Jacob Czech

Export geometry doesn't auto-triangulate meshes

1

When you select "File>Export>MCell MDL Geometry (.mdl)", it doesn't automatically triangulate the selected mesh. In fact, it doesn't fail either. It just exports the element connection list incorrectly.

Add support for OUTPUT_BUFFER_SIZE, TIME_LIST, and ITERATION_LIST

1

Currently, there is no way to adjust the OUTPUT_BUFFER_SIZE for reaction data. Also, instead of simply support a step value, we could support custom time and iteration lists. In MCell,...

We don't expose the ASCII viz data option (`MODE = ASCII`) anywhere in CellBlender. It might be nice to add, so people don't have to edit MDL.

Currently, the simulation runner does not work with Python 2.6. It would be fairly trivial to add support if we simply replace this: ``` if sys.version_info.major == 3: ``` with...

If you try to build the distribution created by sdist (python setup sdist; cd dist; python setup.py build), it will fail when using the [nfsim_dynamic_meshes_pymcell branch](https://github.com/mcellteam/mcell/tree/nfsim_dynamic_meshes_pymcell) because the requirements.py file...

We already have them listed for Ubuntu. We should do the same for OSX.

If you have a molecule with a diffusion constant of zero which is applied to a concentration clamp, MCell will produce the following (unhelpful) error message: `Error: Failed to parse...

Surface molecule CROSSINGS and HITS don't work

1

FRONT, BACK, or ALL CROSSINGS/HITS don't work for surface molecules, although the QRG suggests otherwise: > For a volume molecule output the number of times the named molecule has hit...

A strange bug can be triggered when creating a surface class where all molecules should be absorbed (i.e. **ABSORPTIVE = ALL_MOLECULES**). The problem is that volume molecules are not absorbed...

Intersecting reflective meshes

1

Branch: dynamic_meshes If a molecule is between a set of intersecting reflective meshes, then it's possible for the molecule to leak out of that space (when the meshes move).