Re: fipy diffusion setup

On Mon, Apr 18, 2016 at 12:33 PM, Phil Battle <bat...@advr-inc.com> wrote: > Ok, below works as I would expect ( note Dx and Dz are constants) Thanks for that. I can confirm that it's broken in Python 2.7 as well when the diffusion coefficient is [[Dx, Dy]]. -- Danie

Re: fipy diffusion setup

k 2 for the diffusion coefficient. It's safer to do that for anisotropy. > I see questions posted on this list, Gist and stack overflow - is there a > preference for posting ? I prefer Stackoverflow, but depends on the nature of the question. Stackoverflow isn't good for very o

Re: Memory Leaks with Trilinos

>>> [ 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 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 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 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 ]

Re: Convection-diffusion problem on a 1D cylindrical grid

on exactly overlaps with the analytical solution only if I do >>> S_vap_analytical.setValue(Mf / (xalt*vgas(xalt))) #with xalt >>> defined below in my code > > instead of > >>> S_vap_analytical.setValue(Mf / (x*vgas(x))) Probably the same deal. -- Daniel Wheeler _

Re: Trouble coding a mass conservation + burgers equation system

erLaw== DiffusionTerm(coeff=D, var=c) +alpha > * n - > c/tau; eq3 = TransientTerm(var=c) == DiffusionTerm(coeff=D, var=c) + ImplicitSourceTerm(coeff=alpha, var=n) - ImplicitSourceTerm(var=c, coeff=1. / tau) Remember that the `v` needs to be updated by `vx` and `vy` explicitly. I hope that helps

Re: 3 convection-reaction-diffusion PDEs coupled to a 2nd-order ODE with spatial derivatives in source terms

s b > > I went through the manual and spent several hours on past discussions on the > mailing-list, but I could not find, yet a working solution. > > Your help would be greatly appreciated. > Best, > > Hervé > > --- > Hervé Turlier, PhD > European Molecular Biolo

Re: mesh size changes 2D advection diffusion problem solution

1. 2. ] [ 0. 0. 1. 1. 2. 2. 0.5 0.5 0.5 1.5 1.5 1.5]] In [5]: velocity[0] = 0.0 In [6]: print velocity [[ 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. ] [ 0. 0. 1. 1. 2. 2. 0.5 0.5 0.5 1.5 1.5 1.5]] -- Daniel Wheeler _

Re: mesh size changes 2D advection diffusion problem solution

oeff = velocityVector.faceValue)) > > eq.solve(var = phi) > > viewer.plot() > > ---- > > > > Thank you very much! > > Best, > > Zhekai > > > > ___ > fi

Re: anisotropic diffusion problem: calculate flux

t would be great to have in FiPy. Sorry that it isn't available. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: anisotropic diffusion problem: calculate flux

n unstructured mesh, but always proceed with caution creating small test cases as you go to confirm. Good luck with it. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Speeding up FiPy / FiPy project status / looking for experienced FiPy developer contact

to anyone who has developer experience with FiPy to discuss my implentations to keep them in line of the structure of the FiPy project/code. Let's set up a video chat with Jon Guyer included. Email me offline and we can set up a time. -- Daniel Wheeler

Re: solving a buyoancy problem

including source terms with the correct masks for the faces rather than using constraints. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: The minimum required packages for parallel running

optimizing unless you really know Trilinos well IMO. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: How to split 4th-order DiffusionTerm into two 2nd-order?

something customized then things should work right. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Coupled 1D PDE's on a periodic grid; writing tricky terms and coefficients in FiPy.

for the equations being solved, see http://materialsinnovation.github.io/pymks/rst/elasticity_2D.html#elastostatics-equations Hope that helps. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal

Re: Coupled 1D PDE's on a periodic grid; writing tricky terms and coefficients in FiPy.

in FiPy until we at least have basic coupled elasticity examples. Thanks. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Computing divergence the (x, y) vector field using faceValues from a CellVariable

