mesh = Grid1D(dx = dx, nx = nx)
from fipy.tools import numerix
from fipy.variables.cellVariable import CellVariable
var = CellVariable(mesh = mesh)
from fipy.solvers.linearLUSolver import LinearLUSolver
from fipy.boundaryConditions.nthOrderBoundaryCondition import NthOrderBoundaryCondition
from fipy.terms.implicitDiffusionTerm import ImplicitDiffusionTerm
from fipy.terms.transientTerm import TransientTerm
eq = ImplicitDiffusionTerm((1.0, 1.0))
BCs = (NthOrderBoundaryCondition(mesh.getFacesLeft(), 0., 0),
NthOrderBoundaryCondition(mesh.getFacesRight(), Lx, 0),
NthOrderBoundaryCondition(mesh.getFacesLeft(), 0., 2),
NthOrderBoundaryCondition(mesh.getFacesRight(), 0., 2))
solver = LinearLUSolver(iterations=10)
if __name__ == '__main__':
eq.solve(var,
boundaryConditions = BCs,
solver = solver)
from fipy.viewers import make
viewer = make(var)
viewer.plot()
raw_input("finished")
dx = Lx / nx
mesh = Grid1D(dx=dx, nx=nx)
from fipy.tools import numerix
from fipy.variables.cellVariable import CellVariable
var = CellVariable(mesh=mesh)
from fipy.solvers.linearLUSolver import LinearLUSolver
from fipy.boundaryConditions.nthOrderBoundaryCondition import NthOrderBoundaryCondition
from fipy.terms.implicitDiffusionTerm import ImplicitDiffusionTerm
from fipy.terms.transientTerm import TransientTerm
eq = ImplicitDiffusionTerm((1.0, 1.0))
BCs = (NthOrderBoundaryCondition(mesh.getFacesLeft(), 0., 0),
NthOrderBoundaryCondition(mesh.getFacesRight(), Lx, 0),
NthOrderBoundaryCondition(mesh.getFacesLeft(), 0., 2),
NthOrderBoundaryCondition(mesh.getFacesRight(), 0., 2))
solver = LinearLUSolver(iterations=10)
if __name__ == '__main__':
eq.solve(var, boundaryConditions=BCs, solver=solver)
from fipy.viewers import make
viewer = make(var)
viewer.plot()
raw_input("finished")
KCscCoeff = params['alphaKstar'] * params['lambdaK'] * (
KMVar / (1 + PN / params['kappaK'])).getCellVolumeAverage()
KCspCoeff = params['lambdaKstar'] / (params['kappaKstar'] + KCVar)
KCEq = TransientTerm() - KCscCoeff + ImplicitSourceTerm(KCspCoeff)
eqs = ((KMVar, KMEq), (TMVar, TMEq), (TCVar, TCEq), (P3Var, P3Eq),
(P2Var, P2Eq), (KCVar, KCEq))
if __name__ == '__main__':
from fipy.viewers import make
PNView = PN / PN.getCellVolumeAverage()
PNView.setName('PN')
PNViewer = make(PNView, limits={'datamax': 2., 'datamin': 0.}, title='')
KMView = KMVar / KMVar.getCellVolumeAverage()
KMView.setName('KM')
KMViewer = make(KMView, limits={'datamax': 2., 'datamin': 0.}, title='')
TMView = TMVar / TMVar.getCellVolumeAverage()
TMView.setName('TM')
TMViewer = make(TMView, limits={'datamax': 2., 'datamin': 0.}, title='')
for i in range(100):
for var, eqn in eqs:
var.updateOld()
for var, eqn in eqs:
eqn.solve(var, dt=1.)
