mcell/mdl/testsuite/parser/01-kitchen_sink_viz_everything.mdl

/****************************************************************************
 * Test 01: Nearly every parser option.
 *
 *    A mostly non-sensical test which simply exercises the parser checking for
 *    anomalous behavior.  This test should not provoke any errors, provided
 *    that counting-5.txt does not exist in its reaction output directory.
 *    (This is to test the "no overwrite" output mode for counting.)
 *
 *    This variant produces most types of VIZ output using most of the
 *    different available notations.
 *
 * Author: Jed Wing <[email protected]>
 * Date:   2008-04-04
 ****************************************************************************/

basename = "01-kitchen_sink_viz_everything"
INCLUDE_FILE = "defaults.mdl"
i_notify     = "valid/notifications_off.mdl"
INCLUDE_FILE = "common.mdl"
NOTIFICATIONS {
    VOLUME_OUTPUT_REPORT            = OFF
    REACTION_OUTPUT_REPORT          = OFF
    VIZ_OUTPUT_REPORT               = OFF
    FILE_OUTPUT_REPORT              = OFF
    MOLECULE_COLLISION_REPORT       = OFF
}

/* 01. ASCII-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/01 - ASCII old/"
VIZ_DATA_OUTPUT
{
    MODE = ASCII
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    ITERATION_FRAME_DATA
    {
        ALL_DATA           = [1]
        EFFECTOR_POSITIONS = [[1 TO 100 STEP 10], 102, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        EFFECTOR_STATES    = [[1 TO 100 STEP 10], 103, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        MOLECULE_POSITIONS = [[1 TO 100 STEP 10], 104, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        MOLECULE_STATES    = [11, 105]
    }
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 02. ASCII-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/02 - ASCII old/"
VIZ_DATA_OUTPUT
{
    MODE = ASCII
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    ITERATION_LIST = [[1 TO 100 STEP 10], [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 03. ASCII-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/03 - ASCII old/"
VIZ_DATA_OUTPUT
{
    MODE = ASCII
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    TIME_LIST = [[1e-6 TO 1e-4 STEP 1e-5], [1.01e-4 TO 1e-3 STEP 1e-4], [1.001e-3 TO 1e-2 STEP 1e-3]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 04. ASCII-mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/04 - ASCII new/"
VIZ_OUTPUT
{
    MODE = ASCII
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        ITERATION_NUMBERS
        {
            ALL_DATA     @ [2, 3]
            POSITIONS    @ [[0 TO 100 STEP 10]]
        }
    }
}

/* 05. ASCII-mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/05 - ASCII new/"
VIZ_OUTPUT
{
    MODE = ASCII
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        TIME_POINTS
        {
            ALL_DATA     @ [2e-6, 3e-6]
            POSITIONS    @ [[0 TO 1e-4 STEP 1e-5]]
        }
    }
}

/* 11. RK-mode viz output, VIZ_DATA_OUTPUT notation [secretly ASCII] */
thisvizdir = vizdir & "/11 - RK old ASCII/"
VIZ_DATA_OUTPUT
{
    MODE = CUSTOM_RK
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    ITERATION_LIST = [[1 TO 100 STEP 10], [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 12. RK-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/12 - RK old/"
VIZ_DATA_OUTPUT
{
    MODE = CUSTOM_RK [[-10 TO 10 STEP 0.5]] [1, 0.8, 0.6]
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    ITERATION_LIST = [[1 TO 100 STEP 10], [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 13. RK-mode viz output, VIZ_OUTPUT notation [secretly ASCI] */
thisvizdir = vizdir & "/13 - RK new ASCII/"
VIZ_OUTPUT
{
    MODE = CUSTOM_RK
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        ITERATION_NUMBERS
        {
            ALL_DATA     @ [2, 3]
            POSITIONS    @ [[0 TO 100 STEP 10]]
        }
    }
}

/* 14. RK-mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/14 - RK new/"
VIZ_OUTPUT
{
    MODE = CUSTOM_RK [[-10 TO 10 STEP 0.5]] [1, 0.8, 0.6]
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        TIME_POINTS
        {
            ALL_DATA     @ [2e-6, 3e-6]
            POSITIONS    @ [[0 TO 1e-4 STEP 1e-5]]
        }
    }
}

