mcell/mdl/testsuite/regression/22-rx_reflective_surface_bug.mdl

/***************************************************************************
* Test 22: Testing reaction between volume molecule and surface
*          when surface class is declared REFLECTIVE and when it is
*          REFLECTIVE by default.
*
*	Volume molecules A are released inside boxes "box_refl", and B
*       inside  "box_default".
*	Let one box "box_refl" interior be REFLECTIVE through SURFACE_CLASS
*       "my_refl".  Let another box "box_default" also has interior
*       REFLECTIVE but through the SURFACE_CLASS "my_default" (in fact
*       default property).  
*
*       Reflective surfaces we can specify directly through
*       SURFACE_CLASS "my_refl{REFLECTIVE = A}" or indirectly
*       through SURFACE_CLASS "my_default {} " using the fact that 
*       all surfaces by default are REFLECTIVE.
*
*       The bug in the code prevented reaction 
*       of the type vol_mol' @ my_refl; -> ... [rate] to happen, while
*       reaction of the type vol_mol' @ my_default; -> ...[rate]
*       did happened.
*
*       Here we test the bug fix.
*
* Author: Boris Kaminsky <[email protected]>
* Date: 2011-01-14
***************************************************************************/
basename = "22-rx_reflective_surface_bug"
countdir = "dat/" & basename & "/"

dt = 1e-6
TIME_STEP = dt
TIME_STEP_MAX = dt
ITERATIONS = 100   
EFFECTOR_GRID_DENSITY = 10000
boxdims = 0.13

VACANCY_SEARCH_DISTANCE = 1

DEFINE_MOLECULES
{
   A {DIFFUSION_CONSTANT_3D = 2e-7}  
   B {DIFFUSION_CONSTANT_3D = 2e-7}  
   sm_L {DIFFUSION_CONSTANT_2D = 2e-7}  
   sm_M {DIFFUSION_CONSTANT_2D = 2e-7}  
}


DEFINE_SURFACE_CLASSES
{ 
    my_refl {REFLECTIVE = A; }
    my_default { }
}

DEFINE_REACTIONS
{
   A' @ my_refl; -> sm_L'[1e11]
   B' @ my_default; -> sm_M'[1e11]

}



fuzz = 0.01
x = 2*boxdims + fuzz

box_refl BOX
{
   CORNERS = [-boxdims,-boxdims,-boxdims] , [boxdims,boxdims,boxdims]
   DEFINE_SURFACE_REGIONS
   {
      whole_mesh{
	ELEMENT_LIST = [ALL_ELEMENTS] 

        SURFACE_CLASS = my_refl 
      }
   }
}


box_default BOX
{
   CORNERS = [-boxdims,-boxdims,-boxdims] , [boxdims,boxdims,boxdims]
   DEFINE_SURFACE_REGIONS
   {
      whole_mesh{
	ELEMENT_LIST = [ALL_ELEMENTS] 

        SURFACE_CLASS = my_default
      }
   }
  TRANSLATE = [x,0,0]
}



case1 OBJECT
{
  box_refl OBJECT box_refl {}
  box_default OBJECT box_default {}
  A_release RELEASE_SITE {SHAPE = case1.box_refl MOLECULE = A NUMBER_TO_RELEASE = 100}
  B_release RELEASE_SITE {SHAPE = case1.box_default MOLECULE = B NUMBER_TO_RELEASE = 100}
}


xleft = x - boxdims - fuzz
xright = x + boxdims
PARTITION_X = [[xleft TO xright STEP 0.013]]
PARTITION_Y = [[-boxdims-fuzz TO boxdims+fuzz STEP 0.013]]
PARTITION_Z = [[-boxdims-fuzz TO boxdims+fuzz STEP 0.013]]


INSTANTIATE world OBJECT 
{
   b1 OBJECT case1 {}
}


REACTION_DATA_OUTPUT
{
   ITERATION_LIST = [[10 TO 100 STEP 1]]
   HEADER = "# "
   {
     (COUNT [sm_L, WORLD]): "sm_L",
     (COUNT [sm_M, WORLD]): "sm_M"
   } => countdir & "refl.dat"

}