mcell/mdl/validate/volume_output_2.mdl

iterations = 10000
timestep = 1e-6
boxdims = 1.0 
voldiffconst = 1e-6
numtorelease = 1000

ITERATIONS = iterations
TIME_STEP = timestep

PARTITION_X = [[-5.2 TO 5.2 STEP .1]] 
PARTITION_Y = [[-5.2 TO 5.2 STEP .1]]
PARTITION_Z = [[-5.2 TO 5.2 STEP .1]]

DEFINE_MOLECULES
{
    D {DIFFUSION_CONSTANT_3D = voldiffconst}  
    E {DIFFUSION_CONSTANT_3D = voldiffconst} 
    F {DIFFUSION_CONSTANT_3D = voldiffconst} 
}

DEFINE_REACTIONS
{
    D + E -> F [2e8]
}

DEFINE_RELEASE_PATTERN release_pattern_1 {
    DELAY = 0.0
    RELEASE_INTERVAL = 3 * timestep
    TRAIN_INTERVAL = 1 * timestep
    TRAIN_DURATION = 1 * timestep
    NUMBER_OF_TRAINS = 1
}

all_release_sites OBJECT {
    release_site_1 SPHERICAL_RELEASE_SITE {
        LOCATION = [-0.8*boxdims, -0.8*boxdims, -0.8*boxdims]
        MOLECULE = D
        NUMBER_TO_RELEASE = 1000
        SITE_DIAMETER = 0
        RELEASE_PATTERN = release_pattern_1
    }

    release_site_2 SPHERICAL_RELEASE_SITE {
        LOCATION = [0.8*boxdims, 0.8*boxdims, 0.8*boxdims]
        MOLECULE = E
        NUMBER_TO_RELEASE = 1000
        SITE_DIAMETER = 0
        RELEASE_PATTERN = release_pattern_1
    }
}

main_box BOX 
{
    CORNERS = [-boxdims, -boxdims, -boxdims], [boxdims, boxdims, boxdims]
}

outer_box BOX
{
    CORNERS = [-4,-4,-4], [4,4,4] 
}

INSTANTIATE world OBJECT 
{
    main_box OBJECT main_box {} 
    outer_box OBJECT outer_box{}  
    release_sites OBJECT all_release_sites { }
}

VOLUME_DATA_OUTPUT
{
    FILENAME_PREFIX = "volume_output/d_loc"
    MOLECULES = D
    LOCATION = [-boxdims, -boxdims, -boxdims]
    VOXEL_SIZE = [boxdims/5, boxdims/5, boxdims/5]
    VOXEL_COUNT = [10, 10, 10]
    STEP = 500*timestep
}

VOLUME_DATA_OUTPUT
{
    FILENAME_PREFIX = "volume_output/e_loc"
    MOLECULES = E
    LOCATION = [-boxdims, -boxdims, -boxdims]
    VOXEL_SIZE = [boxdims/5, boxdims/5, boxdims/5]
    VOXEL_COUNT = [10, 10, 10]
    STEP = 500*timestep
}

VOLUME_DATA_OUTPUT
{
    FILENAME_PREFIX = "volume_output/f_loc"
    MOLECULES = F
    LOCATION = [-boxdims, -boxdims, -boxdims]
    VOXEL_SIZE = [boxdims/5, boxdims/5, boxdims/5]
    VOXEL_COUNT = [10, 10, 10]
    STEP = 500*timestep
}