Fipy

From charlesreid1

Installing Fipy

Installing FiPy with Pip

These instructions worked for Mountain Lion and Maverick (OS X 10.7 and 10.8).

Numpy

Keep it simple: 

pip install numpy

Pysparse

Both pip and easy_install are broken for pysparse: 

$ pip install pysparse
Downloading/unpacking pysparse
  Could not find a version that satisfies the requirement pysparse (from versions: 1.1.1-dev, 1.2-dev, 1.2-dev202, 1.2-dev203, 1.2-dev213, 1.3-dev)
Cleaning up...
No distributions matching the version for pysparse
Storing complete log in /Users/charles/.pip/pip.log

$ easy_install pysparse

[...]

1 error generated.
error: Setup script exited with error: Command "/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -DLENFUNC_OK=1 -DNO_ATLAS_INFO=3 -I/private/var/folders/nw/1yytq18n06db0v8r1pvxf5rc0000gn/T/easy_install-dlFghq/pysparse-1.3-dev/pysparse/sparse/src -I/var/folders/nw/1yytq18n06db0v8r1pvxf5rc0000gn/T/easy_install-dlFghq/pysparse-1.3-dev/pysparse/include -I/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -I/var/folders/nw/1yytq18n06db0v8r1pvxf5rc0000gn/T/easy_install-dlFghq/pysparse-1.3-dev/pysparse/include -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c /private/var/folders/nw/1yytq18n06db0v8r1pvxf5rc0000gn/T/easy_install-dlFghq/pysparse-1.3-dev/pysparse/sparse/src/spmatrixmodule.c -o build/temp.macosx-10.6-intel-2.7/private/var/folders/nw/1yytq18n06db0v8r1pvxf5rc0000gn/T/easy_install-dlFghq/pysparse-1.3-dev/pysparse/sparse/src/spmatrixmodule.o -msse3 -I/System/Library/Frameworks/vecLib.framework/Headers" failed with exit status 1

So I built it myself: 

$ git clone git://pysparse.git.sourceforge.net/gitroot/pysparse/pysparse
$ cd pysparse
$ python setup.py build && python setup.py install

Fipy

Using pip: 

$ pip install fipy

Installing Fipy from Source

I was able to mostly follow this guide on Matforge (the site that hosts Fipy source code): http://matforge.org/fipy/wiki/InstallFiPy/MacOSX/SnowLeopard

Here are the steps I took:

  • Skipped virtualenv (because I manage my Python distribution intelligently/carefully, I didn't need to bother with this step. See my Python page for more information.)
  • Already had Gfortran installed.
  • Installed the latest Cmake
  • Skipped FFTW
  • Skipped SparseSuite
    • I was able to skip both of these because my Numpy was working and using the system's LAPACK/BLAS without problems.
  • Already had Numpy installed
  • Already had Matplotlib installed
  • Installed Pysparse from source

Once I had all of these dependencies installed, I was able to download and install Fipy. Note that as of this writing (December 2013), the instructions on http://matforge.org/fipy/wiki/InstallFiPy/MacOSX/SnowLeopard are out of date, because it specifies that you should check out a copy of the source code via SVN. In fact, Fipy now uses git.

Either download the latest release from this page: http://www.ctcms.nist.gov/fipy/download/ or by cloning a copy with git: 

$ git clone git://code.matforge.org/nist/fipy.git


Using Fipy

Vector Equations in Fipy

Notes on using vector equations in Fipy:

Fipy Scripts

I have assembled notes on Fipy scripts solving a number of different types of problems:

Transient

Diffusion

Convection

Fipy and Cantera

Some notes on how to use Fipy with Cantera:

Notes on Fipy Examples

Surface Adsorption Equation

One of the examples included with Fipy is a electrochemical level set example, which defines, among other things, a surface adsorption equation class. I have compiled some scattered notes on this class here:

Fipy/Surface Adsorption Equation

My application was somewhat different - I wasn't so much interested in the evolution of the interface, as much as I was interested in the evolution of adsorbed surface species on a stationary catalyst surface.


