Re: Source Term in KWC model

your C++ model, you may want to compare 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

s 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

t;> C = CellVariable(name="concentration", mesh = mesh,value=0.) >> >> *C.faceGrad.constrain(beta*(C.faceValue-Cw)/D, mesh.facesLeft)* >> >> *C.constrain(Cl,mesh.facesRight)* >> >> eqI =TransientTerm()==ImplicitDiffusionTerm(coeff=D) >> >> >> viewer

Re: Constrain combined derivatives of multi-variables

guess in the FEM these are applied as constraints on the boundary and I'm not sure how to do this in the FVM in a natural way. 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

Re: Constrain combined derivatives of multi-variables

best way to do this would be with source terms 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'l

Re: question on source term

variable won't buy you anything. Use a Taylor expansion to make the correct explicit / implicit choice S = Sc + var1 * dS / dvar1 + var2 * dS / dvar2 if S is the source term. The other choice would be to do full Newton iteration. > So, I would need an equation for U, would that be >

Re: viewers not found

nfo It is a bit odd that the viewers need that, but "python setup.py develop" should deal with any issues like that if you are hacking 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: Product between matrix and vectors

ge velo = DOT(D,epsilon.grad) to velo = epsilon.grad.dot(D) and it should work for you. Not sure why "DOT" isn't returning a variable object. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov

Re: Product between matrix and vectors

ell, 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

Re: 2D cylindrical convection + heat transfer problem

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

Re: stress / strain equations

enting it using coupled 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: Question about Diffusion Under Temperature Gradient

using unrealistic values for the > parameters not explicitly listed in the paper. Could you provide the > thermodynamic system parameters you used and maybe a workflow for the code > so I can check with my work? Unfortunately, I am not sure what you're referring to. Which code / exa

Re: questions in fipy about flux boundary condition

e boundary, and introduce an implicit source term with "v" 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

Re: Thermal simulation

lobal value as part of the calculation and not just a post-process 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 htt

Re: Pysparse TypeError with vector equations

contributors. > (By the way, someone used Markov-chain natural language processing to > generate hilarious fake git documentation, which is not that much different > from git documentation, here: http://www.antichipotle.com/git/) Very amusing. Did you tweet that? -- Daniel Wheeler __

Re: Variable <--> Term

as you only seem to be doing one step above, maybe you should be using an ExplicitConvectionTerm rather 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

voked? 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: Parallel meshing

he best solution. But in my case it works!! Good. I hope you make good progress with your 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 ]

Re: Pysparse TypeError with vector equations

hat 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 [

Re: Parallel meshing

ross two nodes import tempfile tempfile.tempdir = './' import fipy as fp geoFile = 'tmsh3d.geo' mesh = fp.Gmsh3D(geoFile) mx,my,mz = mesh.getCellCenters() print mx Going forward, it would be nice to automate this. Probably always reset &

Re: Parallel meshing

On Fri, Mar 21, 2014 at 12:35 PM, Daniel Wheeler 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@nist.gov h

Re: Parallel meshing

d a randomized > list of integers 0 through 31. With other information from PBS I could see > 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/fipy ]

Re: Pysparse TypeError with vector equations

will get recognition and have your name on the list 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

Re: Parallel meshing

> node to print out status as the program runs. Can you send me the script and geo file and I'll try running it on multiple nodes 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: Scalar variable

econd 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 <><><><>___ 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

s are utilized (we have a show_loads command) 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.

Re: parallel execution with nonUniformGrid3D

rk in the IPython notebook. http://thread.gmane.org/gmane.comp.python.ipython.user/9728 You might be interested in a notebook I just wrote 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. ht

Re: Reference for van Leer convection term?

