def define_uniform_comp_domain_ax(
self, no_of_nodes,
normalised_domain_thickness): # Uniform axial domain, electrodes
self.nx = int(no_of_nodes)
self.L_normalised = normalised_domain_thickness
self.dx = numerix.full((self.nx, ), (self.L_normalised / self.nx))
self.axial_mesh = Grid1D(nx=self.nx, Lx=self.L_normalised)
self.axial_mesh = Grid1D(nx=self.nx, Lx=self.L_normalised)
self.axialfaces = self.axial_mesh.faceCenters # Create a shorthand name for accessing axial faces
def create_mesh(self):
"""
Create the :mod:`fipy` mesh for the domain using :attr:`cell_size` and :attr:`total_cells`.
The arrays :attr:`depths` and :attr:`distances` are created, which provide the
coordinates and distances of the mesh cells.
"""
self.logger.info(
'Creating UniformGrid1D with {} sediment and {} DBL cells of {}'.
format(self.sediment_cells, self.DBL_cells, self.cell_size))
self.mesh = Grid1D(
dx=self.cell_size.numericValue,
nx=self.total_cells,
)
self.logger.debug('Created domain mesh: {}'.format(self.mesh))
#: An array of the scaled cell distances of the mesh
self.distances = Variable(value=self.mesh.scaledCellDistances[:-1],
unit='m',
name='distances')
Z = self.mesh.x()
Z = Z - Z[self.idx_surface]
#: An array of the cell center coordinates, with the 0 set at the sediment surface
self.depths = Variable(Z, unit='m', name='depths')
def define_non_uniform_comp_domain_ax(
self, no_of_nodes, normalised_domain_thickness
): # Non-uniform axial domain, electrodes
self.nx = int(no_of_nodes)
self.L_normalised = normalised_domain_thickness
self.dx = compute_cheb_pts(self.L_normalised, self.nx)
self.axial_mesh = Grid1D(dx=self.dx, Lx=self.L_normalised)
self.axialfaces = self.axial_mesh.faceCenters # Create a shorthand name for accessing axial faces
def solve_pde(
xmin, # domain min
xmax, # domain max
Tmax, # time max
theta=1, # dynamics drift
mu=0, # dynamics stable level
sigma=1, # dynamics noise
dx=0.01, # space discretization
dt=0.01, # time discretization
gbm=False): # state-dependent drift
mesh = Grid1D(dx=dx, nx=(xmax - xmin) / dx) + xmin
Tsteps = int(Tmax / dt) + 1
x_face = mesh.faceCenters
x_cell = mesh.cellCenters[0]
V = CellVariable(name="V", mesh=mesh, value=0.)
# PDE
if gbm:
eq = TransientTerm(
var=V) == (DiffusionTerm(coeff=float(sigma) * sigma / 2, var=V) -
UpwindConvectionTerm(
coeff=float(theta) * (x_face - float(mu)), var=V) +
V * (float(theta) - x_cell))
else:
eq = TransientTerm(
var=V) == (DiffusionTerm(coeff=float(sigma) * sigma / 2, var=V) -
UpwindConvectionTerm(coeff=float(theta) *
(x_face - float(mu)),
var=V) + V * float(theta))
# Boundary conditions
V.constrain(1., mesh.facesRight)
V.faceGrad.constrain([0.], mesh.facesLeft)
# Solve by stepping in time
sol = np.zeros((Tsteps, mesh.nx))
for step in range(Tsteps):
eq.solve(var=V, dt=dt)
sol[step] = V.value
X = mesh.cellCenters.value[0]
T = dt * np.arange(Tsteps)
return T, X, sol
((x / l)**(k1 - 1)) * (1 - (x / l))**(p1 - 1)) / 7.3572
def y02(x):
""""Initial negative ion charge density"""
return nini * ((special.gamma(k2 + p2)) /
(special.gamma(k2) * special.gamma(p2)) *
