Make ca2+ example run and add submit scripts for HPC cluster

[finsberg]

• Remove some unused imports
• Added back some info used in mesh creation (in particular z_PSD which is needed later)
• Edited integratedDomain
  • The line integrateDomain = d.MeshFunction("size_t", spine_mesh, 2, facet_markers_orig) didn't make sense when facet_markers_orig was also a MeshFunction
• Remove print_assembly from config
• Run formatter
• Make it possible to set paths via environment variables which is useful when submitting jobs.

[emmetfrancis]

Looks good! Thanks and sorry again about the mess.

[emmetfrancis]

I went back into the file, should run as intended now. The initial condition with the "NMDAR" species needed to be set according to the facet markers from the mesh file. Right now, the method I used to do this is very inefficient, so please suggest any changes there if possible. The goal is to simply set NMDAR to 1.0 at all the locations where the facet marker is 11 (should be zero everywhere else)

[finsberg]

Added timers, see RangamaniLabUCSD/smart#151

[emmetfrancis]

FYI @finsberg , can add extra config setting for enforcing mass conservation. (could test with vs. without)

configCur.flags.update({"enforce_mass_conservation": True})

[finsberg]

Added option in a38c65f