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].
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:
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 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
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.
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.
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.
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:
will correspond to, e.g.:
Paths will always be rendered using POSIX conventions (path elements separated by “/”). Any references of the form:
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|[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.|