((x / l)**(k2 - 1)) * (1 - (x / l))**(p2 - 1)) / 7.3572
def y03(x):
"""Initial potential"""
return a1 * np.sin(b1 * x + c1) + a2 * np.sin(b2 * x + c2)
mesh = Grid1D(dx=dx, nx=nx) #Establish mesh in how many dimensions necessary
##############################################################################
#################''' SETUP CELLVARIABLES AND EQUATIONS '''####################
##############################################################################
#CellVariable - defines the variables that you want to solve for:
'''Initial value can be established when defining the variable, or later using 'var.value ='
Value defaults to zero if not defined'''
Pion = CellVariable(mesh=mesh,
name='Positive ion Charge Density',
value=y01(x))
Nion = CellVariable(mesh=mesh,
name='Negative ion Charge Density',
from fipy import CellVariable, Grid1D, DiffusionTerm, Viewer, ImplicitSourceTerm from fipy.tools import numerix from fipy.solvers import * from parameters import * # ----------------- Solver -------------------------------- mySolver = LinearGMRESSolver(iterations=1000, tolerance=1.0e-6) # ----------------- Mesh Generation ----------------------- nx = 100 L = 5.0 mesh = Grid1D(nx=nx, Lx=L) x = mesh.cellCenters[0] # Cell position # ----------------- Variable Declarations ----------------- density = CellVariable(name=r"$n$", mesh=mesh, hasOld=True) temperature = CellVariable(name=r"$T$", mesh=mesh, hasOld=True) Z = CellVariable(name=r"$Z$", mesh=mesh, hasOld=True) Diffusivity = CellVariable(name=r"$D$", mesh=mesh, hasOld=True) # ----------- Initial Conditions of Z --------------------- Z0L = 1.0 # L--mode Z0H = Z_S * (1.0 - numerix.tanh((L * x - L) / 2.0)) # H--mode Z.setValue(Z0H) # ----------------- Diffusivities ------------------------- # Itohs'/Zohm's model
from builtins import range
__docformat__ = 'restructuredtext'
from fipy import input
from fipy import CellVariable, FaceVariable, Grid1D, TransientTerm, CentralDifferenceConvectionTerm
from fipy.tools import numerix
L = 2.
X0 = -1.
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__':
# parameter values diffusion = 101. rateConstant = .5 L = 1. siteDensity = 1. cinf = 1. nx = 100 totalTimeSteps = 100 dt = 0.001 ## build the mesh dx = L / (nx - 1.5) mesh = Grid1D(nx=nx, dx=dx, communicator=serialComm) ## build the distance variable value = mesh.cellCenters[0] - 1.499 * dx ##distanceVar = DistanceVariable(mesh = mesh, value = dx * (arange(nx) - 0.999)) distanceVar = DistanceVariable(mesh=mesh, value=value, hasOld=1) ## Build the bulk diffusion equation bulkVar = CellVariable(mesh=mesh, value=cinf) surfactantVar = SurfactantVariable(distanceVar=distanceVar) from .surfactantBulkDiffusionEquation import buildSurfactantBulkDiffusionEquation bulkEqn = buildSurfactantBulkDiffusionEquation(bulkVar,
from mpi4py import MPI
m4comm = MPI.COMM_WORLD
mpi4py_info = "mpi4py: processor %d of %d" % (m4comm.Get_rank(),
m4comm.Get_size())
from PyTrilinos import Epetra
epcomm = Epetra.PyComm()
trilinos_info = "PyTrilinos: processor %d of %d" % (epcomm.MyPID(),
epcomm.NumProc())
from fipy import parallelComm, Grid1D