(since the cell center gradients are calculated from the cell center values). Arguably, setting a faceGrad constraint should influence the extrapolation, but it doesn't currently. Hope this helps. Cheers. -- Daniel Wheeler ___ fipy mailing list fipy

Re: Gmsh2D() error -- Gmsh version must be =2.0

://github.com/usnistgov/fipy/blob/develop/fipy/meshes/gmshMesh.py#L149 and find out what gmshVersion is. I suspect it's None or something like that and Gmsh is not even being found. I often use the Interactive Python Debugger for this sort of thing and it's a great help. Cheers, Daniel -- Daniel

Re: Convective term

is not that great at pure hyperbolic problems, but you can try to use the VanLeerAdvectionTerm to preserve the shocks better. See https://gist.github.com/wd15/22d739ee506f5ebf07eb. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov

Re: phi.grad() question

v.getGrad()[:,0] [[ 0.5 1. 0.5 0.5 1. 0.5 0.5 1. 0.5] [ 0. 0. 0. 0. 0. 0. 0. 0. 0. ]] -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman

Re: Diffusion in a 2D Annulus.

-linear iterations. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: 1D coupled fluid equations in FiPy

the derivatives unless P has n dependence so Riemann does nothing. I probably need to see how your implementing things to be more helpful. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https

Re: Diffusion in a 2D Annulus.

to import the results into Mathematica. You can just use viewer = fipy.Viewer(phi); viewer.plot() to look at the results. Cheers, Daniel -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https

Re: Incorrect Face Value for Neumann Boundaries

it would be a huge issue to make it work correctly. Just a case of carving out some time to do it. Feel free to submit an issue outlining your use case, see https://github.com/usnistgov/fipy/issues. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov

Re: Advection Problem: understandig the boundary conditions

can't get that working. Please do get back to me if you can't get this working. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Fipy gives incorrect solution when using neumann and robin boundary conditions, but no dirichlet

of parameters or equation and for a more general equation or parameters we would see a difference? I'd like the test to reflect the change in some way if possible. Have a test that failed for the old wrong solution and passed for your new solution. Thanks, Daniel -- Daniel Wheeler

Re: Fipy gives incorrect solution when using neumann and robin boundary conditions, but no dirichlet

. I'm beginning to wonder if we shouldn't switch all boundary condition to source terms and do away with constraints because they obfuscate what's going on. I need to think about it. I hope the example helps. Cheers, Daniel -- Daniel Wheeler ___ fipy

Re: Installation failure in Python 3 virtualenv

with FiPy and Python 3 that we need to address. Good luck. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Parallellizing do not have any benefit. Because trilinos is slower than standart solver (Simple Version)

are into HPC. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Parallellizing do not have any benefit. Because trilinos is slower than standart solver (Simple Version)

to determine that Trilinos is actually the issue and not something else. Also, are you certain you are running in parallel. This has caught me out before. Print fipy.parallelComm.procID, also print mpi4py version of procID and Epetra's version Epetra.PyComm().MyPID(). -- Daniel Wheeler

Re: Mailing list archive link

On Tue, Sep 9, 2014 at 10:07 AM, Raymond Smith smit...@mit.edu wrote: Hi, Fipy. I just noticed that when I click on the mailing list archive links at http://www.ctcms.nist.gov/fipy/documentation/MAIL.html Thanks for the heads up, it should work now. -- Daniel Wheeler

Re: Unexpected result, possibly wrong, result solving 1D unsteady heat equation with spatially-varying diffusion coefficient

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 ]

Re: Scaling plotting window

://gist.github.com/wd15/f59005909801df9dd38b -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Scaling plotting window

On Wed, Sep 24, 2014 at 4:15 PM, Daniel Wheeler daniel.wheel...@gmail.com wrote: You could make those changes to your code or pull in the particular commit. Rather than changing your code you can use the viewer's axis attribute to set the limits. viewer.axes.ylim(ymax=3) for example

