Using Dynamic Geometries

Dynamic Geometries

How-To

This is a brief write-up that explains how to use dynamic geometries. This option is currently only available in the dynamic_meshes branch.

In your main MDL, you should include a line like this:

DYNAMIC_GEOMETRY = "list_of_geometry.mdl

The entire main.mdl could be as simple as 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
  }
}

The list_of_geometry.txt file is formatted similar to a variable rate constant file. Time is in one column and a file name is in the other. The contents of it should be similar to this:

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
6e-05 divide.007.mdl
7e-05 divide.008.mdl
8e-05 divide.009.mdl
9e-05 divide.010.mdl
0.0001 divide.011.mdl

These geometry files (e.g. divide.002.mdl) should only contain the polygon objects and a new instantiation block (and optionally partitions) like this:

Icosphere POLYGON_LIST {
  VERTEX_LIST {
    [ 1.30580268820069e-11, -2.61160459374293e-15, -0.999780893325806 ]
    [ 0.723563373088837, -0.525693416595459, -0.447192370891571 ]
    ...
    [ 0.370742291212082, 0.761781990528107, 0.531000852584839 ]
    [ 0.318294435739517, 0.795699238777161, 0.515025854110718 ]
  }
  ELEMENT_CONNECTIONS {
    [ 0, 27, 26 ]
    [ 1, 41, 71 ]
    ...
    [ 2561, 372, 461 ]
    [ 372, 9, 461 ]
  }
}

INSTANTIATE DGScene OBJECT {
  Icosphere OBJECT Icosphere{}
}

Using other MDL commands in one of these "geometry" files may or may not work.

Warnings/Errors

There are a couple of custom warnings/errors that can be useful when using dynamic geometries. As with any warning in MCell, including these in your MDL is optional.

First, there is LARGE_MOLECULAR_DISPLACEMENT, which warns the user if the molecular displacement is larger than the mean radial displacement of any molecule in the simulation. Next, there is ADD_REMOVE_MESH, which warns the user if a mesh has been added to or removed from the simulation.

The default option for both of these are WARNING, but as with other warnings, they can be set to ERROR or IGNORE. These go in the WARNINGS block along with all the other warnings like this:

WARNINGS
{
    LARGE_MOLECULAR_DISPLACEMENT = IGNORED
    ADD_REMOVE_MESH = ERROR
}

Volume Molecule Placement

There are currently two methods for placing volume molecules after a dynamic geometry event. One method places molecules at some random position directly adjacent to the nearest triangle of the enclosing mesh. The other places molecules at the closest point adjacent to the nearest triangle of the enclosing mesh. The first method (currently the default) can be explicitly set like this:

DYNAMIC_GEOMETRY_RANDOM = FALSE

The other method is enableD by setting this same keyword to true:

DYNAMIC_GEOMETRY_RANDOM = TRUE