Overview

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 drug eluting stents [Saylor:2011p2794], reactive wetting [PhysRevE.82.051601], photovoltaics [Hangarter:2011p2795] and a level set treatment of the electrodeposition process [NIST:damascene:2001].

Even if you don’t read manuals...

...please read Installation, Using FiPy and Frequently Asked Questions, as well as examples.diffusion.mesh1D.

What’s new in version 3.0.1-dev139-ge5d2233?

The bump in major version number reflects more on the substantial increase in capabilities and ease of use than it does on a break in compatibility with FiPy 2.x. Few, if any, changes to your existing scripts should be necessary.

The significant changes since version 2.1 are:

• Coupled and Vector Equations are now supported.
• A more robust mechanism for specifying Boundary Conditions is now used.
• Most Meshes can be partitioned by Meshing with Gmsh.
• PyAMG and SciPy have been added to the Solvers.
• FiPy is capable of Running under Python 3.
• “getter” and “setter” methods have been pervasively changed to Python properties.
• The test suite now runs much faster.
• Tests can now be run on a full install using fipy.test().
• The functions of the numerix module are no longer included in the fipy namespace. See examples.updating.update2_0to3_0 for details.
• Equations containing a TransientTerm, must specify the timestep by passing a dt= argument when calling solve() or sweep().

Tickets fixed in this release:

45  Navier Stokes
85  CellVariable hasOld() should set self.old
101 Grids should take Lx, Ly, Lz arguments
145 tests should be run with fipy.tests()
177 remove ones and zeros from numerix.py
178 Default time steps should be infinite
291 term multiplication changes result
296 FAQ gives bad guidance for anisotropic diffusion
297 Use physical velocity in the manual/FAQ
298 mesh manipulation of periodic meshes leads to errors
299 Give helpfull error on - or / of meshes
301 wrong cell to cell normal in periodic meshes
302 gnuplot1d gives error on plot of facevariable
309 pypi is failing
312 Fresh FiPy gives ""ImportError: No viewers found"""
314 Absence of enthought.tvtk causes test failures
319 mesh in FiPy name space
324 --pysparse configuration should never attempt MPI imports
327 factoryMeshes.py not up to date with respect to keyword arguments
331 changed constraints don't propagate
332 anisotropic diffusion and constraints don't mix
333 `--Trilinos --no-pysparse` uses PySparse?!?
336 Profile and merge reconstrain branch
339 close out reconstrain branch
341 Fix fipy.terms._BinaryTerm test failure in parallel
343 diffusionTerm(var=var1).solver(var=var0) should fail sensibly
346 TeX is wrong in examples.phase.quaternary
348 Include Benny's improved interpolation patch
354 GmshExport is not tested and does not work
355 Introduce mesh.x as shorthand for mesh.cellCenters[0] etc
356 GmshImport should support all element types
357 GmshImport should read element colors
363 Reduce the run times for chemotaxis tests
366 tests take *too* long!!!
369 Make DiffusionTermNoCorrection the default
370 Epetra Norm2 failure in parallel
373 remove deprecated `steps=` from Solver
376 remove deprecated `diffusionTerm=` argument to ConvectionTerm
377 remove deprecated `NthOrderDiffusionTerm`
380 remove deprecated Variable.transpose()
381 remove deprecated viewers.make()
382 get running in Py3k
384 gmsh importer and gmsh tests don't clean up after themselves
385 `diffusionTerm._test()` requires PySparse
390 Improve test reporting to avoid inconsequential buildbot failures
391 efficiency_test chokes on liquidVapor2D.py
393 two `--scipy` failures
395 `--pysparse --inline` failures
417 Memory consumption growth with repeated meshing, especially with Gmsh
418 Viewers not working when plotting meshes with zero cells in parallel
419 examples/cahnHilliard/mesh2D.py broken with --trilinos
420 Epetra.PyComm() broken on Debian
421 cellVariable.min() broken in parallel
426 Add in parallel buildbot testing on more than 2 processors
427 Slow PyAMG solutions
434 Gmsh I/O
438 changes to gmshImport.py caused --inline problems
439 gmshImport tests fail on Windows due to shared file
441 Explicit convetion terms should fail when the equation has no TransientTerm (dt=None)
445 getFaceCenters() should return a FaceVariable
446 constraining values with ImplictSourceTerm not documented?
448 Gmsh2D does not respect background mesh
452 Gmsh background mesh doesn't work in parallel
453 faceValue as FaceCenters gives inline failures
454 Py3k and Windows test failures

Warning

FiPy 3 brought unavoidable syntax changes from FiPy 2. Please see examples.updating.update2_0to3_0 for guidance on the changes that you will need to make to your FiPy 2.x scripts.

