// box_def
box1 BOX
{
    CORNERS = [0, 0, 0], [1, 1, 1]
    ASPECT_RATIO = 6.0
    DEFINE_SURFACE_REGIONS
    {
        r1
        {
            INCLUDE_ELEMENTS = [ LEFT, RIGHT ]
            INCLUDE_PATCH = [ 0.2, 0.2, 1 ], [ 0.4, 0.4, 1]
            SURFACE_CLASS = s_sc_0
            MOLECULE_DENSITY
            {
                s_g_0' = 0.1
                s_g_1, = 0.2
                s_g_2; = 0.1
            }
            MOLECULE_NUMBER
            {
                s_g_3' = 100
                s_g_4, = 200
                s_g_5; = 100
            }
            VIZ_VALUE = 5
        }
        r2
        {
            INCLUDE_ELEMENTS = [ BACK ]
            INCLUDE_REGION = r1
            SURFACE_CLASS = s_sc_1
        }
        r3
        {
            INCLUDE_ELEMENTS = [ 0 TO 5 ]
            EXCLUDE_ELEMENTS = [ 4 ]
            SURFACE_CLASS = s_sc_2
        }
        r4
        {
            INCLUDE_ELEMENTS = [ ALL_ELEMENTS ]
            EXCLUDE_ELEMENTS = [ BACK ]
            SURFACE_CLASS = s_sc_4
        }
        r5
        {
            INCLUDE_ELEMENTS = [ FRONT ]
            INCLUDE_REGION = r1
            EXCLUDE_REGION = r1
            SURFACE_CLASS = s_sc_1
        }
    }
    TRANSLATE = [0.1, 0.1, 2.1]
    SCALE = [0.75, 0.75, 0.75]
    ROTATE = [0.1, 0.2, 0.3], 37
}

box2 BOX
{
    CORNERS = [2, 0, 0], [3, 1, 1]
    ASPECT_RATIO = 2.0
    REMOVE_ELEMENTS
    {
        TOP, BOTTOM, FRONT, BACK, LEFT
    }
    DEFINE_SURFACE_REGIONS
    {
        r5
        {
            INCLUDE_PATCH = [ 3, 0.35, 0.35], [ 3, 0.65, 0.65]
            SURFACE_CLASS = s_sc_3
        }
    }
}

box3 BOX
{
    CORNERS = [-2, 0, 0], [-1, 1, 1]
    ASPECT_RATIO = 5.0  
    DEFINE_SURFACE_REGIONS
    {
        r1
        {
            INCLUDE_ELEMENTS = [ LEFT, RIGHT ]
            /* INCLUDE_PATCH = [-1.4, 0.2, 1 ], [-1.2, 0.4, 1] */
            SURFACE_CLASS = m_sc_0
        }
        r2
        {
            INCLUDE_ELEMENTS = [ BACK ]
            INCLUDE_REGION = r1
            SURFACE_CLASS = m_sc_1
        }
        r3
        {
            INCLUDE_ELEMENTS = [ 0 TO 5 ]
            EXCLUDE_ELEMENTS = [ 4 ]
            SURFACE_CLASS = m_sc_2
        }
        r4
        {
            INCLUDE_ELEMENTS = [ ALL_ELEMENTS ]
            EXCLUDE_ELEMENTS = [ BACK ]
            SURFACE_CLASS = m_sc_3
        }
        r5
        {
            INCLUDE_ELEMENTS = [ ALL_ELEMENTS ]
            EXCLUDE_PATCH = [ -2,0.25,1], [-1,0.75,1] 
            SURFACE_CLASS = m_sc_3
        }
    }
}