Re: dispersion in a radial domain

___ 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

Re: Time-dependent 2D solutions with atypical boundary conditions

trying to implement. More importantly, how are they different from those covered in the examples and usage documentation, such that you're not sure how to proceed? Yun, is there an answer to this question? -- Daniel Wheeler ___ fipy mailing list fipy

Re: Accuracy problem on results

if you can and see if FiPy is closer. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Accuracy problem on results

script (as simplified as possible) with the expected result we could look at it and see if there is anything obvious. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman

Re: Export Grid2D as .mesh or .msh file

, 0.12720232, 0.58384755]) Point being that it is fairly easy to extract the values from FiPy fields and set the Sfepy field at the given locations (to first order accuracy). Of course you still need the reverse mapping, but I imagine there is a way to to do that with SfePy. Hope that helps. -- Daniel

Re: pickle/dump

having. I don't currently have a good solution for long term data storage. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Export Grid2D as .mesh or .msh file

on grid refinement using Gmsh, which involved reading and writing msh files, but I don't think that it has been merged into the main development branch yet. Sorry that I can't be more helpful. Cheers, Daniel -- Daniel Wheeler ___ fipy mailing list fipy

Re: Tensor coefficients in 3D simulations

] -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Tensor coefficients in 3D simulations

try and get that fixed. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: pickle/dump

to the desktop machine. I'm enclosing an example file with nx=100 and ny=10, written on the cluster. Cheers, Bill -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov

Re: Solution stability depends on convectional target?

. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: pickle/dump

://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 ]

Re: Level set methods fail on non-uniform grids under FiPy 3.1

. Maybe at the Scipy conference next year or elsewhere. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Level set methods fail on non-uniform grids under FiPy 3.1

) and would be something that I could possibly participate in. Thanks, Daniel -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Level set methods fail on non-uniform grids under FiPy 3.1

-- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Source Term in KWC model

the output numbers directly for each field with sourceCoeff on and off and see. Cheers, Daniel -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Thermal simulation

for the feedback. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: robin boundary condition

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 ]

Re: Constrain combined derivatives of multi-variables

. I'll try and revisit this in the future when/if I create an elasticity example for FiPy. Sorry that I can't be more helpful. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https

Re: Constrain combined derivatives of multi-variables

that add directly to the equations. Constraints are not that sophisticated. How this is implemented depends on the equations you are solving and which equation the boundary condition is applied so you'll need to supply some more details. -- Daniel Wheeler

Re: question on source term

an equation for U, would that be eqnhelper = ImplicitSourceTerm(1, var=U) == M1*P0 Or am I making things too complicated now. This doesn't help since you still have an explicit representation for M1 and P0 in one of the equations. Cheers, Daniel -- Daniel Wheeler

Re: Product between matrix and vectors

, as shown in the attached file. You probably just need to reshape the arrays properly. Any chance you could cut and paste the whole code or subset that runs and produces the error so I can reproduce the error on my computer (and not as an image preferably)? Cheers, Daniel -- Daniel Wheeler

Re: 2D cylindrical convection + heat transfer problem

by zero, which are probably not important. It worked with both the master and develop branches of FiPy. Go ahead and update to 3.1 from http://www.ctcms.nist.gov/fipy/download/ or clone the repository with git clone git://code.matforge.org/nist/fipy.git. Good luck. -- Daniel Wheeler

Re: stress / strain equations

. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

stress / strain equations

Does anyone have an example of solving the stress / strain equations using FiPy that they would like to share? I am trying to solve them with a materials parameters, but anything would do to get started. -- Daniel Wheeler ___ fipy mailing list fipy

Re: questions in fipy about flux boundary condition

as the coefficient in the cells adjacent to the boundary. I can't really do this without seeing the full set of equations though. If you can supply those then maybe I could code something. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http

Re: Question about Diffusion Under Temperature Gradient

? -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Thermal simulation

then it might lead to the wrong field values if it is calculated incorrectly * check that the solver is converging in parallel -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https

