/****************************************************************************
 * Regression test 03: When two surfaces coincide and one of them is
 *       transparent, odd things happen.  Counting, for one, can become
 *       confused.  Essentially, the transparent surface may be re-collided in
 *       certain cases.
 *
 *       Failure: counts go negative, or extremely positive
 *                total count of cannonballs != 500
 *
 *       Success: for entire run, count 122L+122R == 122 == 500  AND
 *                for entire run, count r122L+r122R == r122 == 500
 *
 * Author: Jed Wing <jed@salk.edu>
 * Date:   2008-09-05
 * Note: As of 05/23/2011 we disallow overlapped walls, so the coodinates
 *       of box122R are slightly shifted.
 *       Modified by Boris Kaminsky
 *       Date: 2011-05-23
 ****************************************************************************/

EFFECTOR_GRID_DENSITY = 30000
ITERATIONS = 10000
TIME_STEP = 1e-6

kfwd    = 5e6
kreset  = 1e3
eps     = 0.001
reforient = 1
EPS_C = 1e-12

NOTIFICATIONS
{
  RELEASE_EVENT_REPORT = ON
}

PARTITION_X = [[-2 TO 2 STEP 0.08]]
PARTITION_Y = [[-2 TO 2 STEP 0.08]]
PARTITION_Z = [[-2 TO 2 STEP 0.08]]

DEFINE_MOLECULES
{
  cannonball { DIFFUSION_CONSTANT_3D = 4e-6 }
  tissue26   { DIFFUSION_CONSTANT_2D = 0 }
  kerchief26 { DIFFUSION_CONSTANT_2D = 0 }
  llabnonnac { DIFFUSION_CONSTANT_3D = 4e-6 }
  eussit26   { DIFFUSION_CONSTANT_2D = 0 }
  feihcrek26 { DIFFUSION_CONSTANT_2D = 0 }
}

DEFINE_REACTIONS
{
  cannonball,, + tissue26,  -> cannonball'' + kerchief26,   [kfwd] : reac_26  kerchief26' -> tissue26' [kreset]     // INVALID
  llabnonnac,, + eussit26,  -> llabnonnac'' + feihcrek26,   [kfwd] : caer_26  feihcrek26' -> eussit26' [kreset]     // INVALID
}

p122a = [-0.2, -0.2, -0.2]
p122b = [ 0.0,  0.2,  0.2]
p122c = [ 0.0 + 2*EPS_C, -0.2, -0.2]
p122d = [ 0.2 + 2*EPS_C,  0.2,  0.2]

/* p122c = [ 0.0, -0.2, -0.2]
p122d = [ 0.2,  0.2,  0.2] */

boxes_reduced OBJECT
{
  box122L BOX { CORNERS = p122a, p122b DEFINE_SURFACE_REGIONS { r { INCLUDE_ELEMENTS = [RIGHT] } } }
  box122R BOX { CORNERS = p122c, p122d DEFINE_SURFACE_REGIONS { l { INCLUDE_ELEMENTS = [LEFT] } } }
}

INSTANTIATE world OBJECT
{
  boxes OBJECT boxes_reduced { }

  rscb26 RELEASE_SITE { SHAPE = SPHERICAL SITE_RADIUS = 0 MOLECULE = cannonball NUMBER_TO_RELEASE = 500 LOCATION = [- eps, 0, 0] }
  rsbc26 RELEASE_SITE { SHAPE = SPHERICAL SITE_RADIUS = 0 MOLECULE = llabnonnac NUMBER_TO_RELEASE = 500 LOCATION = [- eps, 0, 0] }
  rs_t26 RELEASE_SITE { SHAPE = world.boxes.box122L[r]  MOLECULE = tissue26{-reforient}  NUMBER_TO_RELEASE = 500 }
  rs_e26 RELEASE_SITE { SHAPE = world.boxes.box122R[l]  MOLECULE = eussit26{-reforient}  NUMBER_TO_RELEASE = 500 }
}

DEFINE_SURFACE_CLASS trans_cannon { TRANSPARENT = cannonball }
DEFINE_SURFACE_CLASS trans_nonnac { TRANSPARENT = llabnonnac }

MODIFY_SURFACE_REGIONS {
  world.boxes.box122R[l] { SURFACE_CLASS = trans_cannon }
  world.boxes.box122L[r] { SURFACE_CLASS = trans_nonnac }
}

REACTION_DATA_OUTPUT
{
  OUTPUT_BUFFER_SIZE = 1000
  STEP = 1e-6
  HEADER = "# "
  {
    COUNT[cannonball, world.boxes.box122L] : "122L",
    COUNT[cannonball, world.boxes.box122R] : "122R",
    COUNT[cannonball, world.boxes.box122L] + COUNT[cannonball, world.boxes.box122R] : "122",
    COUNT[llabnonnac, world.boxes.box122L] : "r122L",
    COUNT[llabnonnac, world.boxes.box122R] : "r122R",
    COUNT[llabnonnac, world.boxes.box122L] + COUNT[llabnonnac, world.boxes.box122R] : "r122"
  } => "cannonballs.txt"
}

/*
VIZ_OUTPUT
{
  MODE = DREAMM_V3_GROUPED
   FILENAME = "world"
   MOLECULES
   {
     NAME_LIST { ALL_MOLECULES }
     TIME_POINTS { ALL_DATA @ [[0 TO 1e-3 STEP 1e-5]] }
   }
  MESHES
  {
    NAME_LIST { ALL_MESHES }
    TIME_POINTS { ALL_DATA @ [0] }
  }
}
*/