mcell/mdl/testsuite/reactions/09-region_borders.mdl

/************************************************************************** 
* Test 09: Region borders properties tested on cube.
*
*	REFLECTIVE/ABSORPTIVE/TRANSPARENT properties of REGION border tested 
*	on the cube for ALL_MOLECULES and ALL_SURFACE_MOLECULES keywords.
* 
* Author: Boris Kaminsky <[email protected]>
* Date: 2011-03-04
****************************************************************************/


basename = "09-region_borders"
countdir = "dat/" & basename & "/"
boxdims = 0.25
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_2D = 2e-4}
   B {DIFFUSION_CONSTANT_2D = 2e-4}
}


DEFINE_SURFACE_CLASSES 
{
   my_surf_1
   {
      TRANSPARENT = ALL_MOLECULES;
   }
   my_surf_2
   {
        REFLECTIVE = ALL_MOLECULES;  
   }
   my_surf_3
   {
       ABSORPTIVE = ALL_MOLECULES;
   }
   my_surf_4
   {
      TRANSPARENT = ALL_SURFACE_MOLECULES;  
   }
   my_surf_5
   {
      REFLECTIVE = ALL_SURFACE_MOLECULES;
   }
   my_surf_6
   {
      ABSORPTIVE = ALL_SURFACE_MOLECULES;
   }
}

/* Starting X position for box placement */
x = 0
fuzz = 0.01
xleft = x - boxdims - fuzz

/* TRANSPARENT for ALL_MOLECULES */
case1 BOX
{
   CORNERS = [-boxdims,-boxdims,-boxdims] , [boxdims,boxdims,boxdims]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [TOP] 
                MOLECULE_NUMBER{
                  A' = 100
                  B' = 100
                }
                SURFACE_CLASS = my_surf_1  
	     }
           r2{
              ELEMENT_LIST = [RIGHT, LEFT,FRONT, BACK, BOTTOM]
           }
	}
    TRANSLATE = [x,0,0]
}
x = x + 2*boxdims + fuzz

/* REFLECTIVE for ALL_MOLECULES */
case2 BOX
{
   CORNERS = [-boxdims,-boxdims,-boxdims] , [boxdims,boxdims,boxdims]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [TOP] 
                MOLECULE_NUMBER{
                  A' = 100
                  B' = 100
                }
                SURFACE_CLASS = my_surf_2 
	     }
           r2{
              ELEMENT_LIST = [RIGHT, LEFT,FRONT, BACK, BOTTOM]
           }
	}
    TRANSLATE = [x,0,0]
}
x = x + 2*boxdims + fuzz

/* ABSORPTIVE for ALL_MOLECULES */
case3 BOX
{
   CORNERS = [-boxdims,-boxdims,-boxdims] , [boxdims,boxdims,boxdims]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [TOP] 
                MOLECULE_NUMBER{
                  A' = 100
                  B' = 100
                }
                SURFACE_CLASS = my_surf_3
	     }
           r2{
              ELEMENT_LIST = [RIGHT, LEFT,FRONT, BACK, BOTTOM]
           }
	}
    TRANSLATE = [x,0,0]
}
x = x + 2*boxdims + fuzz

/* TRANSPARENT for ALL_SURFACE_MOLECULES */
case4 BOX
{
   CORNERS = [-boxdims,-boxdims,-boxdims] , [boxdims,boxdims,boxdims]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [TOP] 
                MOLECULE_NUMBER{
                  A' = 100
                  B' = 100
                }
                SURFACE_CLASS = my_surf_4
	     }
           r2{
              ELEMENT_LIST = [RIGHT, LEFT,FRONT, BACK, BOTTOM]
           }
	}
    TRANSLATE = [x,0,0]
}
x = x + 2*boxdims + fuzz