#Laplacian=0
nx = 50
dx = 1.
from fipy.meshes.grid1D import Grid1D
mesh = Grid1D(nx=nx, dx=dx)
from fipy.variables.cellVariable import CellVariable
phi = CellVariable(name="solution variable", mesh=mesh, value=0)
z = CellVariable(name="dummy", mesh=mesh, value=0)
valueLeft = 1
valueRight = 0
from fipy.boundaryConditions.fixedValue import FixedValue
BCs = (FixedValue(faces=mesh.getFacesRight(), value=valueRight),
FixedValue(faces=mesh.getFacesLeft(), value=valueLeft))
from fipy.terms.explicitDiffusionTerm import ExplicitDiffusionTerm
eqX = ExplicitDiffusionTerm(coeff=1)
from fipy import viewers
viewer = viewers.make(vars=(phi), limits={'datamin': 0., 'datamax': 1.})
viewer.plot()
eqX.solve(var=phi, boundaryConditions=BCs)
viewer.plot()
def runGold(faradaysConstant=9.6e4,
consumptionRateConstant=2.6e+6,
molarVolume=10.21e-6,
charge=1.0,
metalDiffusion=1.7e-9,
metalConcentration=20.0,
catalystCoverage=0.15,
currentDensity0=3e-2 * 16,
currentDensity1=6.5e-1 * 16,
cellSize=0.1e-7,
trenchDepth=0.2e-6,
aspectRatio=1.47,
trenchSpacing=0.5e-6,
boundaryLayerDepth=90.0e-6,
numberOfSteps=10,
taperAngle=6.0,
displayViewers=True):
cflNumber = 0.2
numberOfCellsInNarrowBand = 20
cellsBelowTrench = 10
from fipy.tools import numerix
from fipy import TrenchMesh
mesh = TrenchMesh(cellSize=cellSize,
trenchSpacing=trenchSpacing,
trenchDepth=trenchDepth,
boundaryLayerDepth=boundaryLayerDepth,
aspectRatio=aspectRatio,
angle=numerix.pi * taperAngle / 180.,
bowWidth=0.,
overBumpRadius=0.,
overBumpWidth=0.)
narrowBandWidth = numberOfCellsInNarrowBand * cellSize
from fipy.models.levelSet.distanceFunction.distanceVariable import DistanceVariable
distanceVar = DistanceVariable(name='distance variable',
mesh=mesh,
value=-1,
narrowBandWidth=narrowBandWidth)
distanceVar.setValue(1, where=mesh.getElectrolyteMask())
distanceVar.calcDistanceFunction(narrowBandWidth=1e10)
from fipy.models.levelSet.surfactant.surfactantVariable import SurfactantVariable
catalystVar = SurfactantVariable(name="catalyst variable",
value=catalystCoverage,
distanceVar=distanceVar)
from fipy.variables.cellVariable import CellVariable
metalVar = CellVariable(name='metal variable',
mesh=mesh,
value=metalConcentration)
exchangeCurrentDensity = currentDensity0 + currentDensity1 * catalystVar.getInterfaceVar(
)
currentDensity = metalVar / metalConcentration * exchangeCurrentDensity
depositionRateVariable = currentDensity * molarVolume / charge / faradaysConstant
extensionVelocityVariable = CellVariable(name='extension velocity',
mesh=mesh,
value=depositionRateVariable)
from fipy.models.levelSet.surfactant.adsorbingSurfactantEquation \
import AdsorbingSurfactantEquation
catalystSurfactantEquation = AdsorbingSurfactantEquation(
catalystVar,
distanceVar=distanceVar,
bulkVar=0,
rateConstant=0,
consumptionCoeff=consumptionRateConstant * extensionVelocityVariable)
from fipy.models.levelSet.advection.higherOrderAdvectionEquation \
import buildHigherOrderAdvectionEquation
advectionEquation = buildHigherOrderAdvectionEquation(
advectionCoeff=extensionVelocityVariable)
from fipy.boundaryConditions.fixedValue import FixedValue
from fipy.models.levelSet.electroChem.metalIonDiffusionEquation \
import buildMetalIonDiffusionEquation
