mcell/mdl/testsuite/regression/28-unimolecular_reaction_after_chkpt.mdl

/****************************************************************************
* Regression test 28: The results of unimolecular reaction with variable 
*                     rection rate were incorrect due to the bug.
*
*  This is a bug encountered by Jun Ma.  It represents itself as molecule's
*  negative lifetime. It happened under two simultaneous conditions:
*  checkpointing and unimolecular reactions with variable rates.
*  It appeared that variable rates files were not properly read and
*  and molecule's scheduling times were not properly set up.
*  For this test file the bug showed up as number of molecules B
*  equal to 10 right after checkpoint.
*
*  Failure: final number of molecules B is 10
*  Success: final number of molecules B is less than 10
*
****************************************************************************/
dt = 1e-6
TIME_STEP = dt
TIME_STEP_MAX = 1000
ITERATIONS = 10
EFFECTOR_GRID_DENSITY = 10000
 
CHECKPOINT_INFILE = "chkpt.tmp"
CHECKPOINT_ITERATIONS = 5
CHECKPOINT_OUTFILE = "chkpt.tmp"

DEFINE_MOLECULES
{
   A {DIFFUSION_CONSTANT_2D = 0}
   B {DIFFUSION_CONSTANT_2D = 0}
}


DEFINE_REACTIONS
{
   A; -> B; ["28-A_B_rates.txt"] 
}

box BOX
{
   CORNERS = [-1,-1,-1] , [1,1,1]
   DEFINE_SURFACE_REGIONS
	{
	   r1{
		ELEMENT_LIST = [TOP,BOTTOM,LEFT,RIGHT,FRONT,BACK]
                MOLECULE_NUMBER{A' = 10}
	     }
	}
}

INSTANTIATE world OBJECT 
{
   box OBJECT box {}
}


REACTION_DATA_OUTPUT
{
   STEP = dt
   {COUNT [B, WORLD]} => "B_World.dat"
}