Re: Pysparse TypeError with vector equations

git documentation, here: http://www.antichipotle.com/git/) Very amusing. Did you tweet that? -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Variable -- Term

than trying to construct MyConvectionTerm.old(). Cheers, Daniel -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Parallel meshing

? No. If the .msh file is already available, the Gmsh3D class shouldn't make any more calls to Gmsh. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Pysparse TypeError with vector equations

for that specific class/class method? $ python fipy/matrices/pysparseMatrix.py -v will run your tests in verbose mode so you can see it is actually being tested. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST

Re: Parallel meshing

= fp.Gmsh3D(geoFile) mx,my,mz = mesh.getCellCenters() print mx Going forward, it would be nice to automate this. Probably always reset tempdir in parallel just to be safe. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http

Re: Parallel meshing

the names of the 4 nodes that were allocated (I believe I didn't have 32 processes on one node). -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo

Re: Parallel meshing

On Fri, Mar 21, 2014 at 12:35 PM, Daniel Wheeler daniel.wheel...@gmail.com wrote: Anyway, there is a workaround, which I will send to you offline. The workaround: https://gist.github.com/wd15/9693712 -- Daniel Wheeler ___ fipy mailing list fipy

Re: Pysparse TypeError with vector equations

of contributors. You could just push your changes to a public repository (Github for example) and then I can pull from there. Thanks. BTW We will be switching to Github soon, which will make this process much easier. -- Daniel Wheeler ___ fipy mailing list

Re: Parallel meshing

and check that it at least works for me or try and debug it. Thanks. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Parallel meshing

) only one of the nodes has busy cores. Hi Bill, I think that the first step is to confirm that Trilinos is working correctly independent of FiPy. To do this just run from PyTrilinos import Epetra print Epetra.PyComm().MyPID() in a script. Does this work on more than one node? -- Daniel

Re: Scalar variable

to joining the equations and solving with a single matrix. The dependence on A* in the second equation is in the integral so there is no easy to get tighter coupling than by simply using alternating solutions of the equations separately (Peclet iteration). -- Daniel Wheeler inline: tblatex-1.pnginline

Re: parallel execution with nonUniformGrid3D

up. It uses Sumatra to record the simulations and then port the records into Pandas. It's a more sophisticated way to record the simulations. http://nbviewer.ipython.org/github/wd15/smt-demo/blob/master/demo.ipynb -- Daniel Wheeler ___ fipy mailing

Re: Reference for van Leer convection term?

in 1979 http://dx.doi.org/10.1016/0021-9991(79)90145-1 I hope that's correct. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: parallel execution with nonUniformGrid3D

into using FiPy in parallel a little bit more, just with a very simple problem in 3D. The results are in two IPython notebooks. See http://nbviewer.ipython.org/github/wd15/fipy-efficiency/tree/master/notebooks/ Parallel efficiency is anything between 0.25 and 0.6 for 48 processes. -- Daniel

Re: Jacobian of a DiffusionTerm

On Wed, Feb 19, 2014 at 8:10 PM, Caleb Hattingh caleb.hatti...@gmail.com wrote: On 20 February 2014 01:48, Daniel Wheeler daniel.wheel...@gmail.com wrote: Thank you very much for your time. Thanks for all the feedback and good luck with your work. -- Daniel Wheeler

Re: Jacobian of a DiffusionTerm

On Tue, Feb 18, 2014 at 6:04 PM, Caleb Hattingh caleb.hatti...@gmail.com wrote: On 19 February 2014 02:25, Daniel Wheeler daniel.wheel...@gmail.com wrote: And this continues all the way down into the bottom right-hand corner such that J[nx,nx] * dx^2 is again -3. I found this by using

Re: Windows 7 (both x64 and x32) installation tests errors

say that FiPy is working on your system. Which version of Gmsh is installed? -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Jacobian of a DiffusionTerm

you on this, but I know that others have used FiPy in this way. If you just want the numerical Jacobian, I would guess that Trilinos can do this. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY

