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

2016-03-10 Thread Guyer, Jonathan E. Dr. (Fed)
Properly, I think it should be (A*Ca*zmu).grad.dot([[1]]), but in 1D it shouldn't be any different. On Mar 10, 2016, at 3:46 PM, Hervé Turlier wrote: > Dear Jonathan, > > Thanks for your inputs. > While I agree that the ConvectionTerm(var=A, coeff=Ca[None]*zmu) would not > work for higher dim

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

2016-03-10 Thread Hervé Turlier
Dear Jonathan, Thanks for your inputs. While I agree that the ConvectionTerm(var=A, coeff=Ca[None]*zmu) would not work for higher dimensions, this should be okay for now in 1-dimension, right ? Also, replacing, in this term, A and Ca should lead to the same numerical result ? For 2-dimensions,

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

2016-03-10 Thread Guyer, Jonathan E. Dr. (Fed)
> I'm not entirely sure why the tuple version breaks, but the convection > terms do store different variables. A tuple of Variable fields is never a higher rank field. It might work occasionally, but it really shouldn't be counted on. I have no idea why V[None] produces a vector from a scalar, b

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

2016-03-10 Thread Hervé Turlier
Hi Daniel, Wonderful ! Indeed that works like you propose. Many thanks. Best, Hervé --- Hervé Turlier, PhD European Molecular Biology Laboratory, Meyerhofstrasse 1 69117 Heidelberg, Germany herve.turl...@embl.de herve.turl...@polytechnique.org Tel: +49 (0)6221 387-8182 > On Mar 10, 2016, at

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

2016-03-10 Thread Daniel Wheeler
Hi Hervé, As you correctly stated, the issue is the scalar/vector velocity and the convection terms. Writing the equations using `V[None]` worked for me rather than using a tuple, `(V,)`, to make the velocity a vector. I don't know why exactly. Try this though, V_vec = V[None] # DEFINE EQUA

Re: mesh size changes 2D advection diffusion problem solution

2016-03-10 Thread Daniel Wheeler
On Wed, Mar 9, 2016 at 12:21 PM, Zhekai Deng wrote: > Thank for you taking the time clarify this to me. I implemented your > suggestions, and it works right now. I understand the TransientTerm part > now. And I have a quick follow up question regarding to velocity field > part: So in my original

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

2016-03-10 Thread Hervé Turlier
Dear FiPy developers,Thanks a lot for sharing the very useful FiPy software and providing reactive support.I’ve got a set of equations for which FiPy should be the right tool to use I think.I have 3 simple convection-reaction-diffusion PDEs (convection-diffusion with reactive source term) in 1-dime