 0<x<nx*dx, y=ny*dy
# vertexIndex[3] = [2,3], right boundary, x=nx*dx, 0<y<ny*dy
vertexIndex = np.array([ [1,2], [1,0], [0,3], [2,3] ])
for i in range(4): # 4 edges for 2D rect area
p = np.arange(self.gsize/2, self.gsize*self.xy_n[i%2], self.gsize)
vx = np.interp(p, [0.0, self.gsize*self.xy_n[i%2]], \
[vertexWindVec[vertexIndex[0,0], 0], \
vertexWindVec[vertexIndex[0,1], 0]]).T.reshape(1,-1)[0]
vy = np.interp(p, [0.0, self.gsize*self.xy_n[i%2]], \
[vertexWindVec[vertexIndex[0,0], 1], \
vertexWindVec[vertexIndex[0,1], 1]]).T.reshape(1,-1)[0]
print 'vx = ' + str(vx)
if i == 0: # down boundary
grad_phi_bc[:, mesh.facesDown()] = np.array([vx, vy])
elif i == 1: # left boundary
grad_phi_bc[:, mesh.facesLeft()] = np.array([vx, vy])
elif i == 2: # up boundary
grad_phi_bc[:, mesh.facesUp()] = np.array([vx, vy])
elif i == 3: # right boundary
grad_phi_bc[:, mesh.facesRight()] = np.array([vx, vy])
# set neumann boundary condition
phi.faceGrad.constrain(((grad_phi_bc[0]),(grad_phi_bc[1])), where=mesh.exteriorFaces)
# step 4: Solve
eqn.solve(var=phi)
#print str(phi)
#print str(type(np.array(phi)))
self.wind_phi_field = np.array(phi)
self.wind_mesh_centers = mesh.cellCenters()
def define_uniform_comp_domain_rad(
self, shells_per_particle, normalised_particle_radius
): # Uniform radial domain, electrode particles
self.nr = int(shells_per_particle)
self.Rs_normalised = normalised_particle_radius
self.dr = self.Rs_normalised / self.nr
self.p2d_mesh = Grid2D(nx=self.nx,
ny=self.nr,
Lx=self.L_normalised,
Ly=self.Rs_normalised)
self.dummy, self.radial_faces = self.p2d_mesh.faceCenters # Create a shorthand name for accessing y-axis faces in the particle mesh
def __init__(self,
X=None,
T=None,
time_steps=5,
max_time=0.4,
num_cells=25,
L=1.):
"""Initialize the objet.
Keyword Arguments:
X --- The sensor locations.
T --- The sensor measurment times.
time_steps --- How many timesteps do you want to measure.
max_time --- The maximum solution time.
num_cells --- The number of cells per dimension.
L --- The size of the computational domain.
"""
assert isinstance(num_cells, int)
self._num_cells = num_cells
assert isinstance(L, float) and L > 0.
self._dx = L / self.num_cells
self._mesh = Grid2D(dx=self.dx,
dy=self.dx,
nx=self.num_cells,
ny=self.num_cells)
self._phi = CellVariable(name='solution variable', mesh=self.mesh)
self._source = CellVariable(name='source term',
mesh=self.mesh,
hasOld=True)
self._eqX = TransientTerm() == ExplicitDiffusionTerm(
coeff=1.) + self.source
self._eqI = TransientTerm() == DiffusionTerm(coeff=1.) + self.source
self._eq = self._eqX + self._eqI
assert isinstance(max_time, float) and max_time > 0.
self._max_time = max_time
#self.max_time / time_steps #.
