mcell/mdl/testsuite/reactions/13-restricted_border_reaction.mdl

/***************************************************************************
* Test-13: Surface reactants cannot search for reaction partners
*          across restrictive region borders.
*
*  If all of the reactants are behind restrictive region border
*  (REFLECTIVE/ABSORPTIVE) the reaction should not happen.
*  Restrictive border is considered "inside-out" when it is
*  e.g. REFLECTIVE relative to the molecule's own region,
*  or "outside-in" when REFLECTIVE to the neighbor region.
*
*  We test here the property that reactant cannot look
*  for potential reaction partners across the restrictive
*  region border.  Static surface molecules occupy all
*  available slots on the meshes.
*
*  Note: all molecule counts except for "box_5.dat" and "box_8.dat"
*        should contain all zeros.
*
* Author: Boris Kaminsky <[email protected]>
* Date: 2011-06-27
*
****************************************************************************/
basename = "13-restricted_border_reaction"
countdir = "dat/" & basename & "/"
dt = 1e-6
TIME_STEP = dt
TIME_STEP_MAX = dt
ITERATIONS = 100 
EFFECTOR_GRID_DENSITY = 10000

VACANCY_SEARCH_DISTANCE = 1

DEFINE_MOLECULES
{
   /* for bimolecular reaction */
   b_A {DIFFUSION_CONSTANT_2D = 0}
   b_B {DIFFUSION_CONSTANT_2D = 0}

   /* for trimolecular reaction */
   t_A {DIFFUSION_CONSTANT_2D = 0}
   t_B {DIFFUSION_CONSTANT_2D = 0}
   t_C {DIFFUSION_CONSTANT_2D = 0}

   /* for products */
   D {DIFFUSION_CONSTANT_2D = 0}
}


DEFINE_SURFACE_CLASSES 
{
  refl_b_A {
     REFLECTIVE = b_A; 
  }
  absorb_b_B {
     ABSORPTIVE = b_B; 
  }
  refl_t_AB {
     REFLECTIVE = t_A; 
     REFLECTIVE = t_B;
  }

}


DEFINE_REACTIONS
{
   b_A; + b_B;  -> D;  [1e2] 
   t_A; + t_B; + t_C; -> D;  [1e-2]
}


/* bimolecular reaction when b_A has restrictive
   region border property "inside_out" */
box_1 BOX
{
   CORNERS = [-0.1,-0.1,-0.1] , [0.1,0.1,0.1]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [RIGHT] 
                      
                MOLECULE_NUMBER{
                  b_A' = 450
                }
                SURFACE_CLASS = refl_b_A 
	     }
	   r2{
		ELEMENT_LIST = [TOP, BOTTOM, LEFT, FRONT, BACK] 
                MOLECULE_NUMBER{
                  b_B' = 2250
                }
	     }
	}
}


/* bimolecular reaction when b_A has restrictive
   region border property "outside_in" */
box_2 BOX
{
   CORNERS = [-0.1,-0.1,-0.1] , [0.1,0.1,0.1]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [RIGHT] 
                      
                MOLECULE_NUMBER{
                  b_A' = 450
                }
	     }
	   r2{
		ELEMENT_LIST = [TOP, BOTTOM, LEFT, FRONT, BACK] 
                MOLECULE_NUMBER{
                  b_B' = 2250
                }
                SURFACE_CLASS = refl_b_A 
	     }
	}
        TRANSLATE = [0.5, 0, 0]
}




/* trimolecular reaction when b_A and b_B have restrictive
   region border property  "inside_out"  */
box_3 BOX
{
   CORNERS = [-0.1,-0.1,-0.1] , [0.1,0.1,0.1]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [RIGHT] 
                      
                MOLECULE_NUMBER{
                  t_A' = 225
                }
                MOLECULE_NUMBER{
                  t_B' = 225
                }

                 SURFACE_CLASS = refl_t_AB
	     }
	   r2{
		ELEMENT_LIST = [TOP, BOTTOM, LEFT, FRONT, BACK] 
                MOLECULE_NUMBER{
                   t_C' = 2250
                }
           }
	}
        TRANSLATE = [1.0, 0, 0]
}

/* trimolecular reaction when b_A and b_B have restrictive
   region border property  "outside_in"  */
box_4 BOX
{
   CORNERS = [-0.1,-0.1,-0.1] , [0.1,0.1,0.1]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [RIGHT] 
                      
                MOLECULE_NUMBER{
                  t_A' = 225
                }
                MOLECULE_NUMBER{
                  t_B' = 225
                }