/* 21. DX-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/21 - DX old/"
VIZ_DATA_OUTPUT
{
    MODE = DX
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    OBJECT_FILE_PREFIXES
    {
        world  = thisvizdir & "objects_a"
        world2 = thisvizdir & "objects_b"
        world.big_object = thisvizdir & "objects_c"
    }
    ITERATION_FRAME_DATA
    {
        EFFECTOR_POSITIONS = [[1 TO 100 STEP 10], 111, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        EFFECTOR_STATES    = [1, [2 TO 100 STEP 10], 112, [102 TO 1000 STEP 100], [1002 TO 10000 STEP 1000]]
        MOLECULE_POSITIONS = [1, [3 TO 100 STEP 10], 113, [103 TO 1000 STEP 100], [1003 TO 10000 STEP 1000]]
        MOLECULE_STATES    = [11, 25, 104]
        SURFACE_POSITIONS  = [1, 2]
        SURFACE_STATES     = [1, 3]
    }
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
        world.big_object.box1     = 5
        world.big_object.box1[r2] = 9
        world.big_object.box1[r3] = 1
        world.big_object.box1[r4] = 2
        world2.big_object.box1    = 44
    }
}

/* 22. DX-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/22 - DX old/"
VIZ_DATA_OUTPUT
{
    MODE = DX
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    OBJECT_FILE_PREFIXES
    {
        world  = thisvizdir & "objects_a"
        world2 = thisvizdir & "objects_b"
    }
    ITERATION_LIST = [[1 TO 100 STEP 10], [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
    STATE_VALUES
    {
        s_g_5                    = 4
        s_v_3                    = 3
        world.big_object.box1[r2] = 9
        world.big_object.box1[r3] = 1
        world.big_object.box1[r4] = 2
    }
}

/* 23. DX-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/23 - DX old/"
VIZ_DATA_OUTPUT
{
    MODE = DX
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    OBJECT_FILE_PREFIXES
    {
        world  = thisvizdir & "objects_a"
        world2 = thisvizdir & "objects_b"
    }
    TIME_LIST = [[1e-6 TO 1e-4 STEP 1e-5], [1.01e-4 TO 1e-3 STEP 1e-4], [1.001e-3 TO 1e-2 STEP 1e-3]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
        world.big_object.box1[r2] = 9
        world.big_object.box1[r3] = 1
        world.big_object.box1[r4] = 2
    }
}

/* 24. DX-mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/24 - DX new/"
VIZ_OUTPUT
{
    MODE = DX
    FILENAME = thisvizdir & "world"
    OBJECT_FILE_PREFIXES
    {
        world  = thisvizdir & "objects_a"
        world2 = thisvizdir & "objects_b"
    }
    MOLECULES
    {
        NAME_LIST {
            s_g_5 = 19
            s_v_3 = 13
            s_g_5 = 4
            s_v_3 = 3
        }
        ITERATION_NUMBERS
        {
            ALL_DATA     @ [[0 TO 100 STEP 10]]
            POSITIONS    @ [2, 3]
        }
    }
    MESHES
    {
        NAME_LIST {
            world.big_object.box1     = 11
            world2.big_object.box1    = 12
            world.big_object.box1[r2] = 9
            world.big_object.box1[r3] = 1
            world.big_object.box1[r4] = 2
        }
        ITERATION_NUMBERS
        {
            ALL_DATA @ [1]
            GEOMETRY @ [2, 3]
        }
    }
}

/* 25. DX-mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/25 - DX new/"
VIZ_OUTPUT
{
    MODE = DX
    FILENAME = thisvizdir & "world"
    OBJECT_FILE_PREFIXES
    {
        world  = thisvizdir & "objects_a"
        world2 = thisvizdir & "objects_b"
    }
    MOLECULES
    {
        NAME_LIST {
            s_g_5 = 29
            s_v_3 = 23
            s_g_5 = 4
            s_v_3 = 3
        }
        TIME_POINTS
        {
            ALL_DATA     @ [2e-6, 3e-6]
            POSITIONS    @ [[0 TO 1e-4 STEP 1e-5]]
        }
    }
    MESHES
    {
        NAME_LIST {
            world.big_object.box1     = 31
            world2.big_object.box1    = 32
            world.big_object.box1[r2] = 9
            world.big_object.box1[r3] = 1
            world.big_object.box1[r4] = 2
        }
        TIME_POINTS
        {
            ALL_DATA @ [1e-6]
            GEOMETRY @ [2e-6, 3e-6]
        }
    }
}

