/* Volume molecules are released inside a set of enclosed meshes.
   Let some of the meshes be located very close one to another
   so that they are within the molecule random walk distance and 
   they have different surface properties, say REFLECTIVE and TRANSPARENT.
   The bug in the diffusion code have resulted in leaking molecules 
   through the REFLECTIVE mesh.   
 */

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

VACANCY_SEARCH_DISTANCE = 1

DEFINE_MOLECULES
{
   A {DIFFUSION_CONSTANT_3D = 2e-7}  
}


DEFINE_SURFACE_CLASS A_refl
{
   REFLECTIVE = A;   
}

DEFINE_SURFACE_CLASS A_transp
{
    TRANSPARENT = A; 
}


box_1 BOX
{
   CORNERS = [-0.13,-0.13,-0.13] , [0.13,0.13,0.13]
   DEFINE_SURFACE_REGIONS
   {
      whole_mesh{
	ELEMENT_LIST = [ALL_ELEMENTS] 

        SURFACE_CLASS = A_refl 
      }
   }
}

box_2 BOX
{
   CORNERS = [-0.11,-0.11,-0.11] , [0.11,0.11,0.11]
   DEFINE_SURFACE_REGIONS
   {
      whole_mesh{
	ELEMENT_LIST = [ALL_ELEMENTS] 

        SURFACE_CLASS = A_refl 
      }
   }
}

box_3 BOX
{
   CORNERS = [-0.1099999999,-0.1099999999,-0.1099999999] , [0.1099999999,0.1099999999,0.1099999999]
   DEFINE_SURFACE_REGIONS
   {
      whole_mesh{
	ELEMENT_LIST = [ALL_ELEMENTS] 

        SURFACE_CLASS = A_transp
      }
   }
}

A_release CUBIC_RELEASE_SITE
{
   LOCATION = [0,0,0]
   MOLECULE = A
   NUMBER_TO_RELEASE = 1000
   SITE_DIAMETER = 0.2


}

INSTANTIATE world OBJECT 
{
   box_1 OBJECT box_1 {}
   box_2 OBJECT box_2 {}
   box_3 OBJECT box_3 {}
   A_release OBJECT A_release {}
}

/* Since "box_2" mesh is REFLECTIVE there should no molecules
   in the space between "box_1" and "box_2". It means that the COUNT
   statement below should be zero for all iterations. */
REACTION_DATA_OUTPUT
{
   STEP = dt
   {
     COUNT [A, world.box_1] -
     COUNT [A, world.box_2]
   } => "./A.dat"

}