Re: Some questions on the viewer

ccounted for. I remember that those orderings are wrong for VTK as that does require a specific ordering (right (or left) hand rule or something like that). -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIS

Re: CylindricalGrid1D mesh volumes

ong as it's clear from the > documentation. The documentation is probably not clear on this, but thanks for raising the 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: CylindricalGrid1D mesh volumes

e, "r" are the cell centers and "dr" is the cell spacing. It's possible that by choosing "theta=1", then the "theta" can be omitted saving an extra operation. > How should I integrate Variables on such a grid? > (2*pi*Var*mesh.cellVolumes).sum()? Make

Re: Query on AdsorbingSurfactantEquation.py consumptionCoeff

Feel free to add any relevant comments to the issue, https://github.com/usnistgov/fipy/issues/690. On Mon, Jan 13, 2020 at 1:36 PM Daniel Wheeler wrote: > > Hi Chaitanya, > > I think you're correct. It seems that term should be multiplied by the > time step. The tests all pass w

Re: Query on AdsorbingSurfactantEquation.py consumptionCoeff

t; if consumptionCoeff is not None: > self.eq += ImplicitSourceTerm(consumptionCoeff*self.dt) > > Please let me know if I am thinking on the right lines. > > Regards, > Chaitanya > > > > ___ > fipy

Re: Re[2]: Need help to set up the model

to the issues that you're seeing. Cheers, Daniel On Sun, Nov 24, 2019 at 4:02 PM Mohammad Madani wrote: > > Thank you for helping me with the mesh. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY:

Re: Fluid Dynamic Basics

g, could you suggest how to set up a > continuity equation coupled with a momentum equation and, perhaps how to > handle a first order differential term like the pressure gradient? > > Thank you, > > -- > Daniel DeSantis > > > ______

Re: Solution to the sine-gordon equation

can be split into two hyperbolic equations, but FiPy doesn't do well with those types of equations. It doesn't have the correct numerical schemes. I think CLAWPACK might be a better bet for that. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://w

Re: Solution to the sine-gordon equation

On Thu, Mar 21, 2019 at 11:48 AM Daniel Wheeler wrote: > > with a transient term in the equation. For small phi, this should > never be negative, since phi should only grow, but for delta_t > 1 That's wrong, phi should shrink, but not go negative. -- Da

Re: Solution to the sine-gordon equation

__ > 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: is it easy to get fipy to make full use of dual CPUs in a single workstation?

being used. If all are being used then you may have threading turned on. This needs to be switched off when compiling Trilinos. 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: Boussinesq Equations

: velocity.divergence == 0 but it doesn’t work. > > Thank you, > > Fabien > > > > > Le 10 oct. 2018 à 17:43, Daniel Wheeler a écrit : > > Don't you still have a $\nabla . \vec{u} = 0$ equation though? It > doesn't go away. That equation becomes like a const

Re: cylindrical coordinates

ave 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://email.nist.gov/mailman/listinfo/fipy ]

Re: Boussinesq Equations

I thank you for trying to solve my problem. > About my set of the equation here is my reasoning. > -- 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: interpolation taking too long in an adaptive meshing effort (remeshing)

arest neighbors, but maybe it is > slowed down by having to do one cell at a time? To get data out of fipy, you don't need to do much more than, import pandas pandas.DataFrame(dict(x=m1.x, y=m1.y, v=v1)).to_csv('test.csv') for example. This will write the position and values of

Re: FiPy Heat Transfer Solution

((60. + 273.15) - T.faceValue, mesh.facesLeft)" and not update in the loop. That doesn't work, however. -- 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 Heat Transfer Solution

that all seems to work at least as far as I can tell. 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: FiPy Heat Transfer Solution

h*(T.faceValue - Tc), mesh.facesLeft) I think that should work. Test it carefully. It's never obvious to me what the sign should be. Don't trust it though. -- 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 contact between two regions

r following up and sharing your code. -- 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 contact between two regions

llDistances)), where=mesh.physicalFaces['thermal contact']) m._cellDistances is the distance between each cell and `dx` is the volume of the cell for a 1D problem. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fip

Re: Integral term

f1.updateOld() -- 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 contact between two regions

ttps://www.mail-archive.com/fipy@nist.gov/msg02626.html by reference. -- 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 contact between two regions

resistance (a pure > resistance); it has zero thickness, and it has zero heat capacity. I need to see it defined mathematically to understand how to implement it in FiPy, but I'm confident it's possible to define it. -- Daniel Wheeler ___ fipy mailing li