metalEquation = buildMetalIonDiffusionEquation(
ionVar=metalVar,
distanceVar=distanceVar,
depositionRate=depositionRateVariable,
diffusionCoeff=metalDiffusion,
metalIonMolarVolume=molarVolume)
metalEquationBCs = FixedValue(mesh.getTopFaces(), metalConcentration)
if displayViewers:
try:
from fipy.viewers.mayaviViewer.mayaviSurfactantViewer import MayaviSurfactantViewer
viewers = (MayaviSurfactantViewer(distanceVar,
catalystVar.getInterfaceVar(),
zoomFactor=1e6,
limits={
'datamax': 1.0,
'datamin': 0.0
},
smooth=1,
title='catalyst coverage'), )
except:
class PlotVariable(CellVariable):
def __init__(self, var=None, name=''):
CellVariable.__init__(self,
mesh=mesh.getFineMesh(),
name=name)
self.var = self._requires(var)
def _calcValue(self):
return numerix.array(
self.var[:self.mesh.getNumberOfCells()])
from fipy.viewers import make
viewers = (make(PlotVariable(var=distanceVar),
limits={
'datamax': 1e-9,
'datamin': -1e-9
}),
make(PlotVariable(var=catalystVar.getInterfaceVar())))
else:
viewers = ()
levelSetUpdateFrequency = int(0.7 * narrowBandWidth / cellSize /
cflNumber / 2)
step = 0
while step < numberOfSteps:
if step % 10 == 0:
for viewer in viewers:
viewer.plot()
if step % levelSetUpdateFrequency == 0:
distanceVar.calcDistanceFunction(deleteIslands=True)
extensionVelocityVariable.setValue(
numerix.array(depositionRateVariable))
argmax = numerix.argmax(extensionVelocityVariable)
dt = cflNumber * cellSize / extensionVelocityVariable[argmax]
distanceVar.extendVariable(extensionVelocityVariable,
deleteIslands=True)
distanceVar.updateOld()
catalystVar.updateOld()
metalVar.updateOld()
advectionEquation.solve(distanceVar, dt=dt)
catalystSurfactantEquation.solve(catalystVar, dt=dt)
metalEquation.solve(metalVar,
boundaryConditions=metalEquationBCs,
dt=dt)
step += 1
try:
from fipy.tools import dump
import os
import examples.levelSet.electroChem
data = dump.read(
os.path.join(examples.levelSet.electroChem.__path__[0],
'goldData.gz'))
n = mesh.getFineMesh().getNumberOfCells()
print numerix.allclose(catalystVar[:n], data[:n], atol=1.0)
except:
return 0
from fipy.boundaryConditions.fixedValue import FixedValue
BC = (NthOrderBoundaryCondition(faces=mesh.getFacesBottom(), value=0,order=1),
FixedValue(faces=mesh.getFacesBottom(), value=0),
NthOrderBoundaryCondition(faces=mesh.getFacesLeft(), value=0,order=1),
NthOrderBoundaryCondition(faces=mesh.getFacesTop(), value=1,order=1),
NthOrderBoundaryCondition(faces=mesh.getFacesTop(), value=0,order=2))
from fipy.boundaryConditions.fixedFlux import FixedFlux
BC = (FixedFlux(faces=mesh.getFacesBottom(), value=0),
FixedValue(faces=mesh.getFacesBottom(), value=0),
FixedValue(faces=mesh.getFacesTop(), value=1),
FixedFlux(faces=mesh.getFacesTop(), value=1),
FixedFlux(faces=mesh.getFacesLeft(), value=0))
from fipy import viewers
viewer = viewers.make(vars=(psi,u,v,U))
eq.solve(var=psi,boundaryConditions=BC)
viewer.plot()
def hit_continue(Prompt='Hit any key to continue'):
raw_input(Prompt)
hit_continue()
phi = CellVariable(name="solution variable",
mesh=mesh,
value=0)
z = CellVariable(name="dummy",
mesh=mesh,
value=0)
valueLeft = 1
valueRight = 0
from fipy.boundaryConditions.fixedValue import FixedValue
BCs = (FixedValue(faces=mesh.getFacesRight(), value=valueRight),