if X is None:
idx = range(self.num_cells**2)
else:
idx = []
x1, x2 = self.mesh.cellCenters
for x in X:
dist = (x1 - x[0])**2 + (x2 - x[1])**2
idx.append(np.argmin(dist))
self._idx = idx
if T is None:
T = np.linspace(0, self.max_time, time_steps)[1:]
self._max_time = T[-1]
self._T = T
self._dt = self.T[0] / time_steps
super(Diffusion, self).__init__(5,
len(self.T) * len(self.idx),
name='Diffusion Solver')
def define_non_uniform_comp_domain_rad(
self, shells_per_particle, normalised_particle_radius
): # Non-uniform radial domain, electrode particles
self.nr = int(shells_per_particle)
self.Rs_normalised = normalised_particle_radius
self.dr = numerix.diff(
numerix.log(1 - numerix.linspace(
0, 1.0 - numerix.exp(self.Rs_normalised), self.nr + 1)))
self.p2d_mesh = Grid2D(dx=self.dx,
dy=self.dr,
Lx=self.L_normalised,
Ly=self.Rs_normalised)
self.dummy, self.radial_faces = self.p2d_mesh.faceCenters # Create a shorthand name for accessing y-axis faces in the particle mesh
def GetAz(Bx, By, Jz, Nc, dl):
mesh = Grid2D(dx=dl[0], dy=dl[1], nx=Nc[0], ny=Nc[1])
_Az = CellVariable(mesh=mesh, value=0.0)
_Bx = CellVariable(mesh=mesh)
_Bx.value = np.reshape(Bx, Nc[0] * Nc[1], order='F')
_By = CellVariable(mesh=mesh)
_By.value = np.reshape(By, Nc[0] * Nc[1], order='F')
_Jz = CellVariable(mesh=mesh)
_Jz.value = np.reshape(Jz, Nc[0] * Nc[1], order='F')
_Az.equation = (DiffusionTerm(coeff=1.0) + _Jz == 0)
#diffcoeff = CellVariable(mesh=mesh, value = 1.0)
#diffTerm = DiffusionTerm(coeff = diffcoeff)
#diffTerm = DiffusionTerm(coeff = 1.0)
#diffcoeff.constrain(0., mesh.exteriorFaces)
# beware of the sign of the flux : always consider outward direction
_Az.faceGrad.constrain(_By.arithmeticFaceValue, where=mesh.facesLeft)
_Az.faceGrad.constrain(-_By.arithmeticFaceValue, where=mesh.facesRight)
_Az.faceGrad.constrain(-_Bx.arithmeticFaceValue, where=mesh.facesBottom)
_Az.faceGrad.constrain(_Bx.arithmeticFaceValue, where=mesh.facesTop)
#_Az.faceGrad.constrain( _By.arithmeticFaceValue[mesh.facesLeft] , where=mesh.facesLeft)
#_Az.faceGrad.constrain(-_By.arithmeticFaceValue[mesh.facesRight] , where=mesh.facesRight)
#_Az.faceGrad.constrain(-_Bx.arithmeticFaceValue[mesh.facesBottom] , where=mesh.facesBottom)
#_Az.faceGrad.constrain( _Bx.arithmeticFaceValue[mesh.facesTop] , where=mesh.facesTop)
#_Az.equation = (diffTerm+_Jz == 0)
#_Az.equation = (DiffusionTerm(diffcoeff)+ (mesh.exteriorFaces*exteriorFlux).divergence + _Jz== 0)
#_Az.equation = (diffTerm + _Jz == 0)
#BCs = [FixedFlux(value= _By.getFaceValue(), faces=mesh.getFacesLeft()),
# FixedFlux(value=-_By.getFaceValue(), faces=mesh.getFacesRight()),
# FixedFlux(value=-_Bx.getFaceValue(), faces=mesh.getFacesBottom()),
# FixedFlux(value= _Bx.getFaceValue(), faces=mesh.getFacesTop())]
#_Az.equation.solve(var=_Az, boundaryConditions=BCs)
_Az.equation.solve(var=_Az)
Az = np.reshape(_Az.value, Nc, order='F')
return Az
steps = 10
timeStepDuration = 0.02
L = 1.5
nx = 100
ny = 100
temperature = 1.
phaseTransientCoeff = 0.1
epsilon = 0.008
s = 0.01
alpha = 0.015
dx = L / nx
dy = L / ny
mesh = Grid2D(dx, dy, nx, ny)
phase = CellVariable(name = 'PhaseField', mesh = mesh, value = 1.)
theta = ModularVariable(name = 'Theta', mesh = mesh, value = 1.)