Re: Moving boundary in FiPy

o formulate my boundary condition as a > source term instead of using faceGrad.constrain... Exactly, formulate the boundary condition as a source and variable diffusion coefficient. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http:

Re: Moving boundary in FiPy

quation in a moving mesh. > > Thanks! > > Zhekai > > ___ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > -- Daniel Wheeler

Re: how to compute interface velocity in examples.phase.anisotropy?

he interface velocity at a given time >> step in examples.phase.anisotropy? >> >> At this time, I was mostly interested in the max and min of the magnitude >> of the interface velocity. >> >> Thanks > > > > ______

Re: Spline interpolation and fipy variable

the moment. Ok, this is only being used for 1D right now so you're fine. > Thank you again very much for your help! 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: Spline interpolation and fipy variable

ote: > Hi Daniel, > > Thank you for taking the time to look at this! My main code calls several > text files and subroutine. I attach everything that is needed to run the > code: -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http:/

Re: Spline interpolation and fipy variable

; dt *= 0.8 > X_var[:] = X_var.old > Xf = X_var.arithmeticFaceValue > > print "Arrived at a temperature step!" > step_T += 1 > id_mean_T = Get_closest_id(X,np.mean(X_var)) > > Mob = M[step_T][id_mean_T] > > > >

Re: Gradient in cylindrical coordinates

Mon, Jan 8, 2018 at 1:39 PM, Daniel Wheeler <daniel.wheel...@gmail.com> wrote: > Hi Leyton, > > I think there is an error in FiPy when calculating gradients with > cylindrical grids. FiPy assumes that the cylindrical faces don't count > towards the face contributions, bu

Re: Gradient in cylindrical coordinates

prohibited. If you receive this in error please contact the sender and > delete the material. The sender does not accept liability for any errors or > missions as a result of the transmission. Please destroy this message and > notify the sender. > > > ___ > 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: Compute total free energy of a system

Sq): > return (0.5 * epsSq * (phi_.grad.mag)**2 + > f(phi_,c_,T)).cellVolumeAverage > > But cellVolumeAverage wouldn't give me the full energy of the domain if I'm > not mistaken? -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.c

Re: 2D anisotropic unstructured mesh and non-classical FV schemes

can make > sure there are no control volume overlaps (and as a result, the > coefficients stay positive, and monotonicity is maintained, and none > of the nice properties are violated) ? No, FiPy is definitely not set up for vertex centered. The above

Re: Error when importing PySparse

t;3.8.4\"" > -Isrc -I/usr/include -I/usr/lib64/python2.6/site-packages/numpy/core/include > -I/usr/include/python2.6 -c src/spmatrixmodule.c -o > build/temp.linux-x86_64-2.6/src/spmatrixmodule.o" failed with exit status 1 > > Would anyone have an idea on how to fix t

Re: Time varying boundary conditions

nt one. How can I do to remove the > fixed value bc? Is there a way to check the boundary conditions on a > variable? > > Thanks, > Adrian. > > ___ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fi

Re: Conda installation not working

s import ModuleDeprecationWarning, > VisibleDeprecationWarning > ImportError: No module named _globals > > As far as I could figure out anaconda updated python to Python 2.7.13 > and the numpy version that ships with fipy is incompatible with this > version. Could you update numpy in the anac

Re: python 3

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: solvers for elliptic equations with dominant lower order terms

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

Re: Complex conjugates in FiPY

alue before the > given PDE...when I thought that the phi value was found exactly by FipY? Setting the value before solving the PDEs provide the initial value if it's an initial value problem. Even a non-initial value problem needs to be start somewhere for the non-

Re: Complex conjugates in FiPY

ix.exp((1j*X))) At this point your script is broken, "phi.value.imag" is all zero while "(0.5-0.5*numerix.exp((1j*X))).value.imag" is non-zero. The type of the CellVariable is wrong initially and the type doesn't change when the value is reset. -- Daniel Wheeler _

Re: Compressible euler equations

tually updating the solution in time. But I don’t know what > equations i am supposed to be sweeping here, I think I lack the experience. > The whole system should be swept, like so : You need to sweep all of them as you're doing. I don't think that the order matters. -- Daniel Wheeler _

Re: Compressible euler equations

c equation (the EoS) in a coupled manner ? > > 2/ If it is not possible to include the equation of state in the system, how > would you take the -dp/dx and the -dp/dy from the momentum equations (with p > expanded as a function of rhoE, rhoU and rhoV) into account ? > > Than

Re: Fresh installation tests fail

or name in names] > File > "/Users/langrock/anaconda/envs/MYFIPYENV/lib/python2.7/unittest/loader.py", > line 100, in loadTestsFromName > parent, obj = obj, getattr(obj, part) > AttributeError: 'module' object has no attribute 'testFiPy' > > ___ > 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: Compressible euler equations

ipy 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: Complex Valued CellVariables?

