Fipy - Revision history

Admin at 07:30, 17 April 2017

2017-04-17T07:30:34Z

← Older revision		Revision as of 07:30, 17 April 2017
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	~~Fipy is a finite-volume partial differential equation solver written in [[Python]].~~

	=Installing Fipy=		=Installing Fipy=

Admin: Admin moved page Category:Fipy to Fipy without leaving a redirect

2017-04-17T07:30:20Z

Admin moved page Category:Fipy to Fipy without leaving a redirect

← Older revision	Revision as of 07:30, 17 April 2017
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Admin: /* Pysparse Error Using Vector Equations */

2014-03-19T20:08:37Z

Pysparse Error Using Vector Equations

← Older revision		Revision as of 20:08, 19 March 2014
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	=Fipy Errors=		=Fipy Errors=

	==Pysparse ~~Error~~ Using Vector Equations==		==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:		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:

Admin: /* Pysparse Error Using Vector Equations */

2014-03-19T20:07:45Z

Pysparse Error Using Vector Equations

← Older revision		Revision as of 20:07, 19 March 2014
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	This patch file is available here: http://files.charlesmartinreid.com/pysparseMatrix.patch		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:

			<source lang="bash">
			$ patch -p1 < pysparseMatrix.patch
			</source>

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

	[[Category:Python]]		[[Category:Python]]

Admin: /* Using Fipy */

2014-03-19T19:58:39Z

Using Fipy

← Older revision		Revision as of 19:58, 19 March 2014
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			=Fipy Errors=

			==Pysparse Error 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:

			<pre>
			---------------------------------------------------------------------------
			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:
			</pre>

			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 <code>ravel()</code> function. This unfurls a square matrix into a single-column vector.

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

			<pre>
			*** 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
			</pre>

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

	[[Category:Python]]		[[Category:Python]]

Admin: /* Diffusion */

2014-01-16T20:01:56Z

Diffusion

← Older revision		Revision as of 20:01, 16 January 2014
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	* [[Fipy/Diffusion 1D]] - solves a steady 1D diffusion problem		* [[Fipy/Diffusion 1D]] - solves a steady 1D diffusion problem
	* [[Fipy/Transient Diffusion 1D]] - solves a transient 1D diffusion problem		* [[Fipy/Transient Diffusion 1D]] - solves a transient 1D diffusion problem
			* [[Fipy and Cantera/Diffusion 1D]] - solves a transient 1D diffusion problem with variable diffusivities, and uses Cantera to calculate the diffusivities as a function of composition

	===Convection===		===Convection===

Admin: /* Transient */

2014-01-16T20:00:55Z

Transient

← Older revision		Revision as of 20:00, 16 January 2014
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	* [[Fipy/Transient 0D]] - solves a transient 0D equation with a constant source term		* [[Fipy/Transient 0D]] - solves a transient 0D equation with a constant source term
	* [[Fipy and Cantera/Reaction 0D]] - solves a transient 0D equation with a reaction source term		* [[Fipy and Cantera/Reaction 0D]] - solves a transient 0D equation with a reaction source term calculated with Cantera

	===Diffusion===		===Diffusion===

Admin: /* Transient */

2014-01-16T20:00:44Z

Transient

← Older revision		Revision as of 20:00, 16 January 2014
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	* [[Fipy/Transient 0D]] - solves a transient 0D equation with a constant source term		* [[Fipy/Transient 0D]] - solves a transient 0D equation with a constant source term
	* [[Fipy/Reaction 0D]] - solves a transient 0D equation with a reaction source term		* [[Fipy and Cantera/Reaction 0D]] - solves a transient 0D equation with a reaction source term

	===Diffusion===		===Diffusion===

Admin: /* Fipy and Cantera */

2014-01-16T20:00:33Z

Fipy and Cantera

← Older revision		Revision as of 20:00, 16 January 2014
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	==Fipy and Cantera==		==Fipy and Cantera==

	~~This section contains some~~ notes on how to use Fipy with Cantera.		Some notes on how to use Fipy with Cantera:
			* [[Fipy and Cantera]]
	[[Fipy and Cantera]]

	==Notes on Fipy Examples==		==Notes on Fipy Examples==

Admin: /* Using Fipy */

2014-01-16T20:00:17Z

Using Fipy

← Older revision		Revision as of 20:00, 16 January 2014
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	=Using Fipy=		=Using Fipy=

			==Vector Equations in Fipy==

			Notes on using vector equations in Fipy:
			* [[Fipy/Vector Equations]]

	==Fipy Scripts==		==Fipy Scripts==