All geometry files in dynamic geometry file

Branch: dynamic_meshes

Currently, the initial set of meshes are treated differently than meshes that appear later via dynamic geometry events. Those initial meshes are included in the main mdl (object definition and instantiation), whereas meshes that appear later have their geometry files listed in the dynamic geometry file. We should change this such that those initial meshes are treated just like the meshes from dynamic geometry events (i.e. the meshes should be in a separate file that is listed in the dynamic geometry file).

Here's an example of how it would work.

Previously, you would have something like this in the dynamic geometry file:

1e-05 divide.002.mdl
2e-05 divide.003.mdl
3e-05 divide.004.mdl
4e-05 divide.005.mdl
5e-05 divide.006.mdl

With this change, you would instead do this (notice the first line):

0 divide.001.mdl
1e-05 divide.002.mdl
2e-05 divide.003.mdl
3e-05 divide.004.mdl
4e-05 divide.005.mdl
5e-05 divide.006.mdl

And for the main MDL, you previously would have done something like this:

TIME_STEP = 1E-5
ITERATIONS = 152

DYNAMIC_GEOMETRY = "list_of_geometry.txt"

DEFINE_MOLECULES { vm { DIFFUSION_CONSTANT_3D = 1e-05 } }

INCLUDE_FILE = "divide.001.mdl"

INSTANTIATE Scene OBJECT {
  Icosphere OBJECT Icosphere{}
  Release_Site RELEASE_SITE {
    SHAPE = Scene.Icosphere
    MOLECULE = vm
    NUMBER_TO_RELEASE = 100
  }
}

Now, you would do this:

TIME_STEP = 1E-5
ITERATIONS = 152

DYNAMIC_GEOMETRY = "list_of_geometry.txt"

DEFINE_MOLECULES { vm { DIFFUSION_CONSTANT_3D = 1e-05 } }

INSTANTIATE Scene OBJECT {
  Release_Site RELEASE_SITE {
    SHAPE = Scene.Icosphere
    MOLECULE = vm
    NUMBER_TO_RELEASE = 100
  }
}

mcellteam / mcell

All geometry files in dynamic geometry file #20