mesh = Grid1D(nx=10)
fipy_info = "FiPy: %d cells on processor %d of %d" % (
mesh.numberOfCells, parallelComm.procID, parallelComm.Nproc)
print " :: ".join((mpi4py_info, trilinos_info, fipy_info))
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 createPhreeqcInstance(filename, kinetics):
nx = 100
ny = 1
nz = 1
dx = 1.5
mesh = Grid1D(nx=nx, dx=dx)
v_cell = mesh.cellVolumes
nxyz = nx * ny * nz # number of cells
nthreads = 1 # number of threads
phreeqc_rm = PhreeqcRM(nxyz, nthreads)
# create a phreeqc instance
# Set properties
status = phreeqc_rm.RM_SetErrorHandlerMode(1)
status = phreeqc_rm.RM_SetComponentH2O(0)
status = phreeqc_rm.RM_SetRebalanceFraction(0.5)
status = phreeqc_rm.RM_SetRebalanceByCell(1)
status = phreeqc_rm.RM_UseSolutionDensityVolume(0)
status = phreeqc_rm.RM_SetPartitionUZSolids(0)
status = phreeqc_rm.RM_SetFilePrefix("Advect_cpp")
status = phreeqc_rm.RM_OpenFiles()
status = phreeqc_rm.RM_SetUnitsSolution(2) # 1, mg/L 2, mol/L 3, kg/kgs
status = phreeqc_rm.RM_SetUnitsPPassemblage(
1) # 0, mol/L cell 1, mol/L water 2 mol/L rock
status = phreeqc_rm.RM_SetUnitsExchange(
1) # 0, mol/L cell 1, mol/L water 2 mol/L rock
status = phreeqc_rm.RM_SetUnitsSurface(
1) # 0, mol/L cell 1, mol/L water 2 mol/L rock
status = phreeqc_rm.RM_SetUnitsGasPhase(
1) # 0, mol/L cell 1, mol/L water 2 mol/L rock
status = phreeqc_rm.RM_SetUnitsSSassemblage(
1) # 0, mol/L cell 1, mol/L water 2 mol/L rock
status = phreeqc_rm.RM_SetUnitsKinetics(
1) # 0, mol/L cell 1, mol/L water 2 mol/L rock
# Set conversion from seconds to days
# I prefer to work with seconds, so I keep it to 1.0
status = phreeqc_rm.RM_SetTimeConversion(1.0 / 86400)
# Set representative volume
rv = np.ones_like(v_cell, dtype='float64') # volume is in liter
status = phreeqc_rm.RM_SetRepresentativeVolume(rv)
# Set initial porosity
por = np.ones(nxyz, dtype='float64') * 1
status = phreeqc_rm.RM_SetPorosity(por)
# Set initial saturation
sat = np.ones(nxyz, dtype='float64')
status = phreeqc_rm.RM_SetSaturation(sat)
# Set cells to print chemistry when print chemistry is turned on
print_chemistry_mask = np.zeros(nxyz, dtype='int')
print_chemistry_mask[:np.int(nxyz / 2)] = 1
status = phreeqc_rm.RM_SetPrintChemistryMask(print_chemistry_mask)
# Partitioning of uz solids
#status = phreeqc_rm.RM_SetPartitionUZSolids(0)
# Demonstation of mapping, no symmetry, only one row of cells
grid2chem = np.arange(nxyz, dtype='int32')
status = phreeqc_rm.RM_CreateMapping(grid2chem)
if (status < 0):
status = phreeqc_rm.RM_DecodeError(status)
nchem = phreeqc_rm.RM_GetChemistryCellCount()
status = phreeqc_rm.RM_SetPrintChemistryOn(
0, 1, 0) # workers, initial_phreeqc, utility
# Set printing of chemistry file
status = phreeqc_rm.RM_LoadDatabase("minteq.v4.dat")