.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: Pulse Laser Propgation Eqn setup

var=E) \ > -TransientTerm(coeff= Beta2/2.0,var=Estar)+ > (k*n2*((E**2))+((J**2))*E)-(w0*tau*rho*E)\ > -((sigma*rho*J)/2)-((multi(numerix.sqrt((E**2.0)+(J**2)))*J)/(2.0*((E**2)+(J**2.0 > - alpha*J > eqn5 = TransientTerm(var=rho)== > rho*thornber((

Re: axisymmetric solidification problem in FiPy: trying to start with a basic 1D Stefan problem (solidification)

n a finite > domain. I know nothing about the phase field method and whether it is > applicable to the ultimate goal in paragraph 1, in which interface velocity > is a specified function of interface temperature. > > > I found a thread from 2007 > https://www.mail-archive.

Re: derivative boundary condition in 2D problem

might be nonsensical, but I think that the constraints have no impact for any quantity that is tangential to the direction of the outbound normal only the normal direction. That could well be a weakness with the notation as we currently have it in FiPy

Re: Question on accessing internal matrices of the system being solved

2th order central-difference) > order schemes in FiPy? That's not easy at all. I don't think it is designed well enough for that. It would require a major rewrite to easily add new convection schemes. Cheers, Daniel -- Daniel Wheeler ___ fipy mailing list fip

Re: Question on accessing internal matrices of the system being solved

/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: Mailing list archive

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: Adaptive mesh refinement in FiPy?

ed in FiPy? > > If so, is there some sort of manual on how to use it? > > > Thanks and best regards, > > Anders > > > ___ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY:

Re: FW: how to set up data transfer between two adjacent nonuniform meshs

e if it is relevant in your case. -- 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: FW: how to set up data transfer between two adjacent nonuniform meshs

it is probably a good idea to cache the mapping from one grid to the other as this is expensive to calculate (especially of you do this at every time step or sweep). We provided this functionality in FiPY, I'm not sure if Scipy lets you do that. --

Re: FW: how to set up data transfer between two adjacent nonuniform meshs

of worrying about mesh ordering. -- 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: Solving convection only problem

not seem to help very > much > > I have attached my example code in this email. Thank you very much. > > Best, > > Zhekai > > > ___ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST i

Re: Question on time-marching scheme in Fipy

basic here. I am just curious about > understanding fipy’s default scheme and implementing an own time-stepper. It's a very good question, but I don't have any helpful answers. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist

Re: Memory Leakage & Object Build-up with FiPy Sweeps

5po5ccrib9 > > > > With best regards, > > > > - Ian & Krishna > > > > P.S. Daniel, thank you very much for the excellent example solution you > provided in response to our question on obtaining the sharp discontinuity. > > > > Ian Campbell | PhD Candidate > > Electrochemical Science & Engineering Group > > Imperial College London, SW7 2AZ, United Kingdom > > > > ___ > 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: FiPy sweep convergence bottoms out

; >> >> >> >> >> >> >> ___ >> 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: sources errors in advection/diffusion problems, and one solution

he interesting question is if the formulation of the boundary >condition at x=0 could be altered to less excite the spurious mode? > >Also, why does the "initial" condition have any effect on the >steady equation? > >Cheers, >Jamie > > > ___

Re: JOR solver to help in accelerating sweeps?

t Regards > > > > Krishna > > > > > > > > > > > _______ > 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: Interesting (perhaps unique) approach to parallelising FiPy sweeps

preciated if you can help us by > pointing it out. I don't see a red flag there. Try to set it up so that the equations are not redefined for every sweep. Also, do an in place update of the variables using [:] or setValue (return the array rather than t

