/****************************************************************************
 * Regression test 12: MCell fails to count oriented surface molecule reaction
 *    products in a simulation which has no waypoints.  This is a modified
 *    version of the test case Boris sent when he reported the bug.
 *
 *    Failure: Any of the first 7 columns in the count differ at any time
 *             Any of the next 14 columns in the count differ at any time
 *             Any of the last 12 columns are non-zero at any time
 *             The first and 8th column ever sum to anything other than 500
 *             The first column does not eventually decrease from 500
 *    Success: Run completes successfully, counts do not trigger the
 *             above failure criteria.
 *
 * Author: Jed Wing <jed@salk.edu>
 * Date:   2009-03-28
 ****************************************************************************/

dt = 1e-6
iterations = 100
TIME_STEP = dt
TIME_STEP_MAX = dt
ITERATIONS = iterations
EFFECTOR_GRID_DENSITY = 10000 
INTERACTION_RADIUS = 0.003 

ACCURATE_3D_REACTIONS =  FALSE

VACANCY_SEARCH_DISTANCE = 1

DEFINE_MOLECULES
{
   A {DIFFUSION_CONSTANT_2D = 2e-3}
   B {DIFFUSION_CONSTANT_2D = 2e-3}
   C {DIFFUSION_CONSTANT_2D = 2e-3}
}

DEFINE_REACTIONS
{
    A' -> B' + C' [0.015e5]:rxn
} 

triangle POLYGON_LIST
{
   VERTEX_LIST
   {
     [0,0,0]
     [1.0,0,0]
     [0.5,0.866,0]
   }
   ELEMENT_CONNECTIONS
   {
     [0,1,2]
   }
   DEFINE_SURFACE_REGIONS
   {
      r1{
	   ELEMENT_LIST = [0] 
                                                                         
           MOLECULE_NUMBER{ 
                A' = 500  
           }
                      
       }
    }
}

INSTANTIATE test OBJECT 
{
     my_triangle OBJECT triangle {}
}

REACTION_DATA_OUTPUT
{
     STEP = dt 
     HEADER = OFF
                
        /* this COUNT statements works */ 
     {
        COUNT [A,     WORLD],
        COUNT [A{1},  test.my_triangle[r1]],
        COUNT [A{2},  test.my_triangle[r1]],
        COUNT ["A'",  test.my_triangle[r1]],
        COUNT ["A''", test.my_triangle[r1]],
        COUNT ["A',", test.my_triangle[r1]],
        COUNT ["A;",  test.my_triangle[r1]],

        COUNT [B,     WORLD],
        COUNT [B{1},  test.my_triangle[r1]],
        COUNT [B{2},  test.my_triangle[r1]],
        COUNT ["B'",  test.my_triangle[r1]],
        COUNT ["B''", test.my_triangle[r1]],
        COUNT ["B',", test.my_triangle[r1]],
        COUNT ["B;",  test.my_triangle[r1]],

        COUNT [C,     WORLD],
        COUNT [C{1},  test.my_triangle[r1]],
        COUNT [C{2},  test.my_triangle[r1]],
        COUNT ["C'",  test.my_triangle[r1]],
        COUNT ["C''", test.my_triangle[r1]],
        COUNT ["C',", test.my_triangle[r1]],
        COUNT ["C;",  test.my_triangle[r1]],

        COUNT [A{-1}, test.my_triangle[r1]],
        COUNT [B{-1}, test.my_triangle[r1]],
        COUNT [C{-1}, test.my_triangle[r1]],
        COUNT [A{-2}, test.my_triangle[r1]],
        COUNT [B{-2}, test.my_triangle[r1]],
        COUNT [C{-2}, test.my_triangle[r1]],
        COUNT ["A,", test.my_triangle[r1]],
        COUNT ["B,", test.my_triangle[r1]],
        COUNT ["C,", test.my_triangle[r1]],
        COUNT ["A,,", test.my_triangle[r1]],
        COUNT ["B,,", test.my_triangle[r1]],
        COUNT ["C,,", test.my_triangle[r1]]
     } => "counts.txt" 
}