Dear Martin, Many thanks for your message.
I think your approach is not too dissimilar from mine, but you are accessing *.value* of CellVariable whereas I am accessing *._array*. I have no problem switching to that, I'd just like confirmation that we can directly set the values by modifying the properties and that we are not omitting any other configuration that would be handled by using the otherwise provided setter methods. Kind Regards, Dario On Mon, Apr 8, 2019 at 5:04 PM Martinus WERTS <martinus.we...@ens-rennes.fr> wrote: > 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", > mesh=mesh, > value=0.) > k = CellVariable(name="capture rate", > mesh=mesh, > value=0.) > > # 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 > u.value=Ceq > 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, > Martin > > > > > > On 08/04/2019 17:30, Dario Panada wrote: > > Hello, > > 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, > Dario > > > > On Mon, Apr 8, 2019 at 3:04 PM Guyer, Jonathan E. Dr. (Fed) via fipy < > fipy@nist.gov> 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 operations. >> >> 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 <dario.pan...@gmail.com> >> wrote: >> > >> > Good Afternoon (Morning) to all, >> > >> > I have an equation of type >> > >> > eq = TransientTerm() == DiffusionTerm(coeff=D) + sourceGrid - sinkGrid >> > >> > 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 >> setupSinkGrid): >> > 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 >> > fipy@nist.gov >> > http://www.ctcms.nist.gov/fipy >> > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >> >> >> _______________________________________________ >> fipy mailing list >> fipy@nist.gov >> http://www.ctcms.nist.gov/fipy >> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >> > > _______________________________________________ > fipy mailing listfipy@nist.govhttp://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > > > _______________________________________________ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >
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