# Demonstration of error handling if ErrorHandlerMode is 0
# commented out for now (AAE)
# if (status != Iphreeqc_rm.RM_OK)
# {
# l = phreeqc_rm.RM_GetErrorStringLength()
# errstr = (char *) malloc((size_t) (l * sizeof(char) + 1))
# phreeqc_rm.RM_GetErrorString(errstr, l+1)
# fprintf(stderr,"Beginning of error string:\n")
# fprintf(stderr,"%s", errstr)
# fprintf(stderr,"End of error string.\n")
# free(errstr)
# errstr = NULL
# phreeqc_rm.RM_Destroy()
# exit(1)
# }
# Run file to define solutions and reactants for initial conditions, selected output
# There are three types of IPhreeqc instances in Phreeqcphreeqc_rm.RM
# Argument 1 refers to the workers for doing reaction calculations for transport
# Argument 2 refers to the InitialPhreeqc instance for accumulating initial and boundary conditions
# Argument 3 refers to the Utility instance
status = phreeqc_rm.RM_RunFile(1, 1, 1, filename)
# Clear contents of workers and utility
Str = "DELETE -all"
status = phreeqc_rm.RM_RunString(1, 0, 1,
Str) # workers, initial_phreeqc, utility
# Determine number of components to transport
ncomps = phreeqc_rm.RM_FindComponents()
gfw = np.zeros(ncomps, dtype='float64')
status = phreeqc_rm.RM_GetGfw(gfw)
#for i in range(ncomps):
# I consider the maximum number of characters for components' name to be 10
components = np.zeros(ncomps, dtype='U10')
for i in range(ncomps):
status = phreeqc_rm.RM_GetComponent(i, components, 10)
# print(components[i].encode(), "\t", gfw[i], "\n")
ic1 = -1 * np.ones(nxyz * 7, dtype=np.int32)
ic2 = -1 * np.ones(nxyz * 7, dtype=np.int32)
f1 = np.ones(nxyz * 7, dtype=np.float64)
for i in np.arange(nxyz):
ic1[i] = 1 # Solution 1
ic1[i + nxyz] = -1 # Equilibrium phases none
ic1[i + 2 * nxyz] = -1 # Exchpdange 1
ic1[i + 3 * nxyz] = -1 # Surface none
ic1[i + 4 * nxyz] = -1 # Gas phase none
ic1[i + 5 * nxyz] = -1 # Solid solutions none
ic1[i + 6 * nxyz] = kinetics # Kinetics none
status = phreeqc_rm.RM_InitialPhreeqc2Module(ic1, ic2, f1)
t = 0.0 # changed time to time1 to avoid conflicts with julia time function
time_step = 0.0
c = np.zeros(ncomps * nxyz, dtype=np.float64)
status = phreeqc_rm.RM_SetTime(t)
status = phreeqc_rm.RM_SetTimeStep(time_step)
status = phreeqc_rm.RM_SetSpeciesSaveOn(1)
status = phreeqc_rm.RM_RunCells()
status = phreeqc_rm.RM_GetConcentrations(c)
nbound = 1
bc1 = np.zeros(nbound, dtype='int32')
bc2 = -1 * np.ones(nbound, dtype='int32')
bc_f1 = np.ones(nbound, dtype='float64')
bc_conc = np.zeros(ncomps * nbound, dtype='float64')
status = phreeqc_rm.RM_InitialPhreeqc2Concentrations(
bc_conc, nbound, bc1, bc2, bc_f1)
density = np.ones(nxyz, dtype=np.float64)
volume = np.zeros(nxyz, dtype=np.float64)
pressure = 2 * np.ones(nxyz, dtype=np.float64)
temperature = 20 * np.ones(nxyz, dtype=np.float64)
sat_calc = np.zeros(nxyz, dtype=np.float64)
status = phreeqc_rm.RM_SetDensity(density)
status = phreeqc_rm.RM_SetPressure(pressure)
status = phreeqc_rm.RM_SetTemperature(temperature)
return bc_conc, mesh, ncomps, components, c, nxyz, phreeqc_rm