x, y = mesh.cellCenters
theta.setValue(0., where=(x - L / 2.)**2 + (y - L / 2.)**2 < (L / 4.)**2)
mPhiVar = phase - 0.5 + temperature * phase * (1 - phase)
thetaMag = theta.old.grad.mag
implicitSource = mPhiVar * (phase - (mPhiVar < 0))
implicitSource += (2 * s + epsilon**2 * thetaMag) * thetaMag
phaseEq = TransientTerm(phaseTransientCoeff) == \
ExplicitDiffusionTerm(alpha**2) \
- ImplicitSourceTerm(implicitSource) \
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from fipy import Variable, CellVariable, Grid2D, TransientTerm, DiffusionTerm
from fipy import ImplicitSourceTerm, Viewer, Matplotlib2DGridViewer
from fipy import MultiViewer, MatplotlibViewer
from fipy.tools import numerix
#%% Initial grid set up
if __name__ == '__main__':
NX = NY = 300
else:
NX = NY = 30
X_SIZE = Y_SIZE = 9
DX = X_SIZE / NX
DY = Y_SIZE / NY
mesh = Grid2D(dx=DX, dy=DY, nx=NX, ny=NY)
D_time = 0.0005
#%% Constants and Other Parameters
TAU = 0.0003 # Tau CONSTANT
ALPHA = 0.9 # Constant
GAMMA = 10.0 # Nondimensionalized
A_noise = 0.01 # Amplitude of the Noise
EPSILON_BAR = 0.01 # Compute Param, Thickness of layer at interface
#%% Anisotropy Functions
def m_temp(alpha, gamma, temp_eq, temp):
"""
Parameters
L = 1.
dx = 0.1
velocity = 1.
cfl = 0.1
distanceToTravel = L / 5.
boxSize = .2
nx = int(L / dx)
ny = int(L / dx)
steps = int(distanceToTravel / dx / cfl)
timeStepDuration = cfl * dx / velocity
mesh = Grid2D(dx=dx, dy=dx, nx=nx, ny=ny)
x0 = (L - boxSize) / 2
x1 = (L + boxSize) / 2
distanceVariable = DistanceVariable(mesh=mesh, value=1., hasOld=1)
x, y = mesh.cellCenters
distanceVariable.setValue(-1,
where=((x0 < x) & (x < x1)) & ((x0 < y) & (y < x1)))
surfactantVariable = SurfactantVariable(distanceVar=distanceVariable, value=1.)
from fipy.variables.surfactantConvectionVariable import SurfactantConvectionVariable
surfactantEquation = TransientTerm() - \
ExplicitUpwindConvectionTerm(SurfactantConvectionVariable(distanceVariable))
def runSimpleTrenchSystem(faradaysConstant=9.6e4,
gasConstant=8.314,
transferCoefficient=0.5,
rateConstant0=1.76,
rateConstant3=-245e-6,
catalystDiffusion=1e-9,
siteDensity=9.8e-6,
molarVolume=7.1e-6,
charge=2,
metalDiffusion=5.6e-10,
temperature=298.,
overpotential=-0.3,
metalConcentration=250.,
catalystConcentration=5e-3,
catalystCoverage=0.,
currentDensity0=0.26,
currentDensity1=45.,
cellSize=0.1e-7,
trenchDepth=0.5e-6,
aspectRatio=2.,
trenchSpacing=0.6e-6,
boundaryLayerDepth=0.3e-6,
numberOfSteps=5,
displayViewers=True):
cflNumber = 0.2
numberOfCellsInNarrowBand = 10
cellsBelowTrench = 10
yCells = cellsBelowTrench \
+ int((trenchDepth + boundaryLayerDepth) / cellSize)
xCells = int(trenchSpacing / 2 / cellSize)
from fipy.tools import serialComm
mesh = Grid2D(dx=cellSize,
dy=cellSize,
nx=xCells,
ny=yCells,
communicator=serialComm)
narrowBandWidth = numberOfCellsInNarrowBand * cellSize
distanceVar = DistanceVariable(name='distance variable',
mesh=mesh,
value=-1.,
hasOld=1)
bottomHeight = cellsBelowTrench * cellSize
trenchHeight = bottomHeight + trenchDepth
trenchWidth = trenchDepth / aspectRatio
sideWidth = (trenchSpacing - trenchWidth) / 2
x, y = mesh.cellCenters
distanceVar.setValue(1.,
where=(y > trenchHeight) |
((y > bottomHeight) &
(x < xCells * cellSize - sideWidth)))
distanceVar.calcDistanceFunction(order=2)
catalystVar = SurfactantVariable(name="catalyst variable",
value=catalystCoverage,
distanceVar=distanceVar)
bulkCatalystVar = CellVariable(name='bulk catalyst variable',
mesh=mesh,
value=catalystConcentration)