Re: Solving advection, segregation and diffusion equation

nvetionTerm isn't necessary as the accuracy is not important in a steady state problem. -- 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 Boundary Condition of one PDE with source term of another PDE

valent to what Jon is saying and similar to what you suggested. It should work fine. -- 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: Periodic BC

177369/fipy-simple-convection https://github.com/usnistgov/fipy/blob/64f7866c8dbe50e2c36adfd23c464a53e4a2b763/examples/diffusion/steadyState/mesh1D/inputPeriodic.py Hope that helps. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://

Re: Extremely Slow .sweep & Updating CellVariable-dependent Boundary Conditions

his approach may be better, though. Yup. It's just that you might be defining many constraints for a CellVariable. Are they updated or do they all apply or what? I'm not sure, but I don't think they were designed to work like that. Have you tried defining the constraint once and upd

Re: Dynamic under-relaxation factors for FiPy sweep

pful resource that the users of FiPy may be able to point me > to ? I don't think there are any FiPy specific resources on that. Your issue is with the algorithm or theory rather than how to implement it in Python / FiPy, right? -- Daniel Wheeler _

Re: reaction-advection-diffusion; problems making the solution converge

Vector? can i get those > for the individual terms on the rhs as well? > > cheers, n. > > ___ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > -- Daniel Wheeler ___

Re: reaction-advection-diffusion; problems making the solution converge

ery small. Is ||lhs - rhs|| getting smaller without normalization? -- 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: Applying Bounding Limits to PDE Solution Variables

.sweep' to compute the residual, so that > I may use the same one? I think it's the L2 norm of "A * x - b" without any normalization, where x is the variable value before the linear solve. See, https://github.com/usnistgov/fipy/blob/develop/fipy/solvers/sol

Re: reaction-advection-diffusion; problems making the solution converge

e > any difference; reducing the tolerance -- some effect, and reducing the > temporal step size, which did not help much. > > should i be doing something differently? > > thanks for any help! > > n. > _______ &

Re: error in gradient even with orthogonal grid

ble to average the gradient over space to reduce the error? I don't think so unless it can be shown to improve the accuracy with analysis. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: htt

Re: Improving non-orthogonality issue in FiPy

issue. Cheers, Daniel On Wed, Jul 20, 2016 at 4:30 PM, Michael Waters <waters.mik...@gmail.com> wrote: > Hi, I'm not sure I understand the issue. Maybe you could explain more? I > made a diagram to help. > > Cheers, > > -Mike Waters > > > > On 07/20/2016 02:51 PM,

Re: Accuracy of DiffusionTerm for non-uniform mesh

//gist.github.com/raybsmith/b0b6ee7c90efdcc35d6a0658319f1a01#file-fipy_accuracy-py-L44 may still only be first order accurate for non-uniform grids. I'll try and investigate this though and see if it matters. -- Daniel Wheeler ___ fipy mail

Re: Accuracy of DiffusionTerm for non-uniform mesh

rgence. That's strange. Are you sure that all the normalization for grid spacing is correct when calculation the norms in that last case? > I can't really explain either of the non-uniform mesh cases, and was curious > if anyone here had some insight. I

Improving non-orthogonality issue in FiPy

the latest / best / most tractable approach for dealing with non-orthogonality in CC-FV. I haven't followed the literature on this for quite some time. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST int

Re: Accuracy of DiffusionTerm for non-uniform mesh

), > I see 0.5-order convergence. > > I can't really explain either of the non-uniform mesh cases, and was curious > if anyone here had some insight. > > Thanks, > Ray > > ___ > fipy mailing list > fipy@nist.gov >

Re: Diffusion-Convection-Reactive Chemisty

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 ]

Re: casting implicit Boundary Conditions in FiPy

ethods and implementing some 1D test cases to double check. I always do this no matter how much I trust the code. -- 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 for nonlinear, coupled PDEs in multiple independent variables

, just use coefficients of 1 to see if actually having those terms helps the numerical stability. If that helps, see if you can dial down those coefficients to get a more physical solution or use other techniques that maintain the correct physics. -- Daniel Wheeler

Re: casting implicit Boundary Conditions in FiPy

t the surface (right boundary) , does a simple > geometric progression suffice with a very small dx at the right boundary > suffice ? Or is there any other optimal (structured) mesh generation > algorithm for choosing mesh sizes depending on problem-type, that I need to >