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

arallel 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. -- Danie

Re: Jacobian of a DiffusionTerm

On Wed, Feb 19, 2014 at 8:10 PM, Caleb Hattingh wrote: > On 20 February 2014 01:48, Daniel Wheeler wrote: > Thank you very much for your time. Thanks for all the feedback and good luck with your work. -- Daniel Wheeler ___ fipy mailing lis

Re: Jacobian of a DiffusionTerm

On Tue, Feb 18, 2014 at 6:04 PM, Caleb Hattingh wrote: > On 19 February 2014 02:25, Daniel Wheeler 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 > perturbation (forward differencing)

Re: Jacobian of a DiffusionTerm

;phi". I don't have any working code to show 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@nis

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

uld 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: choice of solver and implementing customized solver

problems. Often FiPy is very expensive for the setup stage 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

Re: Assigning values to cellvariable

ther kp['NO3'][:] = numerix.array((k['R2'] * k_O2_NO3/(k_O2_NO3 + O2.var))) to cast the RHS to be an array rather than a variable, if you want to not have kp['NO3'] updated via lazy evaluation. -- 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 8:57 PM, sunghyun Kim 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

Re: Taking Dot Product of faceGrad

eems to be what's needed. 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: 3D periodic boundary condition

On Tue, Jan 28, 2014 at 11:01 AM, Daniel Wheeler wrote: > On Mon, Jan 27, 2014 at 3:24 AM, sunghyun Kim wrote: >> Hi. >> I have found "PeriodicGrid1D" or "PeriodicGrid2D" meshes. >> However, it seems there is no way to use 3D periodic boundary condition

Re: 3D periodic boundary condition

dic mesh? Sunghyun, 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: Assigning values to cellvariable

ray() or .value operation. It's like the > operations are just doing book keeping of the account, but the numpy.array() > method encash the final values. Even though, the operators will work the > same on CellVariables as on numpy arrays. Seems like a good interp

Re: Assigning values to cellvariable

should make "a.value" an actual 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

Re: parallel execution with nonUniformGrid3D

hould give better parallel 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 ___

Re: Taking Dot Product of faceGrad

ust a question of extending the overlaps to join along 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

Re: Taking Dot Product of faceGrad

quot;import fipy; fipy.test()" > > gives > usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] >or: -c --help [cmd1 cmd2 ...] >or: -c --help-commands >or: -c cmd --help > > error:invalid command 'egg_info' Not sure what i

Re: problems using FiPy on Windows 7 computer

decrease the size of the mesh for that problem. The idea about having a progress bar is a good one though. We should probably just have ascii progress bars for all the examples that take some time to run. Thanks. -- Daniel Wheeler ___ fipy mailing

Re: Taking Dot Product of faceGrad

> Grid1D) Can you post the complete output 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: problems using FiPy on Windows 7 computer

all last): > File "sphere.py", line 148, in > raise EnvironmentError("Gmsh version must be >= 2.0.") > EnvironmentError: Gmsh version must be >= 2.0. > What version of Gmsh are you using? Try "gmsh --version" at the command line or fire up the Gmsh GUI a

Re: Computation of finite element integrals

iscretized $\psi$'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: https://email.nist.gov/mailman/listinfo/fipy ]

Re: Convection coefficients for vector equations

error (RuntimeError: Factor is exactly > singular), it is at least 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: Vertex vs Cell-centered finite volume

seems like I see a lot more CC rather 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: 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: Parallel Trilinos under Windows

rallel 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 i

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. --

Re: Taking Dot Product of faceGrad

teps for some equations) and then evolve only one or two of the equations for example. -- 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

small system, I get RuntimeError: Factor is exactly singular Something is obviously not right. Do you have a simpler system for which you know the answer? Also so you have a 1D solution? -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.

Re: Taking Dot Product of faceGrad

On Fri, Dec 20, 2013 at 9:13 AM, Jane Hung wrote: > That definitely helps the simulation run, but the behavior is different from > what I've seen with other methods. So I'm wondering if you think the way I'm > rewriting the equations is alright http://pastebin.com/buFS1NRu I didn't check each equ

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: Taking Dot Product of faceGrad

duals isn't really important, but how much they decrease and whether the error 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

Re: Taking Dot Product of faceGrad

on the RHS, but the term does need to end up being a "CellVariable" not a "FaceVariable". It'll be a "FaceVariable" in its current form. Change the outermost "faceGrad" to "grad" 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 ]

Re: bug in adsorbingSurfactantEquation.py?

at's in Cantera, > 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

Re: bug in adsorbingSurfactantEquation.py?

