/****************************************************************************
 * Regression test 05: When a surface molecule undergoes a reaction to become a
 *       volume molecule, orientation must be respected.
 *
 *       Failure: as g decreases, mi increases faster than m
 *
 *       Success: at all times m == mi
 *                at all times m + g == 1000
 *
 * Author: Jed Wing <jed@salk.edu>
 * Date:   2008-09-10
 ****************************************************************************/

ITERATIONS=5000
TIME_STEP=1e-6
EFFECTOR_GRID_DENSITY=15000

DEFINE_MOLECULES
{
  g { DIFFUSION_CONSTANT_2D = 0 }
  m { DIFFUSION_CONSTANT_3D = 2e-6 }
}

DEFINE_REACTIONS
{
  g' -> m'      [1e3]
}

INSTANTIATE world OBJECT
{
  box BOX
  {
    CORNERS = [-1, -1, -1], [1, 1, 1]
    DEFINE_SURFACE_REGIONS
    {
      all {
        INCLUDE_ELEMENTS = [ ALL_ELEMENTS ]
        MOLECULE_NUMBER
        {
          g, = 1000
        }
      }
    }
  }
}

REACTION_DATA_OUTPUT
{
  OUTPUT_BUFFER_SIZE = 100
  STEP = 1e-4
  HEADER = "# "
  {
    COUNT[g, WORLD]     : "g",
    COUNT[m, WORLD]     : "m",
    COUNT[m, world.box] : "mi"
  } => "molecules.txt"
}

VIZ_OUTPUT
{
  MODE = DREAMM_V3_GROUPED
  FILENAME = "viz_dat/world"
  MOLECULES
  {
    NAME_LIST { ALL_MOLECULES }
    TIME_POINTS
    {
      ALL_DATA     @ [[0 TO 0.1 STEP 1e-4]]
    }
  }
  MESHES
  {
    NAME_LIST { ALL_MESHES }
    TIME_POINTS
    {
      ALL_DATA @ [0]
    }
  }
}