/* REFLECTIVE for ALL_SURFACE_MOLECULES */
case5 BOX
{
   CORNERS = [-boxdims,-boxdims,-boxdims] , [boxdims,boxdims,boxdims]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [TOP] 
                MOLECULE_NUMBER{
                  A' = 100
                  B' = 100
                }
                SURFACE_CLASS = my_surf_5
	     }
           r2{
              ELEMENT_LIST = [RIGHT, LEFT,FRONT, BACK, BOTTOM]
           }
	}
    TRANSLATE = [x,0,0]
}
x = x + 2*boxdims + fuzz

/* ABSORPTIVE for ALL_SURFACE_MOLECULES */
case6 BOX
{
   CORNERS = [-boxdims,-boxdims,-boxdims] , [boxdims,boxdims,boxdims]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [TOP] 
                MOLECULE_NUMBER{
                  A' = 100
                  B' = 100
                }
                SURFACE_CLASS = my_surf_6
	     }
           r2{
              ELEMENT_LIST = [RIGHT, LEFT,FRONT, BACK, BOTTOM]
           }
	}
    TRANSLATE = [x,0,0]
}
x = x + 2*boxdims + fuzz

xright = x + boxdims
PARTITION_X = [[xleft TO xright STEP 0.025]]
PARTITION_Y = [[-boxdims-fuzz TO boxdims+fuzz STEP 0.025]]
PARTITION_Z = [[-boxdims-fuzz TO boxdims+fuzz STEP 0.025]]



INSTANTIATE world OBJECT 
{
   b1 OBJECT case1 {}
   b2 OBJECT case2 {}
   b3 OBJECT case3 {}
   b4 OBJECT case4 {}
   b5 OBJECT case5 {}
   b6 OBJECT case6 {}
}

REACTION_DATA_OUTPUT
{
   STEP = dt
   HEADER = "# "
   {
      COUNT ["A;", world.b1[r1]]: "r1_A",
      COUNT ["B;", world.b1[r1]]: "r1_B",
      COUNT ["A;", world.b1[r2]]: "r2_A",
      COUNT ["B;", world.b1[r2]]: "r2_B"
   }	=> countdir & "transp_all_mols.dat"
   {
      COUNT ["A;", world.b2[r1]]: "r1_A",
      COUNT ["B;", world.b2[r1]]: "r1_B",
      COUNT ["A;", world.b2[r2]]: "r2_A",
      COUNT ["B;", world.b2[r2]]: "r2_B"
   }	=> countdir & "refl_all_mols.dat"
   {
      COUNT ["A;", world.b4[r1]]: "r1_A",
      COUNT ["B;", world.b4[r1]]: "r1_B",
      COUNT ["A;", world.b4[r2]]: "r2_A",
      COUNT ["B;", world.b4[r2]]: "r2_B"
   }	=> countdir & "transp_all_surface_mols.dat"
   {
      COUNT ["A;", world.b5[r1]]: "r1_A",
      COUNT ["B;", world.b5[r1]]: "r1_B",
      COUNT ["A;", world.b5[r2]]: "r2_A",
      COUNT ["B;", world.b5[r2]]: "r2_B"
   }	=> countdir & "refl_all_surface_mols.dat"

}


REACTION_DATA_OUTPUT
{
   TIME_LIST = [9e-5, [9.1e-5 TO 1e-4 STEP 1e-6]]

   HEADER = "# "
   {
      COUNT ["A;", world.b3[r1]]: "r1_A",
      COUNT ["B;", world.b3[r1]]: "r1_B",
      COUNT ["A;", world.b3[r2]]: "r2_A",
      COUNT ["B;", world.b3[r2]]: "r2_B"
   }	=> countdir & "absorb_all_mols.dat"
   {
      COUNT ["A;", world.b6[r1]]: "r1_A",
      COUNT ["B;", world.b6[r1]]: "r1_B",
      COUNT ["A;", world.b6[r2]]: "r2_A",
      COUNT ["B;", world.b6[r2]]: "r2_B"
   }	=> countdir & "absorb_all_surface_mols.dat"

}