FixedValue(faces=mesh.getFacesLeft(), value=valueLeft))
from fipy.terms.explicitDiffusionTerm import ExplicitDiffusionTerm
eqX = ExplicitDiffusionTerm(coeff=1)
from fipy import viewers
viewer = viewers.make(vars=(phi),
limits={'datamin': 0., 'datamax': 1.})
viewer.plot()
eqX.solve(var=phi,
boundaryConditions=BCs)
viewer.plot()
eq= ImplicitDiffusionTerm(coeff=(a,a))+(u.getOld().getOld() - 2*u.getOld() + u) / timeStepDuration ** 2 from fipy.boundaryConditions.fixedValue import FixedValue from fipy.boundaryConditions.fixedFlux import FixedFlux from fipy.boundaryConditions.nthOrderBoundaryCondition import NthOrderBoundaryCondition BCs = ( NthOrderBoundaryCondition(faces=mesh.getFacesRight(), value=0,order=2), NthOrderBoundaryCondition(faces=mesh.getFacesRight(), value=1,order=3), FixedValue(faces=mesh.getFacesLeft(), value=0), FixedFlux(faces=mesh.getFacesLeft(), value=0)) from fipy import viewers viewer = viewers.make(vars=(u)) def hit_continue(Prompt='Hit any key to continue'): raw_input(Prompt) for step in range(steps): u.updateOld() eq.solve(var=u,boundaryConditions=BCs,dt=timeStepDuration) eq= ImplicitDiffusionTerm(coeff=(a,a))+(u.getOld().getOld() - 2*u.getOld() + u) / timeStepDuration ** 2 viewer.plot() hit_continue() #getOld seems to be not working
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.meshes.grid2D import Grid2D
mesh = Grid2D(dx=cellSize, dy=cellSize, nx=xCells, ny=yCells)
narrowBandWidth = numberOfCellsInNarrowBand * cellSize
from fipy.models.levelSet.distanceFunction.distanceVariable import \
DistanceVariable
distanceVar = DistanceVariable(name='distance variable',
mesh=mesh,
value=-1,
narrowBandWidth=narrowBandWidth,
hasOld=1)
bottomHeight = cellsBelowTrench * cellSize
trenchHeight = bottomHeight + trenchDepth
trenchWidth = trenchDepth / aspectRatio
sideWidth = (trenchSpacing - trenchWidth) / 2
x, y = mesh.getCellCenters()[..., 0], mesh.getCellCenters()[..., 1]
distanceVar.setValue(1,
where=(y > trenchHeight) |
((y > bottomHeight) &
(x < xCells * cellSize - sideWidth)))
distanceVar.calcDistanceFunction(narrowBandWidth=1e10)
from fipy.models.levelSet.surfactant.surfactantVariable import \
SurfactantVariable
catalystVar = SurfactantVariable(name="catalyst variable",
value=catalystCoverage,
distanceVar=distanceVar)
from fipy.variables.cellVariable import CellVariable
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.getInterfaceVar()
exchangeCurrentDensity = currentDensity0 + tmp
import fipy.tools.numerix as numerix
expo = numerix.exp(expoConstant * overpotential)
currentDensity = expo * exchangeCurrentDensity * metalVar \
/ metalConcentration
depositionRateVariable = currentDensity * molarVolume \
/ (charge * faradaysConstant)
extensionVelocityVariable = CellVariable(name='extension velocity',
mesh=mesh,
value=depositionRateVariable)
from fipy.models.levelSet.surfactant.adsorbingSurfactantEquation \
import AdsorbingSurfactantEquation
surfactantEquation = AdsorbingSurfactantEquation(
surfactantVar=catalystVar,
distanceVar=distanceVar,
bulkVar=bulkCatalystVar,
rateConstant=rateConstant0 + rateConstant3 * overpotential**3)
from fipy.models.levelSet.advection.higherOrderAdvectionEquation \
import buildHigherOrderAdvectionEquation