metalVar = CellVariable(name='metal variable',
mesh=mesh,
value=metalConcentration)
expoConstant = -transferCoefficient * faradaysConstant \
/ (gasConstant * temperature)
tmp = currentDensity1 * catalystVar.interfaceVar
exchangeCurrentDensity = currentDensity0 + tmp
expo = numerix.exp(expoConstant * overpotential)
currentDensity = expo * exchangeCurrentDensity * metalVar \
/ metalConcentration
depositionRateVariable = currentDensity * molarVolume \
/ (charge * faradaysConstant)
extensionVelocityVariable = CellVariable(name='extension velocity',
mesh=mesh,
value=depositionRateVariable)
surfactantEquation = AdsorbingSurfactantEquation(
surfactantVar=catalystVar,
distanceVar=distanceVar,
bulkVar=bulkCatalystVar,
rateConstant=rateConstant0 + rateConstant3 * overpotential**3)
advectionEquation = TransientTerm() + AdvectionTerm(
extensionVelocityVariable)
metalEquation = buildMetalIonDiffusionEquation(
ionVar=metalVar,
distanceVar=distanceVar,
depositionRate=depositionRateVariable,
diffusionCoeff=metalDiffusion,
metalIonMolarVolume=molarVolume,
)
metalVar.constrain(metalConcentration, mesh.facesTop)
from surfactantBulkDiffusionEquation import buildSurfactantBulkDiffusionEquation
bulkCatalystEquation = buildSurfactantBulkDiffusionEquation(
bulkVar=bulkCatalystVar,
distanceVar=distanceVar,
surfactantVar=catalystVar,
diffusionCoeff=catalystDiffusion,
rateConstant=rateConstant0 * siteDensity)
bulkCatalystVar.constrain(catalystConcentration, mesh.facesTop)
if displayViewers:
try:
from mayaviSurfactantViewer import MayaviSurfactantViewer
viewer = MayaviSurfactantViewer(distanceVar,
catalystVar.interfaceVar,
zoomFactor=1e6,
datamax=0.5,
datamin=0.0,
smooth=1,
title='catalyst coverage')
except:
viewer = MultiViewer(
viewers=(Viewer(distanceVar, datamin=-1e-9, datamax=1e-9),
Viewer(catalystVar.interfaceVar)))
else:
viewer = None
levelSetUpdateFrequency = int(0.8 * narrowBandWidth \
/ (cellSize * cflNumber * 2))
for step in range(numberOfSteps):
if step > 5 and step % 5 == 0 and viewer is not None:
viewer.plot()
if step % levelSetUpdateFrequency == 0:
distanceVar.calcDistanceFunction(order=2)
extensionVelocityVariable.setValue(depositionRateVariable())
distanceVar.updateOld()
distanceVar.extendVariable(extensionVelocityVariable, order=2)
dt = cflNumber * cellSize / extensionVelocityVariable.max()
advectionEquation.solve(distanceVar, dt=dt)
surfactantEquation.solve(catalystVar, dt=dt)
metalEquation.solve(metalVar, dt=dt)
bulkCatalystEquation.solve(bulkCatalystVar,
dt=dt,
solver=GeneralSolver(tolerance=1e-15,
iterations=2000))
try:
import os
filepath = os.path.splitext(__file__)[0] + '.gz'
print catalystVar.allclose(numerix.loadtxt(filepath), rtol=1e-4)
except:
return 0
from __future__ import division from __future__ import unicode_literals from builtins import range from examples.chemotaxis.parameters import parameters from fipy import input from fipy import CellVariable, Grid2D, TransientTerm, DiffusionTerm, ImplicitSourceTerm, Viewer params = parameters['case 2'] nx = 50 ny = 50 dx = 1. L = nx * dx mesh = Grid2D(nx=nx, ny=ny, dx=dx, dy=1.) shift = 1. KMVar = CellVariable(mesh=mesh, value=params['KM'] * shift, hasOld=1) KCVar = CellVariable(mesh=mesh, value=params['KC'] * shift, hasOld=1) TMVar = CellVariable(mesh=mesh, value=params['TM'] * shift, hasOld=1) TCVar = CellVariable(mesh=mesh, value=params['TC'] * shift, hasOld=1) P3Var = CellVariable(mesh=mesh, value=params['P3'] * shift, hasOld=1) P2Var = CellVariable(mesh=mesh, value=params['P2'] * shift, hasOld=1) RVar = CellVariable(mesh=mesh, value=params['R'], hasOld=1) PN = P3Var + P2Var KMscCoeff = params['chiK'] * (RVar + 1) * (1 - KCVar - KMVar.cellVolumeAverage) KMspCoeff = params['lambdaK'] / (1 + PN / params['kappaK'])