Fipy Errors

Pysparse TypeError Using Vector Equations

When you follow the installation procedure above, to install Pysparse and then Fipy, you may see some issues when you sweep vector equations in Fipy. Specifically, you will see TypeErrors coming from Pysparse, but with no explanation at all of what's causing them. For example, an output that looks like this: 

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)

[...]

/home/charles/pkg/transport/git/verification_aris/ConcentrationReactor.pyc in compute_solution(self)
    238
    239             # Solve
--> 240             res = eqn1.sweep(var=C)
    241             print "Residual (Rxn-Diff Eqn) = ",res
    242

/usr/local/lib/python2.7/dist-packages/FiPy-3.1-py2.7.egg/fipy/terms/term.pyc in sweep(self, var, solver, boundaryConditions, dt, underRelaxation, residualFn, cacheResidual, cacheError)
    236         solver = self._prepareLinearSystem(var=var, solver=solver, boundaryConditions=boundaryConditions, dt=dt)
    237         solver._applyUnderRelaxation(underRelaxation=underRelaxation)
--> 238         residual = solver._calcResidual(residualFn=residualFn)
    239
    240         if cacheResidual or cacheError:

/usr/local/lib/python2.7/dist-packages/FiPy-3.1-py2.7.egg/fipy/solvers/solver.pyc in _calcResidual(self, residualFn)
    146             return residualFn(self.var, self.matrix, self.RHSvector)
    147         else:
--> 148             return numerix.L2norm(self._calcResidualVector())
    149
    150     def _calcRHSNorm(self):

/usr/local/lib/python2.7/dist-packages/FiPy-3.1-py2.7.egg/fipy/solvers/solver.pyc in _calcResidualVector(self, residualFn)
    138             return residualFn(self.var, self.matrix, self.RHSvector)
    139         else:
--> 140             Lx = self.matrix * numerix.array(self.var)
    141
    142             return Lx - self.RHSvector

/usr/local/lib/python2.7/dist-packages/FiPy-3.1-py2.7.egg/fipy/matrices/pysparseMatrix.pyc in __mul__(self, other)
    325                                        matrix=spmatrix.matrixmultiply(self.matrix, other.matrix))
    326         else:
--> 327             return _PysparseMatrixFromShape.__mul__(self, other)
    328
    329     def asTrilinosMeshMatrix(self):

/usr/local/lib/python2.7/dist-packages/FiPy-3.1-py2.7.egg/fipy/matrices/pysparseMatrix.pyc in __mul__(self, other)
    167                 return y
    168             else:
--> 169                 raise TypeError
    170
    171     def __rmul__(self, other):

TypeError:

The problem, ultimately, is that the "vector" that Pysparse is trying to turn into a Pysparse vector is not, in fact, a vector, but a square matrix.

Fortunately, the solution is simple, and involves the ravel() function. This unfurls a square matrix into a single-column vector.

You will need to patch Fipy's class that wraps Pysparse matrices: 

*** a/fipy/matrices/pysparseMatrix.py   2013-09-30 19:17:46.000000000 -0700
--- b/fipy/matrices/pysparseMatrix.py   2014-01-16 10:55:13.000000000 -0800
*************** class _PysparseMatrix(_SparseMatrix):
*** 165,170 ****
--- 165,175 ----
                  y = numerix.empty((self.matrix.shape[0],))
                  self.matrix.matvec(other, y)
                  return y
+             elif shape[0]*shape[1] == N:
+                 other = other.ravel()
+                 y = numerix.empty((self.matrix.shape[0],))
+                 self.matrix.matvec(other, y)
+                 return y
              else:
                  raise TypeError

This patch file is available here: http://files.charlesmartinreid.com/pysparseMatrix.patch

Applying the Patch

If you've downloaded Fipy, go into the directory containing the files you downloaded and copy the patch to that location. You can then apply the patch by running the command: 

$ patch -p1 < pysparseMatrix.patch

The -p1 strips off the "a" and "b" directory names in front of the paths to files in the patch.

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