7;dt**2'. > And why do you think it shouldn't take a timestep at all? It needs a time step for the rate of adsorption. No time step is needed simply for evolving a fixed surfactant quantity, which is neither desorbing or adsorbing. The problem is that the equ

Re: bug in adsorbingSurfactantEquation.py?

a problem. Thanks for the patch and don't be shy about submitting more patches. 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: 2 moving boundaries problem

her than the FiPy documentation. The FiPy documentation assumes that you already have a set of equations. Good luck with it. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.

Re: 2 moving boundaries problem

at, hence why it was taken out. -- 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: non-linear boundary conditions

thing to do with boundary conditions can be programmed to work iteratively (explicitly and sometimes implicitly) and of course everything is available for you to tinker with. Whether the iterations converge is a whole other question of course. -- Daniel Wheeler ___

Re: Lake Temperature Modelling with FiPy

line 612, in tempList = runIterations() File "Hostetler3.py", line 608, in runIterations tempArray[step][depth_ind] = temp.value[depth_ind] NameError: global name 'tempArray' is not defined I assume that this isn

Re: Lake Temperature Modelling with FiPy

I am getting temperature values in the negative thousands. Fix the boundary condition issue and see what happens and then send the entire code and we can try and debug it. 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: Defining CellVariable within a class

ttribute, but I got an > error message "Solids instance has no attribute of value". It might be a > silly question, but I could not find an answer online. Hi Yuan, Could you give a code snippet that's fully executable or at least give the full traceback? So that I can reproduce th

Re: richards equation in fipy

ct to S and then the diffusion coefficient is just "K * Hprime". Hope that helps. -- 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: Gmsh Physical Entities & tools.dump

istent storage then creating a ~/.fipy directory in the users home area is probably the way to go. -- 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: Convective-diffusion PDE

Create a function to discretize the convection term and then update a CellVariable that represents this term at every time step. Hope that helps. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: h

Re: What am I doing right? Re: Any such thing as an "open" boundary condition?

dy. Only when a constraint is not already applied to the variable being solved for. > Thanks for all your useful comments! No problem. This is definitely a confusing issue. -- 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: Gmsh Physical Entities & tools.dump

e(6) = {2, 1, 3}; Circle(7) = {3, 1, 4}; Circle(8) = {4, 1, 5}; Circle(9) = {5, 1, 2}; Line Loop(10) = {6, 7, 8, 9}; Plane Surface(11) = {10}; Physical Surface("Circle")

Re: Switch x, y axis in viewer

nge(10))) >>> vi.axes.set_title("Something") >>> vi.axes.set_xlabel("Blah") >>> vi.plot() -- 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: Switch x, y axis in viewer

lues (mesh grid locations). I don't understand why it could not be > plotted. Remember that mostly any array-like thing in FiPy can be cast to a numpy array simply by putting numpy.array(X) around it. -- Daniel Wheeler ___ fipy mailing list

Re: Switch x, y axis in viewer

isotropy.html as an example of how to subclass and customize a viewer. -- 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: What am I doing right? Re: Any such thing as an "open" boundary condition?

non-exit faces ("~" is NOT in numpy-array-like language). I think that the convection term includes the outward flux, but that is being added back in by the source term. There may or may not be a reason why this works better. I don't know for sure -- 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: coupling of equation with 2nd order diffusive terms

ur code or update your code from the repository. Hope that helps. -- 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: coupling of equation with 2nd order diffusive terms

quires more than one shot to reduce the error enough. The LinearLUSolver iterations are obviously different from iterations in a regular iterative solver. Hope that helps. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov

Re: globalValue for faceCenters in parallel

> I'll look into that a little more since it's unexpected. It's been a while > since I've tried to do any debugging of Python with MPI, but I could at > least try and provide some sort of test case that does it for me along with > version information for any of the depende

Re: globalValue for faceCenters in parallel

Python processes still seem to be > pegging the CPUs while I presume they should be waiting on Gmsh to compute a > mesh. Strange, I have no idea what's happening there. -- 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: globalValue for faceCenters in parallel

each process should I use MPI comm > primitives to pull them together or is there a cleaner way to get this > within the existing framework? I'm not really sure what you are trying to do here. What is the purpose? Maybe there is another way. > Also,