advectionEquation = buildHigherOrderAdvectionEquation(
advectionCoeff=extensionVelocityVariable)
from fipy.boundaryConditions.fixedValue import FixedValue
from fipy.models.levelSet.electroChem.metalIonDiffusionEquation \
import buildMetalIonDiffusionEquation
metalEquation = buildMetalIonDiffusionEquation(
ionVar=metalVar,
distanceVar=distanceVar,
depositionRate=depositionRateVariable,
diffusionCoeff=metalDiffusion,
metalIonMolarVolume=molarVolume,
)
metalEquationBCs = FixedValue(mesh.getFacesTop(), metalConcentration)
from fipy.models.levelSet.surfactant.surfactantBulkDiffusionEquation \
import buildSurfactantBulkDiffusionEquation
bulkCatalystEquation = buildSurfactantBulkDiffusionEquation(
bulkVar=bulkCatalystVar,
distanceVar=distanceVar,
surfactantVar=catalystVar,
diffusionCoeff=catalystDiffusion,
rateConstant=rateConstant0 * siteDensity)
catalystBCs = FixedValue(mesh.getFacesTop(), catalystConcentration)
if displayViewers:
try:
from fipy.viewers.mayaviViewer.mayaviSurfactantViewer import MayaviSurfactantViewer
viewers = (MayaviSurfactantViewer(distanceVar,
catalystVar.getInterfaceVar(),
zoomFactor=1e6,
limits={
'datamax': 0.5,
'datamin': 0.0
},
smooth=1,
title='catalyst coverage'), )
except:
from fipy.viewers import make
viewers = (make(distanceVar,
limits={
'datamin': -1e-9,
'datamax': 1e-9
}), make(catalystVar.getInterfaceVar()))
else:
viewers = ()
levelSetUpdateFrequency = int(0.8 * narrowBandWidth \
/ (cellSize * cflNumber * 2))
for step in range(numberOfSteps):
if step % 5 == 0:
for viewer in viewers:
viewer.plot()
if step % levelSetUpdateFrequency == 0:
distanceVar.calcDistanceFunction()
extensionVelocityVariable.setValue(depositionRateVariable())
distanceVar.updateOld()
catalystVar.updateOld()
metalVar.updateOld()
bulkCatalystVar.updateOld()
distanceVar.extendVariable(extensionVelocityVariable)
dt = cflNumber * cellSize / numerix.max(extensionVelocityVariable)
advectionEquation.solve(distanceVar, dt=dt)
surfactantEquation.solve(catalystVar, dt=dt)
metalEquation.solve(metalVar,
dt=dt,
boundaryConditions=metalEquationBCs)
bulkCatalystEquation.solve(bulkCatalystVar,
dt=dt,
boundaryConditions=catalystBCs)
try:
import os
import examples.levelSet.electroChem
filepath = os.path.join(examples.levelSet.electroChem.__path__[0],
'test.gz')
from fipy.tools import dump
from fipy.tools import numerix
print catalystVar.allclose(numerix.array(dump.read(filepath)),
rtol=1e-4)
except:
return 0
def runGold(faradaysConstant=9.6e4,
consumptionRateConstant=2.6e+6,
molarVolume=10.21e-6,
charge=1.0,
metalDiffusion=1.7e-9,
metalConcentration=20.0,
catalystCoverage=0.15,
currentDensity0=3e-2 * 16,
currentDensity1=6.5e-1 * 16,
cellSize=0.1e-7,
trenchDepth=0.2e-6,
aspectRatio=1.47,
trenchSpacing=0.5e-6,
boundaryLayerDepth=90.0e-6,
numberOfSteps=10,
taperAngle=6.0,
displayViewers=True):
cflNumber = 0.2
numberOfCellsInNarrowBand = 20
cellsBelowTrench = 10
from fipy.tools import numerix
from fipy import TrenchMesh
mesh = TrenchMesh(cellSize = cellSize,
trenchSpacing = trenchSpacing,
trenchDepth = trenchDepth,
boundaryLayerDepth = boundaryLayerDepth,
aspectRatio = aspectRatio,
angle = numerix.pi * taperAngle / 180.,
bowWidth = 0.,
overBumpRadius = 0.,
overBumpWidth = 0.)
