mcell/mdl/testsuite/reactions/12-all_enclosed_test.mdl

/***************************************************************************
* Reactions test-12: Testing of the REACTION_DATA_OUTPUT statement
*    COUNT[name, region, ALL_ENCLOSED]
*
*  Surface molecules A are placed on the surfaces of both "outer" and
*  "inner" cubes, such that "inner" cube is completely inside "outer" one.
*  The COUNT statement above written for "outer" cube will effectively
*  calculate number of molecules A for the inner cube.
*
*  Failure: the count of molecules A is incorrect.
*  Success: the count of molecules A is correct.
*
*  Author: Boris Kaminsky <[email protected]>
*  Date: 2011-03-25
***************************************************************************/
basename = "12-all_enclosed_test"
countdir = "dat/" & basename & "/"

dt = 1e-6
TIME_STEP = dt
TIME_STEP_MAX = dt
ITERATIONS = 100   
SURFACE_GRID_DENSITY = 10000

VACANCY_SEARCH_DISTANCE = 1

DEFINE_MOLECULES
{
   A {DIFFUSION_CONSTANT_2D = 2e-7}  
}


outer BOX
{
   CORNERS = [-0.13,-0.13,-0.13] , [0.13,0.13,0.13]
   DEFINE_SURFACE_REGIONS
   {
      whole_mesh{
	ELEMENT_LIST = [ALL_ELEMENTS] 
        MOLECULE_NUMBER {
          A; = 200
        }

      }
   }
}

inner BOX
{
   CORNERS = [-0.05,-0.05,-0.05] , [0.05,0.05,0.05]
   DEFINE_SURFACE_REGIONS
   {
      whole_mesh{
	ELEMENT_LIST = [ALL_ELEMENTS] 
        MOLECULE_NUMBER {
          A; = 100
        }

      }
   }
}



INSTANTIATE world OBJECT 
{
   outer OBJECT outer {}
   inner OBJECT inner {}
}

REACTION_DATA_OUTPUT
{
   STEP = dt
   { COUNT [A, world.outer[whole_mesh], ALL_ENCLOSED] } => countdir & "A.dat"

}