Re: getting simple 1D convection to work

o better. Try the VanLeerConvectionTerm for a second order accurate scheme http://matforge.org/fipy/browser/fipy/fipy/terms/vanLeerConvectionTerm.py#L47 A lot of work uses even higher order schemes. Those aren't in FiPy. CLAWPACK may have some of those if you want to compare. Cheers -- Dani

Re: two questions

se much larger time steps in most cases. However, for Cahn-Hilliard, a spectral method is nearly always better than a lower order method. If you need help with Python code for the spectral method, I have that some place. Just let me know. Cheers, Daniel -- Daniel Wheeler ___

Re: Background information regarding the new constraint system

the semi-discrete form, I assume you mean that the equations are only discretized in space, but not yet in time. If this is in fact your question, I imagine that FiPy makes implicit assumptions regarding the time stepping when implementing the boundary conditions, but I am not entirely sure. Chee

Re: Does fipy support anisotropy and heterogeneous?

100. 100. 10. 100. 100. 10. 100. 100. 10. 10. 100. 100. 10. 10. 100. 100. 10. 10.]]] >>> print X [ 0.5 1.5 2.5 0.5 1.5 2.5 0.5 1.5 2.5 0.5 1.5 2.5 0. 1. 2. 3. 0. 1. 2. 3. 0. 1. 2. 3. ] Seems to work. Hope that helps. --

Re: suggested documentation change

. The faster we can switch to Github the better. Anyway, I created a ticket, see http://matforge.org/fipy/ticket/652. It will probably be dealt with as part of the next release cycle. Thanks. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://w

Re: Mesh Optimisation

t to a FiPy mesh. Unfortunately, most meshing tools only give the vertices and cells with some assumptions about the ordering and cell type. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://

Re: Mesh Optimisation

could help selecting > the optimum cell sizes? > Don't know the answer to this and I'm not sure what you're asking for. Does Dave's answer help? -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fip

Re: different solutions in fipy2 and fipy3

our fault. It's a problem in FiPy. It should really handle this correctly. There is a certain amount of cross-inspection needed between terms to select the correct schemes and this isn't happening correctly at the moment. Thanks for pointing out the issue. -- Daniel Wheeler _

Re: different solutions in fipy2 and fipy3

ighted an issue. FiPy should really throw an informative error when multiple terms of the same kind are used in an equation (or just work properly as in 2.1.3). -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST

Re: fipy tag request on Stackoverflow

estion, and I'll mark it as such. > 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 ]

fipy tag request on Stackoverflow

Is there anyone on this mailing list who has enough Stackoverflow kudos to create a fipy tag? Thanks. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo

Re: Paralell solver problem

an solve I'll share the solution. > Please do. 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: Convection terms and algebraic equations

? For instance, the electroneutrality assumption in > electrochemistry, \sum{z_{i}C_{i} = 0, relates ion concentrations with an > algebraic constraint. > Can't the constrained equation simply be used to eliminate one of the variables? If not, Raymond's solution seems reasonable. -

Re: [Problem] print "faceGrad" or not will change the calculation results

eps will be limited. I'm not certain, but isn't there a way to integrate this to be part of a diffusion term? -- 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: Paralell solver problem

h a simple fix or not ? > > Hi Serbulent, Apologies for the late response. Two questions. * Do the tests run okay with 8 processors. * Does "__main__.py" work with 2 processors? One more thing, you might want to avoid using "__main__.py" as a file name. That m

Re: coupled flow + advection-diffusion-reaction equations

ld you please give your opinion regarding 2D and > curved geometries? > The gemetry should not present a challange to FiPy assuming that Gmsh can generate it and with the caveat that FiPy looses accuracy as the non-orthogonality and non-conjunctinality is increased. If you

Re: Surface/tangential derivatives or Laplace-Beltrami operators

ffusion tensor so that I can > use the usual DiffusionTerm to model tangential diffusion? > You can define an anisotropic diffusion coefficient. See http://www.ctcms.nist.gov/fipy/examples/diffusion/generated/examples.diffusion.anisotropy.html. The nume

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