Dear Dario,

I am currently using Fipy for a slightly different diffusion-reaction problem.

I use a CellVariable on the same grid for the (spatially-dependent) rate constant. One can set its values in a "numpy-vectorized" fashion by accessing the "value" property of the CellVariable.

By using a Boolean expression for indexing the "value" vector one can address individual elements.

Here are bits of code that illustrate the approach. It sets the "capture rate" to Kcap inside a sphere of radius R. Outside the sphere, "capture rate" is zero.

    # create grid (one octant, using symmetry)
    mesh = UniformGrid3D(nx=Nx, ny=Ny, nz=Nz,
                  dx=sx/Nx, dy=sy/Ny, dz=sz/Nz,
                 origin=[[0.],[0.],[0.]] )
    X,Y,Z = mesh.cellCenters

    # variables
    u = CellVariable(name="particles",
    k = CellVariable(name="capture rate",

    # equation
    eq = TransientTerm(var = u) == DiffusionTerm(coeff = Dcoeff, var = u) - k*u

    # I skip the boundary conditions here to keep this message compact

    # initial conditions for u; setting value for rate constant
    k.value[(X**2 + Y**2 + Z**2< Rcap**2)] = Kcap

I also found that it is possible to access the elements on this regular 3D grid via a "reshaped" version of the array

    uvol = u.value.reshape(Nz,Ny,Nx)


    uvol[:,0,:] += np.sum(vvol, axis=1)

This approach, however, requires that one does the book-keeping of the coordinate system oneself, and relies on the specific way that the data is organized by FiPy.

Best wishes,

On 08/04/2019 17:30, Dario Panada wrote:

Many thanks for your reply.

Yes, let me provide a bit more context.

I two initial numpy grids (n*n*n) where each value corresponds to a source/sink. Eg: Given my source grid and coordinates (1,2,3) having value 5, I want to set such value as a source in FiPy. Currently I am dong that by, for each such coordinate, finding the corresponding ravelled index and setting it in _array, as snippet in my previous message;

/i = np.ravel_multi_index([coordinate[0], coordinate[1], coordinate[2]], (20, 20, 20))/
/            sourceGrid._array[i] = sourceRate/
/            sinkGrid._array[i] = sinkRate/
I suppose I could build the entire vector of sources before and then doing a single assignment to _array, but again you correctly mentioned that relying on that is bad practice.

You mention:

/sourceGrid[..., i] = sourceRate/
Can I just please confirm what data type sourceGrid is? In the context of defining the equation

/eq = TransientTerm() == DiffusionTerm(coeff=D) + sourceGrid - sinkGrid/
Can sourceGrid/sinkGrid just be numpy arrays or even simple python lists? I was under the impression they had to be CellVariable objects but could be wrong.

Kind Regards,

On Mon, Apr 8, 2019 at 3:04 PM Guyer, Jonathan E. Dr. (Fed) via fipy < <>> wrote:

    Iterating over a mesh with a Python `for` loop is, as you've
    found, an incredibly inefficient way to do things. FiPy, like
    numpy it relies on, is intended to be used with vectorized

    As far as your approach, things that start with `_` in Python are
    internal implementation details and you should not depend on them.
    If you find cases in FiPy that absolutely require that you access
    `some._propertyName` or `some._methodName()`, then please file an
    issue explaining your need so that we can provide a public interface.

    In this case, there's no need to access `_array`. Just write

    >>> sourceGrid[..., i] = sourceRate
    >>> sinkGrid[..., i] = sinkRate

    HOWEVER, you are still relying on an internal implementation
    detail, specifically that a Grid is an array with known fastest
    and slowest varying axes. We have in FiPy's history switched from
    Fortran to C ordering, and we might conceivably switch back at
    some point. Further, if you every wanted to run your script on an
    unstructured mesh, then your system wouldn't work at all.

    `sourceCoords` presumably comes from some definition in terms of
    geometry rather than discrete mesh indices. FiPy is intended to
    work best with those geometric descriptions. If you described
    where `sourceCoords` came from, we could help with a more FiPyish
    way to get what you want.

    > On Apr 6, 2019, at 9:02 AM, Dario Panada <
    <>> wrote:
    > Good Afternoon (Morning) to all,
    > I have an equation of type
    > eq = TransientTerm() == DiffusionTerm(coeff=D) + sourceGrid -
    > Where sourceGrid and sinkGrid are derived from values in a 3D grid.
    > Is there any downside to declaring the grids as
    > sourceGrid = CellVariable(name="source", mesh=Grid3D(dx=1, dy=1,
    dz=1, nx=20, ny=20, nz=20))
    >         sinkGrid = CellVariable(name="sink", mesh=Grid3D(dx=1,
    dy=1, dz=1, nx=20, ny=20, nz=20))
    > And populating them as:
    >  i = np.ravel_multi_index([coordinate[0], coordinate[1],
    coordinate[2]], (20, 20, 20))
    >             sourceGrid._array[i] = sourceRate
    >             sinkGrid._array[i] = sinkRate
    > The original procedure I was using (given below) where I called
    .setValue on each coordinate is extremely time-consuming. Results
    seem to align, but of course this doesn't mean it's right... Or if
    it's wrong, any specific advice on how to achieve this?
    > Thanks,
    > Dario
    > Original approach (and there is an equivalent function for
    > def setupSourceGrid_(self, sourceCoords, mesh):
    >         sourceGrid = CellVariable(name="source", mesh=mesh, value=0)
    >         sourceGrid.setValue(0.)
    >         for pos, v in sourceCoords.iteritems():
    >             tmpGrid = [False for _ in range(8000)]
    >             i = np.ravel_multi_index([pos[0], pos[1], pos[2]],
    (20, 20, 20))
    >             tmpGrid[i] = True
    >             sourceGrid.setValue(v, where=tmpGrid)
    > _______________________________________________
    > fipy mailing list
    > <>
    >  [ NIST internal ONLY: ]

    fipy mailing list <>
      [ NIST internal ONLY: ]

fipy mailing list
   [ NIST internal ONLY: ]

fipy mailing list
  [ NIST internal ONLY: ]

Reply via email to