/* This example demonstrates the creation of a release site    */
/* that fills an unusual geometry at a specified concentration */

time_step = 1.0e-6
total_time = 1.0e-3

TIME_STEP = time_step
ITERATIONS = total_time/time_step
EFFECTOR_GRID_DENSITY = 10000
INTERACTION_RADIUS = 0.005


PARTITION_X = [ [-0.15 TO 0.15 STEP 0.03] ]
PARTITION_Y = [ [-0.15 TO 0.15 STEP 0.03] ]
PARTITION_Z = [ [-0.15 TO 0.15 STEP 0.03] ]


DEFINE_MOLECULES
{
  A { D_3D = 100e-8 }
  B { D_3D = 100e-8 }
  C { D_3D = 100e-8 }
  D { D_2D = 0 }
}

/* Your basic reversable binding reaction */
DEFINE_REACTIONS
{
  A + B -> C [1e7]
  C -> A + B [1e2]
}

/* Create geometry with release site in here */
bag OBJECT
{
  small_box BOX
  {
    CORNERS = [-0.1,-0.1,-0.1] , [0.1,0.1,0.1]
    ASPECT_RATIO = 3
    DEFINE_SURFACE_REGIONS
    {
      silly { INCLUDE_ELEMENTS = [TOP,LEFT] }
      solly { INCLUDE_ELEMENTS = [TOP,RIGHT] }
    }
  }

  bad_box BOX
  {
    CORNERS = [-0.05,-0.05,-0.2] , [0.05,0.05,0.2]
  }

  surf_release RELEASE_SITE { SHAPE=bag.small_box[silly]*bag.small_box[solly] MOLECULE=D NUMBER_TO_RELEASE=150 }
  vol_release RELEASE_SITE { SHAPE=bag.small_box[ALL]-bag.bad_box[ALL] MOLECULE=A CONCENTRATION=1e-4 }
}


/* 481.76 molecules/volume = 100uM */
INSTANTIATE my_world OBJECT
{
  my_bag OBJECT bag {}
  B_release RELEASE_SITE { SHAPE=CUBIC LOCATION=[0,0,0] MOLECULE=B CONCENTRATION=1e-4 SITE_DIAMETER=0.19999 }
  C_release RELEASE_SITE { SHAPE=CUBIC LOCATION=[0,0,0] MOLECULE=C NUMBER_TO_RELEASE=482 SITE_DIAMETER=0.1999 }  
}  


/* This just dumps molecule positions in text as state_value X Y Z orient */
VIZ_DATA_OUTPUT
{
  MODE=ASCII
  MOLECULE_FILE_PREFIX = "box"
  STATE_VALUES {
    A = 1
    B = 2
    C = 3
    D = 4
  }
  ITERATION_LIST = [0e0,1e0,1e1,1e2,1e3]
}
  

REACTION_DATA_OUTPUT
{
  STEP = 1e-5
  { COUNT [A,WORLD] } => "count_A.dat"
  { COUNT [B,WORLD] } => "count_B.dat"
  { COUNT [C,WORLD] } => "count_C.dat"
  { COUNT [D,WORLD] } => "count_D.dat"
}