from fipy import CellVariable, Grid2D, GaussianNoiseVariable, DiffusionTerm, TransientTerm, ImplicitSourceTerm, VTKCellViewer, LinearLUSolver, parallelComm
from fipy.tools import numerix
import time
from params_fipy import (A_RAW, NOISE_MAGNITUDE, TIME_MAX, DT, N_CELLS,
DOMAIN_LENGTH, TIME_STRIDE, chi_AB, N_A, N_B, GIBBS,
DESIRED_RESIDUAL)
print("Yay")
# # Define mesh
# mesh = Grid2D(dx=dx, dy=dx, nx=N_CELLS, ny=N_CELLS)
mesh = Grid2D(nx=10.0, ny=10.0, dx=1.0, dy=1.0)
print("mesh loaded")
# We need to define the relevant variables:
a = CellVariable(name=r"a", mesh=mesh, hasOld=1)
exp_a = CellVariable(name=r"exp_a", mesh=mesh, hasOld=1)
mu_AB = CellVariable(name=r"mu_AB", mesh=mesh, hasOld=1)
# We need to introduce the noise
noise = GaussianNoiseVariable(mesh=mesh,
mean=numerix.log(A_RAW),
variance=abs(numerix.log(NOISE_MAGNITUDE))).value
a[:] = noise
if GIBBS == "FH":
dgda = (1 + a) * (numerix.exp(a) / N_A) - (numerix.exp(a) / N_B) * (
1 + numerix.log(1.0 - numerix.exp(a))
) + chi_AB * numerix.exp(a) - 2.0 * chi_AB * numerix.exp(2.0 * a)
from __future__ import unicode_literals
from builtins import input
__docformat__ = 'restructuredtext'
from fipy import Grid2D, DistanceVariable, Viewer
from fipy.tools import numerix, serialComm
dx = 1.
dy = 1.
nx = 5
ny = 5
Lx = nx * dx
Ly = ny * dy
mesh = Grid2D(dx=dx, dy=dy, nx=nx, ny=ny, communicator=serialComm)
var = DistanceVariable(name='level set variable',
mesh=mesh,
value=-1.,
hasOld=1)
x, y = mesh.cellCenters
var.setValue(1,
where=((x < dx) | (x > (Lx - dx))
| (y < dy) | (y > (Ly - dy))))
if __name__ == '__main__':
var.calcDistanceFunction(order=1)
viewer = Viewer(vars=var, datamin=-5., datamax=5.)
viewer.plot()
value = valueBottomTop)
var.constrain(valueLeftRight, mesh.facesLeft)
var.constrain(valueLeftRight, mesh.facesRight)
var.constrain(valueBottomTop, mesh.facesTop)
var.constrain(valueBottomTop, mesh.facesBottom)
#do the 2D problem for comparison
nx = 8 # FIXME: downsized temporarily from 10 due to https://github.com/usnistgov/fipy/issues/622
ny = 5
dx = 1.
dy = 1.
mesh2 = Grid2D(dx = dx, dy = dy, nx = nx, ny = ny)
var2 = CellVariable(name = "solution variable 2D",
mesh = mesh2,
value = valueBottomTop)
var2.constrain(valueLeftRight, mesh2.facesLeft)
var2.constrain(valueLeftRight, mesh2.facesRight)
var2.constrain(valueBottomTop, mesh2.facesTop)
var2.constrain(valueBottomTop, mesh2.facesBottom)
eqn = DiffusionTerm()
if __name__ == '__main__':
eqn.solve(var2)
viewer = Viewer(var2)
##### The first type of functions###### # y01 = np.zeros(nx) # y01[0:500] = 0.5e21 # # y02 = np.zeros(nx) # y02[0:500] = 0.5e21 # # y03 = np.zeros(nx) s=(nx, ny) B01=np.full(s, 0.5e21) B02=np.full(s, 0.5e21) B03=np.full(s, 0) # print(np.shape(B01)) mesh = Grid2D(dx=dx,dy=dy,nx=nx,ny=ny) # Establish mesh in how many dimensions necessary mesh_2D = Grid2D(dx=dx,dy=dy,nx=nx,ny=ny) Pion = CellVariable(mesh=mesh_2D, name='Positive ion Charge Density', value= B01) Nion = CellVariable(mesh=mesh_2D, name='Negative ion Charge Density', value= B02) potential = CellVariable(mesh=mesh_2D, name='Potential', value=0.) # # print(Pion.value.shape) # print(Nion.value.shape) # print(potential.value.shape) # plt.imshow(Pion.value, vmin=0, vmax = 1e22) # plt.colorbar() # plt.show()