// /* 31. DREAMM mode viz output, VIZ_DATA_OUTPUT notation */
// thisvizdir = vizdir & "/31 - DREAMM old/"
// VIZ_DATA_OUTPUT
// {
//     FILENAME = thisvizdir & "world"
//     ITERATION_FRAME_DATA
//     {
//         ALL_DATA           = [1]
//         EFFECTOR_POSITIONS = [[1 TO 100 STEP 10], 102, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
//         EFFECTOR_STATES    = [[1 TO 100 STEP 10], 103, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
//         MOLECULE_POSITIONS = [[1 TO 100 STEP 10], 104, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
//         MOLECULE_STATES    = [11, 105]
//         MOLECULE_POSITIONS = [3]
//         MOLECULE_STATES    = [5]
//     }
//     STATE_VALUES
//     {
//         s_g_5         = 4
//         s_v_3         = 3
//     }
// }
// 
// /* 32. DREAMM mode viz output, VIZ_DATA_OUTPUT notation */
// thisvizdir = vizdir & "/32 - DREAMM old/"
// VIZ_DATA_OUTPUT
// {
//     FILENAME = thisvizdir & "world"
//     ITERATION_LIST = [[1 TO 100 STEP 10], [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
//     STATE_VALUES
//     {
//         s_g_5         = 4
//         s_v_3         = 3
//     }
// }
// 
// /* 33. DREAMM mode viz output, VIZ_DATA_OUTPUT notation */
// thisvizdir = vizdir & "/33 - DREAMM old/"
// VIZ_DATA_OUTPUT
// {
//     FILENAME = thisvizdir & "world"
//     TIME_LIST = [[1e-6 TO 1e-4 STEP 1e-5], [1.01e-4 TO 1e-3 STEP 1e-4], [1.001e-3 TO 1e-2 STEP 1e-3]]
//     STATE_VALUES
//     {
//         s_g_5         = 4
//         s_v_3         = 3
//     }
// }

/* 34. DREAMM mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/34 - DREAMM new/"
VIZ_OUTPUT
{
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        TIME_POINTS
        {
            ALL_DATA     @ [2e-6, 3e-6]
            POSITIONS    @ [[0 TO 1e-4 STEP 1e-5]]
            ORIENTATIONS @ [3e-6, 4e-6]
        }
    }
    MESHES
    {
        NAME_LIST { ALL_MESHES }
        TIME_POINTS
        {
            ALL_DATA @ [1e-6]
            GEOMETRY @ [2e-6, 3e-6]
            REGION_DATA  @ [3e-6, 4e-6]
        }
    }
}

/* 35. DREAMM mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/35 - DREAMM new/"
VIZ_OUTPUT
{
    MODE = DREAMM_V3
    VIZ_MOLECULE_FORMAT = ASCII
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        TIME_POINTS
        {
            ALL_DATA     @ [2e-6, 3e-6]
            POSITIONS    @ [[0 TO 1e-4 STEP 1e-5]]
            ORIENTATIONS @ [3e-6, 4e-6]
        }
    }
    MESHES
    {
        NAME_LIST { ALL_MESHES }
        TIME_POINTS
        {
            ALL_DATA @ [1e-6]
            GEOMETRY @ [3e-6, 4e-6]
            REGION_DATA  @ [2e-6, 4e-6]
        }
    }
}

/* 36. DREAMM mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/36 - DREAMM new/"
VIZ_OUTPUT
{
    VIZ_MESH_FORMAT = ASCII
    VIZ_MOLECULE_FORMAT = BINARY
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        ITERATION_NUMBERS
        {
            ALL_DATA     @ [2, 3]
            POSITIONS    @ [[0 TO 100 STEP 10]]
            ORIENTATIONS @ [3, 4]
        }
    }
    MESHES
    {
        NAME_LIST { ALL_MESHES }
        ITERATION_NUMBERS
        {
            ALL_DATA @ [1]
            GEOMETRY @ [2, 3]
            REGION_DATA  @ [3, 4]
        }
    }
}

/* 37. DREAMM mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/37 - DREAMM new/"
VIZ_OUTPUT
{
    VIZ_MESH_FORMAT = BINARY
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        ITERATION_NUMBERS
        {
            ALL_DATA     @ [2, 3]
            POSITIONS    @ [[0 TO 100 STEP 10]]
            ORIENTATIONS @ [3, 4]
        }
    }
    MESHES
    {
        NAME_LIST { ALL_MESHES }
        ITERATION_NUMBERS
        {
            ALL_DATA @ [1]
            GEOMETRY @ [2, 3]
            REGION_DATA  @ [3, 4]
        }
    }
}

