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
Description: MS-Word 2007 document
modConversionModel_v2.py
Description: Binary data
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