Re: choice of solver and implementing customized solver

of a solution problem and expensive independent of the size of the domain. Once the domain is scaled up a lot of this overhead becomes inconsequential. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY

Re: 3D periodic boundary condition

On Tue, Jan 28, 2014 at 8:57 PM, sunghyun Kim kimsungh...@kaist.ac.kr wrote: thank you so much! It's been merged to the develop branch now. So use $ git clone git://code.matforge.org/nist/fipy.git $ cd fipy $ git checkout develop -- Daniel Wheeler

Re: 3D periodic boundary condition

, this should be easy to implement. I'll file a ticket and see if I can get something working. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: 3D periodic boundary condition

On Tue, Jan 28, 2014 at 11:01 AM, Daniel Wheeler daniel.wheel...@gmail.com wrote: On Mon, Jan 27, 2014 at 3:24 AM, sunghyun Kim kimsungh...@kaist.ac.kr wrote: Hi. I have found PeriodicGrid1D or PeriodicGrid2D meshes. However, it seems there is no way to use 3D periodic boundary condition

Re: Taking Dot Product of faceGrad

. Sorry that I can't implement this right now. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Taking Dot Product of faceGrad

cmd --help error:invalid command 'egg_info' Not sure what is going on there. Try $ python import fipy fipy.test() -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https

Re: Taking Dot Product of faceGrad

the top and bottom of the mesh. The left-right overlaps already work being on the same processor since the partitioning is only along the y-axis. Hope that helps. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy

Re: parallel execution with nonUniformGrid3D

performance as it is partitions in an optimal way using Gmsh. The partitions for Grid3D are suboptimal slices. The Grid3D class in parallel is a proof of concept as much as anything. Cheers, Daniel -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http

Re: Assigning values to cellvariable

array. Also you can always get the array value by simply forcing with numpy.array(b * c), which removing any vestiges of FiPy from the object. There may be a good reason to make the assignment, but it might also indicate that there is a better way. -- Daniel Wheeler

Re: Taking Dot Product of faceGrad

from $ python -c import fipy; fipy.test() Thanks. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Mass and stiffness matrix

) print eqn.matrix This is a mixture of both the stiffness and mass matrices. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Vertex vs Cell-centered finite volume

than VC on the whole if that counts for anything Sorry I can't be more specific. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Convection coefficients for vector equations

a solution to the problem of how to specify coefficients. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Computation of finite element integrals

-averaged discretized $\psi$'s. I don't believe that FiPy has any inbuilt functionality to do this. Hope that helps or at least clarifies things a bit. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY

Re: Parallel Trilinos under Windows

of parallel under windows? Unfortunately not. Jon is currently working on implementing PETC as a backend solver, maybe this will be better on Windows. Good luck. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST

Re: Parallel Trilinos under Windows

seem to find any Windows specific installation instructions at Sandia, but I found these http://hillyuan.blogspot.com/2013/02/build-trilinos-in-windows-by-visual.html Will compiling the trilinos code using cygwin work? Not tried that either. Sorry. -- Daniel Wheeler

Re: Taking Dot Product of faceGrad

also decreases. solve version http://pastebin.com/sBQj7knw I created a notebook with some pointers about how to reformulate the equations so they are mostly implicit. I believe this is possible with your equations. http://nbviewer.ipython.org/gist/wd15/8043375 -- Daniel Wheeler

Re: Taking Dot Product of faceGrad

order diffusion terms and coupled equations can't be trusted. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

Re: bug in adsorbingSurfactantEquation.py?

, which is the tool I'm currently using to solve coverage equations for catalysts. So making that connection was very helpful too! Harry Moffat? Maybe the wrong Moffat. I coauthor papers with someone called Tom Moffat. No connection with Harry. -- Daniel Wheeler

Re: Taking Dot Product of faceGrad

and things should work. -- Daniel Wheeler ___ 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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