TIME_STEP = 1e-6
TIME_STEP_MAX = 1.1e-6
ITERATIONS = 1000
EFFECTOR_GRID_DENSITY = 10000

PARTITION_X = [0.99,1.01,1.99,2.01]
PARTITION_Y = [0.99,1.01,1.99,2.01]
PARTITION_Z = [0.99,1.01,1.99,2.01]

DEFINE_MOLECULES {
  A { DIFFUSION_CONSTANT_3D = 2e-6 }
  B { DIFFUSION_CONSTANT_2D = 0 }
  C { DIFFUSION_CONSTANT_2D = 0 }
  B.A { DIFFUSION_CONSTANT_2D = 0 }
  C.A { DIFFUSION_CONSTANT_2D = 0 }
}

DEFINE_SURFACE_CLASSES {
  transp {
    TRANSPARENT = A
  }
}


DEFINE_REACTIONS {
  A' + B, -> B.A, [2e7]
  A' + C, -> C.A' [2e7]
  B.A, -> B, + A' [1e2]
  C.A' -> C + A' [1e2]
}

A_site CUBIC_RELEASE_SITE {
  LOCATION = [1.5,1.5,1.5]
  MOLECULE = A
  NUMBER_TO_RELEASE = 1000
  SITE_DIAMETER = 0.00001
}

box BOX {
  CORNERS = [1,1,1] , [2,2,2]
  DEFINE_SURFACE_REGIONS {
    r1 {
      ELEMENT_LIST = [TOP,BOTTOM,LEFT,RIGHT,FRONT,BACK]
      MOLECULE_DENSITY { B' = 0 }
    }
  }
}

not_box BOX {
  CORNERS = [1.3,1.3,1.3] , [1.7,1.7,1.7]
  DEFINE_SURFACE_REGIONS {
    r1 {
      ELEMENT_LIST = [ALL_ELEMENTS]
      SURFACE_CLASS = transp
      MOLECULE_DENSITY { C' = 100 }
    }
  }
}

small_box BOX {
  CORNERS = [1.3,1.3,1.3] , [1.7,1.7,1.7]
  DEFINE_SURFACE_REGIONS {
    r1 {
      ELEMENT_LIST = [ALL_ELEMENTS]
      MOLECULE_DENSITY { B' = 100 }
    }
  }
}

INSTANTIATE world OBJECT {
  release_site OBJECT A_site {}
  effectors OBJECT box {}
  container OBJECT small_box {}
  imaginary OBJECT not_box {} 
}