I recommend you work through and check your units in all equations. I don't
have any intuition for what's a big value and what's small when we're talking
kmol. There aren't any units at all specified for D, k, etc.
Is your solution converged when it finishes `while res > 1.e-2`? How did you
pick that value for the residual?
> On Jul 21, 2016, at 2:12 PM, Daniel DeSantis <desan...@gmail.com> wrote:
>
> So, these changes all helped a lot, both in getting results and my general
> understanding. Sorry to come back with more questions but I have been trying
> to extend the model a bit. I've added a second, competing reaction and have
> tried to incorporate a temperature profile. So far, I can get answers that
> seem to match what I expect but I have to use strange values to do so...
>
> The two problems I have are:
> 1) The temperature profile requires a k_eff of 5e6 or 5e7 to not increase
> ridiculously high.
>
> 2) The diffusion coefficient has to be relatively high (D=100) in order to
> get a decent concentration profile. In most models with a reaction that has a
> decent velocity, you can ignore diffusion all together. That does not seem to
> be the case here. Perhaps my understanding of how to code these systems is
> incorrect? In this particular case, is there something I should be doing to
> make the diffusion term second order?
>
> I've included codes and an equation sheet to try and clarify things. As it
> stands, the coefficients (D, k1, k2, keff) in the code give me a
> concentration profile I expect but not a temperature one.
>
> Thank you,
>
> Daniel DeSantis
>
> On Thu, Jul 14, 2016 at 10:36 AM, Daniel DeSantis <desan...@gmail.com>wrote:
> Thank you everyone. This helps a lot!
>
> On Wed, Jul 13, 2016 at 5:04 PM, Guyer, Jonathan E. Dr. (Fed)
> <jonathan.gu...@nist.gov> wrote:
> That should be OK. FiPy automatically maps the constraint onto the faceValue
> of a CellVariable.
>
> > On Jul 13, 2016, at 3:26 PM, Keller, Trevor (Fed) <trevor.kel...@nist.gov>
> > wrote:
> >
> > Is the definition of C_a_BC correct? For a 1D grid, is the behavior of
> > C_a.constrain(C_a_BC, where=mesh.facesRight)
> > with a CellVariable instead of a scalar value
> > C_a_BC= C_a_0*(1-X)
> > meaningful?
> >
> > Trevor
> > From: fipy-boun...@nist.gov <fipy-boun...@nist.gov> on behalf of Daniel
> > DeSantis <desan...@gmail.com>
> > Sent: Wednesday, July 13, 2016 4:08:50 PM
> > To: FIPY
> > Subject: Re: Diffusion-Convection-Reactive Chemisty
> >
> > I'm sorry. I was trying to fix the problem, and forgot to put a line back
> > in, which was masked by me not clearing a variable value for V. My
> > apologies. Please try this code instead. It has the traceback I mentioned
> > before.
> >
> >
> >
> > Traceback (most recent call last):
> >
> > File "<ipython-input-1-d209891ef431>", line 1, in <module>
> > runfile('C:/Users/ddesantis/Dropbox/PythonScripts/CFD
> > Models/ConversionModel.py',
> > wdir='C:/Users/ddesantis/Dropbox/PythonScripts/CFD Models')
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py",
> > line 699, in runfile
> > execfile(filename, namespace)
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py",
> > line 74, in execfile
> > exec(compile(scripttext, filename, 'exec'), glob, loc)
> >
> > File "C:/Users/ddesantis/Dropbox/PythonScripts/CFD
> > Models/ConversionModel.py", line 110, in <module>
> > res = Eq.sweep(dt=dt, solver=solver)
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\term.py",
> > line 236, in sweep
> > solver = self._prepareLinearSystem(var=var, solver=solver,
> > boundaryConditions=boundaryConditions, dt=dt)
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\term.py",
> > line 170, in _prepareLinearSystem
> > buildExplicitIfOther=self._buildExplcitIfOther)
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\coupledBinaryTerm.py",
> > line 122, in _buildAndAddMatrices
> > buildExplicitIfOther=buildExplicitIfOther)
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\binaryTerm.py",
> > line 68, in _buildAndAddMatrices
> > buildExplicitIfOther=buildExplicitIfOther)
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\binaryTerm.py",
> > line 68, in _buildAndAddMatrices
> > buildExplicitIfOther=buildExplicitIfOther)
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\binaryTerm.py",
> > line 68, in _buildAndAddMatrices
> > buildExplicitIfOther=buildExplicitIfOther)
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\unaryTerm.py",
> > line 99, in _buildAndAddMatrices
> > diffusionGeomCoeff=diffusionGeomCoeff)
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\abstractConvectionTerm.py",
> > line 211, in _buildMatrix
> > self.constraintB = -((1 - alpha) * var.arithmeticFaceValue *
> > constraintMask * exteriorCoeff).divergence * mesh.cellVolumes
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\variables\variable.py",
> > line 1151, in __mul__
> > return self._BinaryOperatorVariable(lambda a,b: a*b, other)
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\variables\variable.py",
> > line 1116, in _BinaryOperatorVariable
> > if not v.unit.isDimensionless() or len(v.shape) > 3:
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\variables\variable.py",
> > line 255, in _getUnit
> > return self._extractUnit(self.value)
> >
> > File
> > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\variables\variable.py",
> > line 561, in _getValue
> > value[..., mask] = numerix.array(constraint.value)[..., mask]
> >
> > IndexError: index 100 is out of bounds for axis 0 with size 100
> >
> > On Wed, Jul 13, 2016 at 3:59 PM, Daniel Wheeler <daniel.wheel...@gmail.com>
> > wrote:
> > Hi Daniel,
> >
> > It is giving a different error for me
> >
> > Traceback (most recent call last):
> > File "ConversionModel.py", line 78, in <module>
> > V.constrain(V0,mesh.facesLeft)
> > NameError: name 'V' is not defined
> >
> > Is this the correct script?