""" This file generates the 1D mesh and the 4 cell state variables needed for the model (including Diffusivity). """ from fipy import Grid1D, CellVariable from fipy.tools import numerix, dump from parameters import * # ----------------- Mesh Generation ----------------------- mesh = Grid1D(nx=config.nx, Lx=L) x = mesh.cellCenters[0] # Cell position X = mesh.faceCenters[0] # Face position, if needed # -------------- State Variable Declarations -------------- density = CellVariable(name=r"$n$", mesh=mesh, hasOld=True) temperature = CellVariable(name=r"$T$", mesh=mesh, hasOld=True) U = CellVariable(name=r"$U$", mesh=mesh, hasOld=True) Z = CellVariable(name=r"$Z$", mesh=mesh, hasOld=True) Diffusivity = CellVariable(name=r"$D$", mesh=mesh, hasOld=True) U.setValue(density * temperature / (gamma - 1.0)) # -------------- Other Variable Declarations -------------- # Thermal velocities (most probable)
from fipy import Grid1D, CellVariable, TransientTerm, DiffusionTerm, Viewer m = Grid1D(nx=100, Lx=1.) v0 = CellVariable(mesh=m, hasOld=True, value=0.5) v1 = CellVariable(mesh=m, hasOld=True, value=0.5) v0.constrain(0, m.facesLeft) v0.constrain(1, m.facesRight) v1.constrain(1, m.facesLeft) v1.constrain(0, m.facesRight) eq0 = TransientTerm() == DiffusionTerm(coeff=0.01) - v1.faceGrad.divergence eq1 = TransientTerm() == v0.faceGrad.divergence + DiffusionTerm(coeff=0.01) vi = Viewer((v0, v1)) for t in range(100): v0.updateOld() v1.updateOld() res0 = res1 = 1e100 while max(res0, res1) > 0.1: res0 = eq0.sweep(var=v0, dt=1e-5) res1 = eq1.sweep(var=v1, dt=1e-5) if t % 10 == 0: vi.plot() # eqn0 = TransientTerm(var=v0) == DiffusionTerm(0.01, var=v0) - DiffusionTerm(1, var=v1) # eqn1 = TransientTerm(var=v1) == DiffusionTerm(1, var=v0) + DiffusionTerm(0.01, var=v1)
def __init__(self, dx):
self.mesh = Grid1D(dx=dx)
def __init__(self, nx, dx):
assert np.array(dx).shape == ()
self.mesh = Grid1D(nx=nx, dx=dx)
>>> print KCVar.allclose(params['KC'], atol = accuracy)
1
"""
from examples.chemotaxis.parameters import parameters
from fipy import CellVariable, Grid1D, TransientTerm, DiffusionTerm, ImplicitSourceTerm, Viewer
params = parameters['case 2']
nx = 50
dx = 1.
L = nx * dx
mesh = Grid1D(nx=nx, dx=dx)
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'])
__docformat__ = 'restructuredtext'
from fipy import CellVariable, Grid1D, PeriodicGrid1D, TransientTerm, VanLeerConvectionTerm, DefaultAsymmetricSolver, Viewer
from fipy.tools import numerix
L = 20.
nx = 40
dx = L / nx
cfl = 0.5
velocity = 1.0
dt = cfl * dx / velocity
steps = int(L / 4. / dt / velocity)
mesh = Grid1D(dx=dx, nx=nx)
periodicMesh = PeriodicGrid1D(dx=dx, nx=nx // 2)
startingArray = numerix.zeros(nx, 'd')
startingArray[2 * nx // 10:3 * nx // 10] = 1.
var1 = CellVariable(name="non-periodic", mesh=mesh, value=startingArray)
var2 = CellVariable(name="periodic",
mesh=periodicMesh,
value=startingArray[:nx // 2])
eq1 = TransientTerm() - VanLeerConvectionTerm(coeff=(-velocity, ))
eq2 = TransientTerm() - VanLeerConvectionTerm(coeff=(-velocity, ))
nx = 100
dx = L/nx
timeStep = dx/10.0
steps = 150
phim = 0.10 # mobile zone porosity
phiim = 0.05 # immobile zone porosity
beta = 0.05 # mobile/immobile domain transfer rate
D = 1.0E-1 # mobile domain diffusion coeff
Rm = 1.0 # mobile domain retardation coefficient
Rim = 1.0 # immobile domain retardation coefficient
betaT = phiim*Rim/(phim*Rm)
DR = D/Rm
m = Grid1D(dx=dx, nx=nx)
c0 = np.zeros(nx, 'd')
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)