Download and Installation

Please refer to Installation for details on download and installation. FiPy can be redistributed and/or modified freely, provided that any derivative works bear some notice that they are derived from it, and any modified versions bear some notice that they have been modified.

Support

You can communicate with the FiPy developers and with other users via our mailing list and we welcome you to use the tracking system for bugs, support requests, feature requests and patch submissions <http://matforge.org/fipy/report>. We welcome collaborative efforts on this project.

FiPy is a member of MatForge, a project of the Materials Digital Library Pathway. This National Science Foundation funded service provides management of our public source code repository, our bug tracking system, and a “wiki” space for public contributions of code snippets, discussions, and tutorials.

• Mailing List
  • List Archive

Conventions and Notation

FiPy is driven by Python script files than you can view or modify in any text editor. FiPy sessions are invoked from a command-line shell, such as tcsh or bash.

Throughout, text to be typed at the keyboard will appear like this. Commands to be issued from an interactive shell will appear:

$ like this

where you would enter the text (“like this”) following the shell prompt, denoted by “$”.

Text blocks of the form:

>>> a = 3 * 4
>>> a
12
>>> if a == 12:
...     print "a is twelve"
...
a is twelve

are intended to indicate an interactive session in the Python interpreter. We will refer to these as “interactive sessions” or as “doctest blocks”. The text “>>>” at the beginning of a line denotes the primary prompt, calling for input of a Python command. The text “...” denotes the secondary prompt, which calls for input that continues from the line above, when required by Python syntax. All remaining lines, which begin at the left margin, denote output from the Python interpreter. In all cases, the prompt is supplied by the Python interpreter and should not be typed by you.

Warning

Python is sensitive to indentation and care should be taken to enter text exactly as it appears in the examples.

When references are made to file system paths, it is assumed that the current working directory is the FiPy distribution directory, refered to as the “base directory”, such that:

examples/diffusion/steadyState/mesh1D.py

will correspond to, e.g.:

/some/where/FiPy-X.Y/examples/diffusion/steadyState/mesh1D.py

Paths will always be rendered using POSIX conventions (path elements separated by “/”). Any references of the form:

examples.diffusion.steadyState.mesh1D

are in the Python module notation and correspond to the equivalent POSIX path given above.

We may at times use a

Note

to indicate something that may be of interest

or a

Warning

to indicate something that could cause serious problems.

[BoettingerReview:2002]

Boettinger, W J, et al. 2002. Phase-field simulation of solidification. Annual Review of Materials Research 32, 163-194.

[ProGit]

Chacon, Scott. (2009) Pro Git. : Apress.

[ChenReview:2002]

Chen, L Q. 2002. Phase-field mdoels for microstructure evolution. Annual Review of Materials Research 32, 113-140.

[Hangarter:2011p2795]

Hangarter, C M, et al. 2011. Three dimensionally structured interdigitated back contact thin film heterojunction solar cells. Journal of Applied Physics 109, 073514.

[NIST:damascene:2001]

Josell, D, et al. 2001. Superconformal Electrodeposition in Submicron Features. prl 87, 016102.

[McFaddenReview:2002]

McFadden, G B. 2002. Phase-field models of solidification. Contemporary Mathematics 306, 107-145.

[Saylor:2011p2794]

Saylor, David M, et al. 2011. Predicting microstructure development during casting of drug-eluting coatings. Acta Biomater 7, 604–613.

[InstallingPythonModules]

Ward, Greg. . Installing Python Modules.

[PhysRevE.82.051601]

Wheeler, Daniel, James A Warren, and William J Boettinger. 2010. Modeling the early stages of reactive wetting. Phys. Rev. E 82, 051601.