narrowBandWidth = numberOfCellsInNarrowBand * cellSize
from fipy.models.levelSet.distanceFunction.distanceVariable import DistanceVariable
distanceVar = DistanceVariable(
name = 'distance variable',
mesh = mesh,
value = -1,
narrowBandWidth = narrowBandWidth)
distanceVar.setValue(1, where=mesh.getElectrolyteMask())
distanceVar.calcDistanceFunction(narrowBandWidth = 1e10)
from fipy.models.levelSet.surfactant.surfactantVariable import SurfactantVariable
catalystVar = SurfactantVariable(
name = "catalyst variable",
value = catalystCoverage,
distanceVar = distanceVar)
from fipy.variables.cellVariable import CellVariable
metalVar = CellVariable(
name = 'metal variable',
mesh = mesh,
value = metalConcentration)
exchangeCurrentDensity = currentDensity0 + currentDensity1 * catalystVar.getInterfaceVar()
currentDensity = metalVar / metalConcentration * exchangeCurrentDensity
depositionRateVariable = currentDensity * molarVolume / charge / faradaysConstant
extensionVelocityVariable = CellVariable(
name = 'extension velocity',
mesh = mesh,
value = depositionRateVariable)
from fipy.models.levelSet.surfactant.adsorbingSurfactantEquation \
import AdsorbingSurfactantEquation
catalystSurfactantEquation = AdsorbingSurfactantEquation(
catalystVar,
distanceVar = distanceVar,
bulkVar = 0,
rateConstant = 0,
consumptionCoeff = consumptionRateConstant * extensionVelocityVariable)
from fipy.models.levelSet.advection.higherOrderAdvectionEquation \
import buildHigherOrderAdvectionEquation
advectionEquation = buildHigherOrderAdvectionEquation(
advectionCoeff = extensionVelocityVariable)
from fipy.boundaryConditions.fixedValue import FixedValue
from fipy.models.levelSet.electroChem.metalIonDiffusionEquation \
import buildMetalIonDiffusionEquation
metalEquation = buildMetalIonDiffusionEquation(
ionVar = metalVar,
distanceVar = distanceVar,
depositionRate = depositionRateVariable,
diffusionCoeff = metalDiffusion,
metalIonMolarVolume = molarVolume)
metalEquationBCs = FixedValue(mesh.getTopFaces(), metalConcentration)
if displayViewers:
try:
from fipy.viewers.mayaviViewer.mayaviSurfactantViewer import MayaviSurfactantViewer
viewers = (
MayaviSurfactantViewer(distanceVar, catalystVar.getInterfaceVar(), zoomFactor = 1e6, limits = { 'datamax' : 1.0, 'datamin' : 0.0 }, smooth = 1, title = 'catalyst coverage'),)
except:
class PlotVariable(CellVariable):
def __init__(self, var = None, name = ''):
CellVariable.__init__(self, mesh = mesh.getFineMesh(), name = name)
self.var = self._requires(var)
def _calcValue(self):
return numerix.array(self.var[:self.mesh.getNumberOfCells()])
from fipy.viewers import make
viewers = (
make(PlotVariable(var = distanceVar), limits = {'datamax' : 1e-9, 'datamin' : -1e-9}),
make(PlotVariable(var = catalystVar.getInterfaceVar())))
else:
viewers = ()
levelSetUpdateFrequency = int(0.7 * narrowBandWidth / cellSize / cflNumber / 2)
step = 0
while step < numberOfSteps:
if step % 10 == 0:
for viewer in viewers:
viewer.plot()
if step % levelSetUpdateFrequency == 0:
distanceVar.calcDistanceFunction(deleteIslands = True)
extensionVelocityVariable.setValue(numerix.array(depositionRateVariable))
argmax = numerix.argmax(extensionVelocityVariable)
dt = cflNumber * cellSize / extensionVelocityVariable[argmax]
distanceVar.extendVariable(extensionVelocityVariable, deleteIslands = True)
distanceVar.updateOld()
catalystVar.updateOld()
metalVar.updateOld()
advectionEquation.solve(distanceVar, dt = dt)
catalystSurfactantEquation.solve(catalystVar, dt = dt)
metalEquation.solve(metalVar, boundaryConditions = metalEquationBCs, dt = dt)
step += 1
try:
from fipy.tools import dump
import os
import examples.levelSet.electroChem
data = dump.read(os.path.join(examples.levelSet.electroChem.__path__[0], 'goldData.gz'))
n = mesh.getFineMesh().getNumberOfCells()