> >
> >
> >
> > On Wed, Jul 13, 2016 at 3:27 PM, Daniel DeSantis <desan...@gmail.com> wrote:
> > > Hello,
> > >
> > > I am having some trouble getting a workable convection coefficient on a
> > > reactive chemistry model with a vector velocity. I have reviewed several
> > > examples from the FiPy mailing list and tried several of the variations
> > > listed there. Originally, I was receiving the error that a coefficient
> > > must
> > > be a vector. Now I seem to be getting an error that says the index is out
> > > of
> > > bounds. Specific traceback is shown below, along with the code attachment.
> > >
> > > Could anyone suggest what I am doing wrong and how to fix it?
> > >
> > > I'm relatively new to Python and FiPy, specifically, so please bear with
> > > me
> > > as I am learning.
> > >
> > > Thank you all!
> > >
> > > --
> > > Daniel DeSantis
> > >
> > > Traceback (most recent call last):
> > >
> > > File "<ipython-input-22-d209891ef431>", line 1, in <module>
> > > runfile('C:/Users/ddesantis/Dropbox/PythonScripts/CFD
> > > Models/ConversionModel.py',
> > > wdir='C:/Users/ddesantis/Dropbox/PythonScripts/CFD Models')
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py",
> > > line 699, in runfile
> > > execfile(filename, namespace)
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py",
> > > line 74, in execfile
> > > exec(compile(scripttext, filename, 'exec'), glob, loc)
> > >
> > > File "C:/Users/ddesantis/Dropbox/PythonScripts/CFD
> > > Models/ConversionModel.py", line 107, in <module>
> > > res = Eq.sweep(dt=dt, solver=solver)
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\term.py",
> > > line 236, in sweep
> > > solver = self._prepareLinearSystem(var=var, solver=solver,
> > > boundaryConditions=boundaryConditions, dt=dt)
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\term.py",
> > > line 170, in _prepareLinearSystem
> > > buildExplicitIfOther=self._buildExplcitIfOther)
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\coupledBinaryTerm.py",
> > > line 122, in _buildAndAddMatrices
> > > buildExplicitIfOther=buildExplicitIfOther)
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\binaryTerm.py",
> > > line 68, in _buildAndAddMatrices
> > > buildExplicitIfOther=buildExplicitIfOther)
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\binaryTerm.py",
> > > line 68, in _buildAndAddMatrices
> > > buildExplicitIfOther=buildExplicitIfOther)
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\binaryTerm.py",
> > > line 68, in _buildAndAddMatrices
> > > buildExplicitIfOther=buildExplicitIfOther)
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\unaryTerm.py",
> > > line 99, in _buildAndAddMatrices
> > > diffusionGeomCoeff=diffusionGeomCoeff)
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\terms\abstractConvectionTerm.py",
> > > line 211, in _buildMatrix
> > > self.constraintB = -((1 - alpha) * var.arithmeticFaceValue *
> > > constraintMask * exteriorCoeff).divergence * mesh.cellVolumes
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\variables\variable.py",
> > > line 1151, in __mul__
> > > return self._BinaryOperatorVariable(lambda a,b: a*b, other)
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\variables\variable.py",
> > > line 1116, in _BinaryOperatorVariable
> > > if not v.unit.isDimensionless() or len(v.shape) > 3:
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\variables\variable.py",
> > > line 255, in _getUnit
> > > return self._extractUnit(self.value)
> > >
> > > File
> > > "C:\Users\ddesantis\AppData\Local\Continuum\Anaconda2\lib\site-packages\fipy\variables\variable.py",
> > > line 561, in _getValue
> > > value[..., mask] = numerix.array(constraint.value)[..., mask]
> > >
> > > IndexError: index 100 is out of bounds for axis 0 with size 100
> > >
> > > _______________________________________________
> > > fipy mailing list
> > > fipy@nist.gov
> > > http://www.ctcms.nist.gov/fipy
> > > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy]
> > >
> >
> >
> >
> > --
> > Daniel Wheeler
> > _______________________________________________
> > fipy mailing list
> > fipy@nist.gov
> > http://www.ctcms.nist.gov/fipy
> > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy]
> >
> >
> >
> > --
> > Daniel DeSantis
> >
> >
> > _______________________________________________
> > 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 ]
>
>
>
> --
> Daniel DeSantis
>
>
>
>
>
> --
> Daniel DeSantis
>
>
> <FiPy Equations for Conversion
> Model.docx><modConversionModel_v2.py>_______________________________________________
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