// polygon_list_def

poly1 POLYGON_LIST
{
    VERTEX_LIST
    {
        [5, 5, 5] 
        [5, 7, 5] 
        [5, 5, 7] 
        [7, 5, 5] 
    }
    ELEMENT_CONNECTIONS
    {
        [0, 1, 2]
        [1, 0, 3]
        [2, 1, 3]
        [0, 2, 3]
    }
}

poly2 POLYGON_LIST
{
    VERTEX_LIST
    {
        [15, 15, 15]
        [15, 17, 15]
        [15, 15, 17]
        [17, 15, 15]
    }
    ELEMENT_CONNECTIONS
    {
        [0, 1, 2]
        [1, 0, 3]
        [2, 1, 3]
        [0, 2, 3]
    }
    REMOVE_ELEMENTS { 1 }
    DEFINE_SURFACE_REGIONS
    {
      r1
      {
        INCLUDE_ELEMENTS = [ ALL_ELEMENTS ]
      }
    }
}

// voxel_list_def
vox1 VOXEL_LIST
{
    VERTEX_LIST
    {
        [15, 15, 15]        // 000
        [15, 17, 15]        // 001
        [15, 17, 15]        // 010
        [15, 17, 17]        // 011
        [17, 15, 15]        // 100
        [17, 17, 15]        // 101
        [17, 17, 15]        // 110
        [17, 17, 17]        // 111
    }
    TET_ELEMENT_CONNECTIONS
    {
        [0, 1, 2, 4]
        [7, 6, 5, 3]
    }
    TRANSLATE = [-1, -1, -1]
    SCALE = [0.5, 0.5, 0.5]
}

radius = 0.25
diameter = [0.4, 0.5, 0.6]

// release_site_def
rs1 RELEASE_SITE
{
    SHAPE = SPHERICAL
    LOCATION = [0.1, 0.1, 0.1]
    MOLECULE = s_v_0
    NUMBER_TO_RELEASE = 1000
    SITE_RADIUS = radius
    RELEASE_PROBABILITY = 1.0
}

rs2 RELEASE_SITE
{
    SHAPE = CUBIC
    LOCATION = [1.1, 0.1, 0.1]
    MOLECULE = s_v_1
    GAUSSIAN_RELEASE_NUMBER { MEAN_NUMBER = 1000 }
    SITE_DIAMETER = 0.5
    RELEASE_PROBABILITY = 0.99
}

rs3 RELEASE_SITE
{
    SHAPE = ELLIPTIC
    LOCATION = [2.1, 0.1, 0.1]
    MOLECULE = s_v_2
    CONCENTRATION = 1. / 25225.5
    SITE_DIAMETER = [0.2, 0.5, 0.8]
    RELEASE_PROBABILITY = 0.98
}

rs4 RELEASE_SITE
{
    SHAPE = RECTANGULAR
    LOCATION = [3.1, 0.1, 0.1]
    MOLECULE = s_v_3
    VOLUME_DEPENDENT_RELEASE_NUMBER { MEAN_DIAMETER = 0.01 STANDARD_DEVIATION = 0.0005 CONCENTRATION = 1. / .26 }
    SITE_DIAMETER = diameter
    RELEASE_PROBABILITY = 0.97
}

rs5 RELEASE_SITE
{
    SHAPE = SPHERICAL_SHELL
    LOCATION = [4.1, 0.1, 0.1]
    MOLECULE = s_v_4
    GAUSSIAN_RELEASE_NUMBER { MEAN_NUMBER = 1000 STANDARD_DEVIATION = 50 }
    SITE_DIAMETER = [0.1, 0.5, 0.9]
    RELEASE_PROBABILITY = 0.96
}

rs6 RELEASE_SITE
{
    SHAPE = LIST
    LOCATION = [5.1, 0.1, 0.1]
    MOLECULE = s_v_5
    SITE_DIAMETER = 0.5
    RELEASE_PROBABILITY = 0.95
    MOLECULE_POSITIONS
    {
        s_v_5 [5.1, 0.1, 0.1]
        s_v_5 [5.2, 0.1, 0.1]
        s_v_5 [5.1, 0.2, 0.1]
        s_v_5 [5.1, 0.1, 0.2]
    }
    MOLECULE_POSITIONS
    {
        s_v_5 [5.1, 0.2, 0.2]
        s_v_5 [5.2, 0.1, 0.2]
        s_v_5 [5.2, 0.2, 0.1]
    }
    MOLECULE_POSITIONS
    {
        s_v_5 [5.2, 0.2, 0.2]
    }
    TRANSLATE = [0, 0, -2]
}

rs6_2 RELEASE_SITE
{
    SHAPE = LIST
    SITE_DIAMETER = 0.5
    RELEASE_PROBABILITY = 0.95
    MOLECULE_POSITIONS
    {
        s_v_5 [5.3, 0.2, 0.2]
    }
    TRANSLATE = [0, 0, -2]
}