print numerix.allclose(catalystVar[:n], data[:n], atol=1.0)
except:
return 0
## Define boundary condition values
leftValue = 1.0
rightValue = 0
## Creation of boundary conditions
from fipy.boundaryConditions.fixedValue import FixedValue
BCs = (FixedValue(faces = mesh_example.getFacesRight(), value=rightValue),
FixedValue(faces=mesh_example.getFacesLeft(),value=leftValue))
D = 1.0 ## diffusivity (m^2/s)
## Transient diffusion equation is defined next
from fipy.terms.explicitDiffusionTerm import ExplicitDiffusionTerm
from fipy.terms.transientTerm import TransientTerm
eqX = TransientTerm() == ExplicitDiffusionTerm(coeff = D)
timeStep = 0.09*deltax**2/(2*D) ## size of time step
steps = 9000 ## number of time-steps
## create a GUI
from fipy import viewers
viewer = viewers.make(vars = phi, limits={'datamin':0.0, 'datamax':1.0})
## iterate until you get tired
for step in range(steps):
eqX.solve(var = phi, boundaryConditions = BCs, dt = timeStep) ## solving the equation
viewer.plot() ## update the GUI
steps = 1000
eq = ImplicitDiffusionTerm(coeff=(
a, a)) + (u.getOld().getOld() - 2 * u.getOld() + u) / timeStepDuration**2
from fipy.boundaryConditions.fixedValue import FixedValue
from fipy.boundaryConditions.fixedFlux import FixedFlux
from fipy.boundaryConditions.nthOrderBoundaryCondition import NthOrderBoundaryCondition
BCs = (NthOrderBoundaryCondition(faces=mesh.getFacesRight(), value=0, order=2),
NthOrderBoundaryCondition(faces=mesh.getFacesRight(), value=1, order=3),
FixedValue(faces=mesh.getFacesLeft(),
value=0), FixedFlux(faces=mesh.getFacesLeft(), value=0))
from fipy import viewers
viewer = viewers.make(vars=(u))
def hit_continue(Prompt='Hit any key to continue'):
raw_input(Prompt)
for step in range(steps):
u.updateOld()
eq.solve(var=u, boundaryConditions=BCs, dt=timeStepDuration)
eq = ImplicitDiffusionTerm(coeff=(a, a)) + (
u.getOld().getOld() - 2 * u.getOld() + u) / timeStepDuration**2
viewer.plot()
hit_continue()
#getOld seems to be not working
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.meshes.grid2D import Grid2D
mesh = Grid2D(dx = cellSize,
dy = cellSize,
nx = xCells,
ny = yCells)
narrowBandWidth = numberOfCellsInNarrowBand * cellSize
from fipy.models.levelSet.distanceFunction.distanceVariable import \
DistanceVariable
distanceVar = DistanceVariable(
name = 'distance variable',
mesh = mesh,
value = -1,
narrowBandWidth = narrowBandWidth,
hasOld = 1)
bottomHeight = cellsBelowTrench * cellSize
trenchHeight = bottomHeight + trenchDepth
trenchWidth = trenchDepth / aspectRatio
sideWidth = (trenchSpacing - trenchWidth) / 2
x, y = mesh.getCellCenters()[...,0], mesh.getCellCenters()[...,1]
distanceVar.setValue(1, where=(y > trenchHeight) | ((y > bottomHeight) & (x < xCells * cellSize - sideWidth)))
distanceVar.calcDistanceFunction(narrowBandWidth = 1e10)
from fipy.models.levelSet.surfactant.surfactantVariable import \
SurfactantVariable
catalystVar = SurfactantVariable(
name = "catalyst variable",
value = catalystCoverage,
distanceVar = distanceVar)
from fipy.variables.cellVariable import CellVariable
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.getInterfaceVar()
exchangeCurrentDensity = currentDensity0 + tmp
import fipy.tools.numerix as numerix
expo = numerix.exp(expoConstant * overpotential)
currentDensity = expo * exchangeCurrentDensity * metalVar \
/ metalConcentration
depositionRateVariable = currentDensity * molarVolume \
/ (charge * faradaysConstant)
extensionVelocityVariable = CellVariable(
name = 'extension velocity',
mesh = mesh,
value = depositionRateVariable)
from fipy.models.levelSet.surfactant.adsorbingSurfactantEquation \
import AdsorbingSurfactantEquation
surfactantEquation = AdsorbingSurfactantEquation(
surfactantVar = catalystVar,
distanceVar = distanceVar,
bulkVar = bulkCatalystVar,
