examples.updating.update1_0to2_0

How to update scripts from version 1.0 to 2.0.

FiPy 2.0 introduces several syntax changes from FiPy 1.0. We appreciate that this is very inconvenient for our users, but we hope you’ll agree that the new syntax is easier to read and easier to use. We assure you that this is not something we do casually; it has been over three years since our last incompatible change (when FiPy 1.0 superceded FiPy 0.1).

All examples included with version 2.0 have been updated to use the new syntax, but any scripts you have written for FiPy 1.0 will need to be updated. A complete listing of the changes needed to take the FiPy examples scripts from version 1.0 to version 2.0 can be found with:

$ git diff version-1_2 version-2_0 examples/

but we summarize the necessary changes here. If these tips are not sufficient to make your scripts compatible with FiPy 2.0, please don’t hesitate to ask for help on the mailing list.

The following items must be changed in your scripts

  • The dimension axis of a Variable is now first, not last

    >>> x = mesh.getCellCenters()[0]
    

    instead of

    >>> x = mesh.getCellCenters()[..., 0]
    

    This seemingly arbitrary change simplifies a great many things in FiPy, but the one most noticeable to the user is that you can now write

    >>> x, y = mesh.getCellCenters()
    

    instead of

    >>> x = mesh.getCellCenters()[..., 0]
    >>> y = mesh.getCellCenters()[..., 1]
    

    Unfortunately, we cannot reliably automate this conversion, but we find that searching for “...,” and “:,” finds almost everything. Please don’t blindly “search & replace all” as that is almost bound to create more problems than it’s worth.

    Note

    Any vector constants must be reoriented. For instance, in order to offset a Mesh, you must write

    >>> mesh = Grid2D(...) + ((deltax,), (deltay,))
    

    or

    >>> mesh = Grid2D(...) + [[deltax], [deltay]]
    

    instead of

    >>> mesh = Grid2D(...) + (deltax, deltay)
    
  • VectorCellVariable and VectorFaceVariable no longer exist. CellVariable and and FaceVariable now both inherit from MeshVariable, which can have arbitrary rank. A field of scalars (default) will have rank=0, a field of vectors will have rank=1, etc. You should write

    >>> vectorField = CellVariable(mesh=mesh, rank=1)
    

    instead of

    >>> vectorField = VectorCellVariable(mesh=mesh)
    

    Note

    Because vector fields are properly supported, use vector operations to manipulate them, such as

    >>> phase.getFaceGrad().dot((( 0, 1),
    ...                          (-1, 0)))
    

    instead of the hackish

    >>> phase.getFaceGrad()._take((1, 0), axis=1) * (-1, 1)
    
  • For internal reasons, FiPy now supports CellVariable and FaceVariable objects that contain integers, but it is not meaningful to solve a PDE for an integer field (FiPy should issue a warning if you try). As a result, when given, initial values must be specified as floating-point values:

    >>> var = CellVariable(mesh=mesh, value=1.)
    

    where they used to be quietly accepted as integers

    >>> var = CellVariable(mesh=mesh, value=1)
    

    If the value argument is not supplied, the CellVariable will contain floats, as before.

  • The faces argument to BoundaryCondition now takes a mask, instead of a list of Face IDs. Now you write

    >>> X, Y = mesh.getFaceCenters()
    >>> FixedValue(faces=mesh.getExteriorFaces() & (X**2 < 1e-6), value=...)
    

    instead of

    >>> exteriorFaces = mesh.getExteriorFaces()
    >>> X = exteriorFaces.getCenters()[..., 0]
    >>> FixedValue(faces=exteriorFaces.where(X**2 < 1e-6), value=...)
    

    With the old syntax, a different call to getCenters() had to be made for each set of Face objects. It was also extremely difficult to specify boundary conditions that depended both on position in space and on the current values of any other Variable.

    >>> FixedValue(faces=(mesh.getExteriorFaces()
    ...                   & (((X**2 < 1e-6)
    ...                       & (Y > 3.))
    ...                      | (phi.getArithmeticFaceValue()
    ...                         < sin(gamma.getArithmeticFaceValue())))), value=...)
    

    although it probably could have been done with a rather convoluted (and slow!) filter function passed to where. There no longer are any filter methods used in FiPy. You now would write

    >>> x, y = mesh.cellCenters
    >>> initialArray[(x < dx) | (x > (Lx - dx)) | (y < dy) | (y > (Ly - dy))] = 1.
    

    instead of the much slower

    >>> def cellFilter(cell):
    ...     return ((cell.center[0] < dx)
    ...             or (cell.center[0] > (Lx - dx))
    ...             or (cell.center[1] < dy)
    ...             or (cell.center[1] > (Ly - dy)))
    
    >>> positiveCells = mesh.getCells(filter=cellFilter)
    >>> for cell in positiveCells:
    ...     initialArray[cell.ID] = 1.
    

