rxd, crxd and dx

Extending NEURON to handle reaction-diffusion problems.

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ziemek
Posts: 43
Joined: Thu May 23, 2019 8:02 am
Location: Warsaw, Poland
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rxd, crxd and dx

Post by ziemek »

Hi!

I have 2 related question:
  • What is the difference between rxd and crxd?
  • What exactly define dx param for Region when I use:

Code: Select all

rxd.set_solve_type(dimension=3)
I understand that this is the maximum size of 3D mesh element. But how exactly the mesh is defined? Does rxd create the mesh automaticaly on each x,y,z direction assuming that each element of the mesh has the area of dx?

Thanks for your help!

adamjhn
Posts: 40
Joined: Tue Apr 18, 2017 10:05 am

Re: rxd, crxd and dx

Post by adamjhn »

In previous versions of NEURON crxd was a faster implementation of rxd using a C/C++ backend. In the current release (7.7.2) there is no difference as crxd has become rxd.

When using the 3D solver, dx is set when creating a region, by default it is 0.25μm.
e.g.

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cyt = rxd.Region(h.allsec(), nrn_region='i', dx=0.25)
The mesh is then generated by rxd using cubic voxels with a maximum volume of dx³.

ziemek
Posts: 43
Joined: Thu May 23, 2019 8:02 am
Location: Warsaw, Poland
Contact:

Re: rxd, crxd and dx

Post by ziemek »

That's the exact answer I was looking for, thanks so much!

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