/*
rs7 RELEASE_SITE
{
    SHAPE = existing_object
    LOCATION = [6.1, 0.1, 0.1]
    MOLECULE = s_v_6
    SITE_DIAMETER = 0.5
    RELEASE_PROBABILITY = 0.94
    RELEASE_PATTERN = rp9
}

rs8 RELEASE_SITE
{
    SHAPE = release_region_expr
    LOCATION = [7.1, 0.1, 0.1]
    MOLECULE = s_v_7
    SITE_DIAMETER = 0.5
    RELEASE_PROBABILITY = 0.93
    RELEASE_PATTERN = rp9
}
*/

rs9 SPHERICAL_RELEASE_SITE
{
    LOCATION = [0.1, 3.1, 9.1]
    MOLECULE = s_v_0
    NUMBER_TO_RELEASE = 1000
    SITE_RADIUS = 0.25
    RELEASE_PROBABILITY = 1.0
}

rs10 CUBIC_RELEASE_SITE
{
    LOCATION = [1.1, 3.1, 9.1]
    MOLECULE = s_v_1
    GAUSSIAN_RELEASE_NUMBER { MEAN_NUMBER = 1000 }
    SITE_DIAMETER = 0.5
    RELEASE_PROBABILITY = 0.99
    TRANSLATE = [1, 1, 1]
}

rs11 ELLIPTIC_RELEASE_SITE
{
    LOCATION = [2.1, 3.1, 9.1]
    MOLECULE = s_v_2
    CONCENTRATION = 1. / 25225.5
    SITE_DIAMETER = [0.2, 0.5, 0.8]
    RELEASE_PROBABILITY = 0.98
}

rs12 RECTANGULAR_RELEASE_SITE
{
    LOCATION = [3.1, 3.1, 9.1]
    MOLECULE = s_v_3
    VOLUME_DEPENDENT_RELEASE_NUMBER { MEAN_DIAMETER = 0.01 STANDARD_DEVIATION = 0.0005 CONCENTRATION = 1. / .26 }
    SITE_DIAMETER = [0.4, 0.5, 0.6]
    RELEASE_PROBABILITY = 0.97
}

rs13 SPHERICAL_SHELL_SITE
{
    LOCATION = [4.1, 3.1, 9.1]
    MOLECULE = s_v_4
    GAUSSIAN_RELEASE_NUMBER { MEAN_NUMBER = 1000 STANDARD_DEVIATION = 50 }
    SITE_DIAMETER = [0.1, 0.5, 0.9]
    RELEASE_PROBABILITY = 0.96
}

// meta_object_def
big_object OBJECT
{
    box1  OBJECT box1  { }  
    box2  OBJECT box2  { } 
    box3  OBJECT box3  { } 
    poly1 OBJECT poly1 { } 
    poly2 OBJECT poly2 { } 

    newbox BOX
    {
        CORNERS = [-20, -20, -20], [20, 20, 20]
        ROTATE = [0, 0, 1], 10
    }

    all_release_sites OBJECT
    {
        rs1  OBJECT rs1  { }
        rs2  OBJECT rs2  { }
        rs3  OBJECT rs3  { }
        rs4  OBJECT rs4  { }
        rs5  OBJECT rs5  { }
        rs6  OBJECT rs6  { }
    /*
        rs7  OBJECT rs7  { }
        rs8  OBJECT rs8  { }
     */
        rs9  OBJECT rs9  { }
        rs10 OBJECT rs10 { }
        rs11 OBJECT rs11 { }
        rs12 OBJECT rs12 { }
        rs13 OBJECT rs13 { }
    }
}