Re: bug in linearBicgstabSolver.py

<jprin...@unh.edu> wrote: > thanks > Jamie -- 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: scipy's Delaunay output to fipy mesh2D object

ntri,[1,2]] > else: > face=tri.simplices[ntri,[2,0]] > faceKey=tuple(sort(face)) > cellFaceIDs[nface,ntri]=faceMap[faceKey] > > #ok, now instantiate a mesh2D object with this data > print 'Making mesh' > mesh=fipy.meshes.mesh2D.Mesh2D(vertexCoord

Re: how to create large grid with holes and odd geometry

ny documentation on the details of the Mesh2D object. > > Thanks, > Jamie Pringle > University of New Hampshire > > On Wed, Jun 15, 2016 at 12:21 PM, Daniel Wheeler <daniel.wheel...@gmail.com> > wrote: >> >> Hi Jamie, >> >> There is no automated wa

Re: casting implicit Boundary Conditions in FiPy

piz Awesome that it worked. I think that you're right though regarding first versus second order boundary condition. I think it is first order in space. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal

Re: how to create large grid with holes and odd geometry

> 0=J(Psi,A(x,y)) + \Del(B(x,y)*\Del Psi) > > > and I can get the coefficients A(x,y) and B(x,y) on either the faces or in > the cell centers are needed. > > Thank you. > Jamie Pringle > University of New Hampshire -- Daniel Wheeler ___

Re: casting implicit Boundary Conditions in FiPy

oblem in 1D. The issues you pointed > out about using this approach in 2D went right over my head. I have to > think about this, when I implement them perhaps in a week or so. 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: casting implicit Boundary Conditions in FiPy

to make sure, do you mean that the boundary condition is a >> derivative with respect to the spatial variable or with respect to time >> as-written? If you mean spatial, such that d\phi/dx = k*phi, have you tried >> >> phi.faceGrad.constrain

Re: how to create large grid with holes and odd geometry

e, but would be very happy with suggestions of the best > way to start. > > Thanks > Jamie Pringle > University of New Hampshire > > ___ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST interna

Re: transient term with coefficient

, Spain > > fv...@unex.es > > > > > > ___ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] -- Daniel Wheeler _

Re: IndexError: index is out of bounds for axis 1 with size

t;>> functions of time (they represent pressure at downstream and upstream >>> tanks). When I solve this problem, I will get a vector for Pd and Pu (at >>> last timestep) which varies with location. For example, for Pu, >>> > >>> > print Pu &

Re: IndexError: index is out of bounds for axis 1 with size

since the constraint is on the faces. I hope this 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: IndexError: index is out of bounds for axis 1 with size

On Fri, May 6, 2016 at 12:09 PM, Daniel Wheeler <daniel.wheel...@gmail.com> wrote: > Hi Mo, Apologies for that. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.go

Re: IndexError: index is out of bounds for axis 1 with size

.58 > D=1e-6 > tmax = 1000 > sigma = 400 > k0 = 10e-16 > T = 300 > M = 0.0399 > R = 8.314 > muf=1.96e-5 > hf=30e-6 > phif=0.25 > A1=1.14 > A2=0.28 > wkf=4 > wkd=4 > wku=4 > Kn=sqrt((3.14*R*T/(2*M))*muf/(Pf*hf)) At this point "Pf"

Re: understanding convection terms

ond order accurate. The other schemes are first order. Of course it's unstable when the Peclet number is above 2 that's why we use the other schemes. Basically, the schemes (hybrid, exponential etc) are ways to swap between central difference and upwind based on the local Peclet number.

Re: understanding convection terms

c0944c21 > > Is this expected behavior? > > Kris > > > ___ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > -- Daniel Wheeler

Re: Thermal Diffusion with Source

ld like to just make it an IPython notebook (rather than doctest/restructured text script) then please do that and we'll try and link to it from the documentation. -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIS

Re: squared partial derivatives

e form. In the case of (f f_y)_y, "f" will be a coefficient in a diffusion term. 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: fipy diffusion setup

[[-1 -1 -1 -1] [-1 -1 -1 -1]] [[-1 -1 -1 -1] [-1 -1 -1 -1]]] ~~~ If you're trying to do fancy indexing with FiPy, you might want check with Numpy first so that you can trust the FiPy result. -- 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 diffusion setup

= v00.dot([[1, 0], [0, 0]]) + v11.dot([[0, 0], [0, 1]]) On Mon, Apr 18, 2016 at 3:33 PM, Daniel Wheeler <daniel.wheel...@gmail.com> wrote: > 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

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