    Although they still exist, we find very little cause to ever call getCells() or fipy.meshes.mesh.Mesh.getFaces().

  • Some modules, such as fipy.solvers, have been significantly rearranged. For example, you need to change

    >>> from fipy.solvers.linearPCGSolver import LinearPCGSolver
    

    to either

    >>> from fipy import LinearPCGSolver
    

    or

    >>> from fipy.solvers.pysparse.linearPCGSolver import LinearPCGSolver
    
  • The numerix.max() and numerix.min() functions no longer exist. Either call max() and min() or the max() and min() methods of a Variable.

  • The Numeric module has not been supported for a long time. Be sure to use

    >>> from fipy import numerix
    

    instead of

    >>> import Numeric
    

The remaining changes are not required, but they make scripts easier to read and we recommend them. FiPy may issue a DeprecationWarning for some cases, to indicate that we may not maintain the old syntax indefinitely.

  • All of the most commonly used classes and functions in FiPy are directly accessible in the fipy namespace. For brevity, our examples now start with

    >>> from fipy import *
    

    instead of the explicit

    >>> from fipy.meshes.grid1D import Grid1D
    >>> from fipy.terms.powerLawConvectionTerm import PowerLawConvectionTerm
    >>> from fipy.variables.cellVariable import CellVariable
    

    imports that we used to use. Most of the explicit imports should continue to work, so you do not need to change them if you don’t wish to, but we find our own scripts much easier to read without them.

    All of the numerix module is now imported into the fipy namespace, so you can call numerix functions a number of different ways, including:

    >>> from fipy import *
    >>> y = exp(x)
    

    or

    >>> from fipy import numerix
    >>> y = numerix.exp(x)
    

    or

    >>> from fipy.tools.numerix import exp
    >>> y = exp(x)
    

    We generally use the first, but you may see us use the others, and should feel free to use whichever form you find most comfortable.

    Note

    Internally, FiPy uses explicit imports, as is considered best Python practice, but we feel that clarity trumps orthodoxy when it comes to the examples.

  • The function fipy.viewers.make() has been renamed to fipy.viewers.Viewer(). All of the limits can now be supplied as direct arguments, as well (although this is not required). The result is a more natural syntax:

    >>> from fipy import Viewer
    >>> viewer = Viewer(vars=(alpha, beta, gamma), datamin=0, datamax=1)
    

    instead of

    >>> from fipy import viewers
    >>> viewer = viewers.make(vars=(alpha, beta, gamma),
    ...                       limits={'datamin': 0, 'datamax': 1})
    

    With the old syntax, there was also a temptation to write

    >>> from fipy.viewers import make
    >>> viewer = make(vars=(alpha, beta, gamma))
    

    which can be very hard to understand after the fact (make? make what?).

  • A ConvectionTerm can now calculate its Péclet number automatically, so the diffusionTerm argument is no longer required

    >>> eq = (TransientTerm()
    ...       == DiffusionTerm(coeff=diffCoeff)
    ...       + PowerLawConvectionTerm(coeff=convCoeff))
    

    instead of

    >>> diffTerm = DiffusionTerm(coeff=diffCoeff)
    >>> eq = (TransientTerm()
    ...       == diffTerm
    ...       + PowerLawConvectionTerm(coeff=convCoeff, diffusionTerm=diffTerm))
    
  • An ImplicitSourceTerm now “knows” how to partition itself onto the solution matrix, so you can write

    >>> S0 = mXi * phase * (1 - phase) - phase * S1
    >>> source = S0 + ImplicitSourceTerm(coeff=S1)
    

    instead of

    >>> S0 = mXi * phase * (1 - phase) - phase * S1 * (S1 < 0)
    >>> source = S0 + ImplicitSourceTerm(coeff=S1 * (S1 < 0))
    

    It is definitely still advantageous to hand-linearize your source terms, but it is no longer necessary to worry about putting the “wrong” sign on the diagonal of the matrix.

  • To make clearer the distinction between iterations, timesteps, and sweeps (see FAQ Iterations, timesteps, and sweeps? Oh, my!) the steps argument to a Solver object has been renamed iterations.

  • ImplicitDiffusionTerm has been renamed to DiffusionTerm.

Last updated on Jan 14, 2021. Created using Sphinx 3.4.3.