mcellteam / mcell

MCell Monte Carlo Simulator of Cellular Microphysiology
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Concentration clamp with non-diffusing molecule #29

Open jczech opened 7 years ago

jczech commented 7 years ago

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 input file

Here's an MDL that produces this error:

ITERATIONS = 1
TIME_STEP = 1e-6

DEFINE_MOLECULES { vol1 { DIFFUSION_CONSTANT_3D = 0 } }

DEFINE_SURFACE_CLASSES { Surface_Class { CLAMP_CONCENTRATION vol1; = 1e-5 } }

Plane POLYGON_LIST {
  VERTEX_LIST {
    [ -0.899999976158142, -0.899999976158142, 0 ]
    [ 0.899999976158142, -0.899999976158142, 0 ]
    [ -0.899999976158142, 0.899999976158142, 0 ]
    [ 0.899999976158142, 0.899999976158142, 0 ]
  }
  ELEMENT_CONNECTIONS {
    [ 1, 2, 0 ]
    [ 1, 3, 2 ]
  }
}

MODIFY_SURFACE_REGIONS { Plane[ALL] { SURFACE_CLASS = Surface_Class } }

INSTANTIATE Scene OBJECT
{
  Plane OBJECT Plane {}
}