Questions tagged [fipy]

FiPy: A Finite Volume PDE Solver Using Python. FiPy is an object oriented, partial differential equation (PDE) solver, written in Python, based on a standard finite volume (FV) approach.

FiPy: A Finite Volume PDE Solver Using Python. FiPy is an object oriented, partial differential equation (PDE) solver, written in Python, based on a standard finite volume (FV) approach.

The framework has been developed in the Materials Science and Engineering Division (MSED) and Center for Theoretical and Computational Materials Science (CTCMS), in the Material Measurement Laboratory (MML) at the National Institute of Standards and Technology (NIST).

The solution of coupled sets of PDEs is ubiquitous to the numerical simulation of science problems. Numerous PDE solvers exist, using a variety of languages and numerical approaches. Many are proprietary, expensive and difficult to customize. As a result, scientists spend considerable resources repeatedly developing limited tools for specific problems.

Our approach, combining the FV method and Python, provides a tool that is extensible, powerful and freely available. A significant advantage to Python is the existing suite of tools for array calculations, sparse matrices and data rendering.

The FiPy framework includes terms for transient diffusion, convection and standard sources, enabling the solution of arbitrary combinations of coupled elliptic, hyperbolic and parabolic PDEs.

Currently implemented models include phase field [BoettingerReview:2002] [ChenReview:2002] [McFaddenReview:2002] treatments of polycrystalline, dendritic, and electrochemical phase transformations as well as a level set treatment of the electrodeposition process [NIST:damascene:2001].

Source:http://www.ctcms.nist.gov/fipy/index.html

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How to combine an ODE system with a FEM system

I have a dynamic model set up as a (stiff) system of ODEs. I currently solve this with CVODE (from the SUNDIALS package in the Assimulo python package) and all is good. I now want to add a new 3D heat sink (with temperature-dependent thermal…
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Problem while solving a minimal 1D Poisson-Nernst-Planck equation

I am trying to solve the Poisson-Nernst-Planck equation in Python with the library FiPy. It is basically a set of equations that describes - in my example - the separation of two ion concentrations in a solution with a potential gradient. Like…
Nadav
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Plotting FiPy equation on a map

I would like to model the biodiffusion of stork through migration. I have an equation that gives me that kind of results, and I would like to plot it on a map to represent the movements. My code equation : D = Variable(value=(0)) ux =…
Jouline
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Space dependent diffusion in fipy

I'm using fipy to model the linearized Poisson-Boltzmann equation, which is essentially I'll assume I can model f(x) as a boundary condition. If epsilon(x) is a constant, fipy can handle this: phi = CellVariable(mesh) dielectric_solvent =…
Hooked
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How to extract a plane from a 3D variable in FiPy (3D to 2D)

I have a variable on a 3D mesh and I am trying to cut a plan. I am surprised this question hasn't been asked before, it looks an easy and common problem but I haven't found any good way. I would appreciate any advice. Let's say that I have a…
user4745703
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Solving complex PDEs in Python with FiPY

I'm attempting to solve a complex PDE with FiPy. It would appear that FiPY does not support complex arguments and the general advice seems to be to split the PDE, solve separately and then recombine. Is this still the case? Secondly, I can't see any…
Ashiataka
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how to Install Fipy on Python 3.3

I would like to install Fipy on Python3.3 (Windows 7 or Linux/ubuntu-mint), is possible? I need to use Fipy for improving my python3.3 coding. Do I have to translate that in python 2.7 ? Please does anyone know? any suggestion?
user1640255
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Fipy error:’’The Factor is exactly singular’’, when applying Neumann boundary conditions

We’re trying to solve a one-dimensional Coupled Continuity-Poisson problem in Fipy. When applying Dirichlet’s conditions, it gives the correct results, but when we change the boundaries conditions to Neumann’s which is closer to our problem, it…
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Solving PDE on 1D cylindrical coordinates with FiPy

Let me start by saying that I have found similar problems to mine on the NARKIVE FiPy mailing list archive but since the equations won't load, they are not very useful. For example Convection-diffusion problem on a 1D cylindrical grid, or on another…
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fipy: 2D Laplace equation: boundary conditions not taken

from fipy import CellVariable, Grid2D, DiffusionTerm nx = 20 # grid size on coordinate axes dx = 1 # grid spacing ny = nx; dy = dx; L = dx*nx mesh = Grid2D(dx=dx, dy=dy, nx=nx, ny=ny) phi = CellVariable(name = "phi", mesh = mesh,…
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Examples for using fipy.steppers.pidStepper

I'm using FiPy to simulate a moderately large system of coupled PDEs (11 equations) that calculate the time-dependent evolution of a biochemical advection-diffusion-reaction network. Currently I'm using a fixed time step, and it works fine. However,…
jmrohwer
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Fixed flux boundary conditions in FiPy

I have a follow-up question for this thread Coupled non-linear equations in FyPi. I managed to set up the system and get the reasonable results when using the Neumann boundary conditions for all variables (i.e. keeping the constant concentrations of…
josefT
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Non-linear HJB PDE using Fipy, PDE translation

I'm trying to solve a non-linear PDE HJB equation using FiPy, but i have some difficulties translating the PDE into the proper FiPy syntax: I tried something like : eqX = TransientTerm() == -DiffusionTerm(coeff=1) + (phi.faceGrad *…
jessi_123
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Modelling a chemical engineering diffusion problem in 1D with FiPy

I want to simulate an adsorbent bed for a chemical reactor by solving a set of partial differential equations. I want to reduce eq_1 and eq_2 to a set of ordinary differential equations via finite volume techniques for spatial terms. Ct , DL and eb…
GOKAY AVCI
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How to write equation terms with independent variable in FiPy?

I am looking to solve a diffusion equation using FiPy and have read some of their documentation, but can't seem to find anything that relates to writing a diffusion term that includes additional terms that are functions of the independent variable…
tooty44
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