rateConstant = rateConstant0 + rateConstant3 * overpotential**3)
from fipy.models.levelSet.advection.higherOrderAdvectionEquation \
import buildHigherOrderAdvectionEquation
advectionEquation = buildHigherOrderAdvectionEquation(
advectionCoeff = extensionVelocityVariable)
from fipy.boundaryConditions.fixedValue import FixedValue
from fipy.models.levelSet.electroChem.metalIonDiffusionEquation \
import buildMetalIonDiffusionEquation
metalEquation = buildMetalIonDiffusionEquation(
ionVar = metalVar,
distanceVar = distanceVar,
depositionRate = depositionRateVariable,
diffusionCoeff = metalDiffusion,
metalIonMolarVolume = molarVolume,
)
metalEquationBCs = FixedValue(mesh.getFacesTop(), metalConcentration)
from fipy.models.levelSet.surfactant.surfactantBulkDiffusionEquation \
import buildSurfactantBulkDiffusionEquation
bulkCatalystEquation = buildSurfactantBulkDiffusionEquation(
bulkVar = bulkCatalystVar,
distanceVar = distanceVar,
surfactantVar = catalystVar,
diffusionCoeff = catalystDiffusion,
rateConstant = rateConstant0 * siteDensity
)
catalystBCs = FixedValue(mesh.getFacesTop(), catalystConcentration)
if displayViewers:
try:
from fipy.viewers.mayaviViewer.mayaviSurfactantViewer import MayaviSurfactantViewer
viewers = (MayaviSurfactantViewer(distanceVar, catalystVar.getInterfaceVar(), zoomFactor = 1e6, limits = { 'datamax' : 0.5, 'datamin' : 0.0 }, smooth = 1, title = 'catalyst coverage'),)
except:
from fipy.viewers import make
viewers = (
make(distanceVar, limits = { 'datamin' :-1e-9 , 'datamax' : 1e-9 }),
make(catalystVar.getInterfaceVar()))
else:
viewers = ()
levelSetUpdateFrequency = int(0.8 * narrowBandWidth \
/ (cellSize * cflNumber * 2))
for step in range(numberOfSteps):
if step % 5 == 0:
for viewer in viewers:
viewer.plot()
if step % levelSetUpdateFrequency == 0:
distanceVar.calcDistanceFunction()
extensionVelocityVariable.setValue(depositionRateVariable())
distanceVar.updateOld()
catalystVar.updateOld()
metalVar.updateOld()
bulkCatalystVar.updateOld()
distanceVar.extendVariable(extensionVelocityVariable)
dt = cflNumber * cellSize / numerix.max(extensionVelocityVariable)
advectionEquation.solve(distanceVar, dt = dt)
surfactantEquation.solve(catalystVar, dt = dt)
metalEquation.solve(metalVar, dt = dt,
boundaryConditions = metalEquationBCs)
bulkCatalystEquation.solve(bulkCatalystVar, dt = dt,
boundaryConditions = catalystBCs)
try:
import os
import examples.levelSet.electroChem
filepath = os.path.join(examples.levelSet.electroChem.__path__[0], 'test.gz')
from fipy.tools import dump
from fipy.tools import numerix
print catalystVar.allclose(numerix.array(dump.read(filepath)), rtol = 1e-4)
except:
return 0
P2spCoeff = params['lambda2'] * (TMVar + params['zeta2T'])
P2Eq = TransientTerm() - ImplicitDiffusionTerm(params['diffusionCoeff']) - P2scCoeff + ImplicitSourceTerm(P2spCoeff)
KCscCoeff = params['alphaKstar'] * params['lambdaK'] * (KMVar / (1 + PN / params['kappaK'])).getCellVolumeAverage()
KCspCoeff = params['lambdaKstar'] / (params['kappaKstar'] + KCVar)
KCEq = TransientTerm() - KCscCoeff + ImplicitSourceTerm(KCspCoeff)
eqs = ((KMVar, KMEq), (TMVar, TMEq), (TCVar, TCEq), (P3Var, P3Eq), (P2Var, P2Eq), (KCVar, KCEq))
if __name__ == '__main__':
from fipy.viewers import make
PNView = PN / PN.getCellVolumeAverage()
PNView.setName('PN')
PNViewer = make(PNView, limits = {'datamax' : 2., 'datamin' : 0.}, title = '')
KMView = KMVar / KMVar.getCellVolumeAverage()
KMView.setName('KM')
KMViewer = make(KMView, limits = {'datamax' : 2., 'datamin' : 0.}, title = '')
TMView = TMVar / TMVar.getCellVolumeAverage()
TMView.setName('TM')
TMViewer = make(TMView, limits = {'datamax' : 2., 'datamin' : 0.}, title = '')
for i in range(100):
for var, eqn in eqs:
var.updateOld()
for var, eqn in eqs:
eqn.solve(var, dt = 1.)