	     }
	   r2{
		ELEMENT_LIST = [TOP, BOTTOM, LEFT, FRONT, BACK] 
                MOLECULE_NUMBER{
                  t_C' = 2250
                }
                SURFACE_CLASS = refl_t_AB 

	     }
	}
        TRANSLATE = [1.5, 0, 0]
}

/* "box_5" is a copy of "box_1" only
    the restrictive region border is removed */
box_5 BOX
{
   CORNERS = [-0.1,-0.1,-0.1] , [0.1,0.1,0.1]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [RIGHT] 
                      
                MOLECULE_NUMBER{
                  b_A' = 450
                }
	     }
	   r2{
		ELEMENT_LIST = [TOP, BOTTOM, LEFT, FRONT, BACK] 
                MOLECULE_NUMBER{
                  b_B' = 2250
                }
	     }
	}
        TRANSLATE = [2.0, 0, 0]
}



/* bimolecular reaction when b_A has restrictive
   region border property "inside_out". 
   Also there are multiple overlapped regions
 */
box_6 BOX
{
   CORNERS = [-0.1,-0.1,-0.1] , [0.1,0.1,0.1]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [RIGHT] 
                      
                MOLECULE_NUMBER{
                  b_A' = 450
                }
                SURFACE_CLASS = refl_b_A 
	     }
	   r2{
		ELEMENT_LIST = [TOP] 
                MOLECULE_NUMBER{
                  b_B' = 450
                }
	     }
           r3{
		ELEMENT_LIST = [TOP, LEFT, RIGHT] 
             }
           r4{
		ELEMENT_LIST = [TOP] 
             }
           r5{
		ELEMENT_LIST = [RIGHT] 
             }

	}
        TRANSLATE = [2.5, 0, 0]
}

/* bimolecular reaction when b_B has restrictive
   region border property "outside_in". 
   Also there are multiple overlapped regions
 */
box_7 BOX
{
   CORNERS = [-0.1,-0.1,-0.1] , [0.1,0.1,0.1]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [RIGHT] 
                      
                MOLECULE_NUMBER{
                  b_A' = 450
                }
                SURFACE_CLASS = absorb_b_B 
	     }
	   r2{
		ELEMENT_LIST = [TOP] 
                MOLECULE_NUMBER{
                  b_B' = 450
                }
	     }
           r3{
		ELEMENT_LIST = [TOP, RIGHT] 
                SURFACE_CLASS = refl_b_A
             }

	}
        TRANSLATE = [3.0, 0, 0]
}

/* bimolecular reaction when b_A has restrictive
   region border property "inside_out". 
   Also there are overlapped regions and restricted border
   constitutes the outer boundary for both regions.
 */
box_8 BOX
{
   CORNERS = [-0.1,-0.1,-0.1] , [0.1,0.1,0.1]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [RIGHT] 
                      
                MOLECULE_NUMBER{
                  b_A' = 450
                }
	     }
	   r2{
		ELEMENT_LIST = [TOP] 
                MOLECULE_NUMBER{
                  b_B' = 450
                }
	     }
           r3{
		ELEMENT_LIST = [TOP, RIGHT] 
                SURFACE_CLASS = refl_b_A
             }

	}
        TRANSLATE = [3.5, 0, 0]
}

INSTANTIATE world OBJECT 
{
   box_1 OBJECT box_1 {}
   box_2 OBJECT box_2 {}
   box_3 OBJECT box_3 {}
   box_4 OBJECT box_4 {}
   box_5 OBJECT box_5 {}
   box_6 OBJECT box_6 {}
   box_7 OBJECT box_7 {}
   box_8 OBJECT box_8 {}
}

REACTION_DATA_OUTPUT
{
   STEP = dt
   HEADER = "# "
   
                                
   { COUNT [D, world.box_1]: "D"
   }	=> countdir & "box_1.dat"
        

   { COUNT [D, world.box_2]: "D"
   }	=> countdir & "box_2.dat"

   { COUNT [D, world.box_3]: "D"
   }	=> countdir & "box_3.dat"

   { COUNT [D, world.box_4]: "D"
   }	=> countdir & "box_4.dat"
   
   { COUNT [D, world.box_6]: "D"
   }	=> countdir & "box_6.dat"

   { COUNT [D, world.box_7]: "D"
   }	=> countdir & "box_7.dat"
   
}


REACTION_DATA_OUTPUT
{

  ITERATION_LIST = [[90 TO 100 STEP 1]]
   
  { COUNT [D, world.box_5]: "D"
  }	=> countdir & "box_5.dat"

   { COUNT [D, world.box_8]: "D"
   }	=> countdir & "box_8.dat"

}