/* 41. DREAMM grouped mode viz output, VIZ_DATA_OUTPUT notation */
// thisvizdir = vizdir & "/41 - DREAMM grouped old/"
// VIZ_DATA_OUTPUT
// {
//     MODE = DREAMM_V3_GROUPED
//     FILENAME = thisvizdir & "world"
//     ITERATION_FRAME_DATA
//     {
//         ALL_DATA           = [1]
//         EFFECTOR_POSITIONS = [[1 TO 100 STEP 10], 102, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
//         EFFECTOR_STATES    = [[1 TO 100 STEP 10], 103, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
//         MOLECULE_POSITIONS = [[1 TO 100 STEP 10], 104, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
//         MOLECULE_STATES    = [11, 105]
//         MOLECULE_POSITIONS = [3]
//         MOLECULE_STATES    = [5]
//     }
//     STATE_VALUES
//     {
//         s_g_5         = 4
//         s_v_3         = 3
//     }
// }
// 
// /* 42. DREAMM grouped mode viz output, VIZ_DATA_OUTPUT notation */
// thisvizdir = vizdir & "/42 - DREAMM grouped old/"
// VIZ_DATA_OUTPUT
// {
//     MODE = DREAMM_V3_GROUPED
//     FILENAME = thisvizdir & "world"
//     ITERATION_LIST = [[1 TO 100 STEP 10], [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
//     STATE_VALUES
//     {
//         s_g_5         = 4
//         s_v_3         = 3
//     }
// }
// 
// /* 43. DREAMM grouped mode viz output, VIZ_DATA_OUTPUT notation */
// thisvizdir = vizdir & "/43 - DREAMM grouped old/"
// VIZ_DATA_OUTPUT
// {
//     MODE = DREAMM_V3_GROUPED
//     FILENAME = thisvizdir & "world"
//     TIME_LIST = [[1e-6 TO 1e-4 STEP 1e-5], [1.01e-4 TO 1e-3 STEP 1e-4], [1.001e-3 TO 1e-2 STEP 1e-3]]
//     STATE_VALUES
//     {
//         s_g_5         = 4
//         s_v_3         = 3
//     }
// }

/* 44. DREAMM grouped mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/44 - DREAMM grouped new/"
VIZ_OUTPUT
{
    MODE = DREAMM_V3_GROUPED
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        TIME_POINTS
        {
            ALL_DATA     @ [[0 TO 1e-4 STEP 1e-5]]
            POSITIONS    @ [2e-6, 3e-6]
            ORIENTATIONS @ [3e-6, 4e-6]
        }
    }
    MESHES
    {
        NAME_LIST { ALL_MESHES }
        TIME_POINTS
        {
            ALL_DATA @ [1e-6]
            GEOMETRY @ [2e-6, 3e-6]
            REGION_DATA  @ [3e-6, 4e-6]
        }
    }
}

/* 45. DREAMM grouped mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/45 - DREAMM grouped new/"
VIZ_OUTPUT
{
    MODE = DREAMM_V3_GROUPED
    FILENAME = thisvizdir & "world2"
    MOLECULES
    {
        NAME_LIST { "s_*" c_s_0 }
        TIME_POINTS
        {
            ALL_DATA     @ [[0 TO 1e-4 STEP 1e-5]]
            POSITIONS    @ [2e-6, 3e-6]
            ORIENTATIONS @ [3e-6, 4e-6]
        }
    }
    MESHES
    {
        NAME_LIST { "world2.*" world.big_object.box1 }
        TIME_POINTS
        {
            ALL_DATA @ [1e-6]
            GEOMETRY @ [2e-6, 3e-6]
            REGION_DATA  @ [3e-6, 4e-6]
        }
    }
}

/* 46. DREAMM grouped mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/46 - DREAMM grouped new/"
VIZ_OUTPUT
{
    MODE = DREAMM_V3_GROUPED
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { "m_*" }
        NAME_LIST { m_g_0=5 m_g_1=4 }
        TIME_POINTS
        {
            POSITIONS    @ [[0 TO 1e-4 STEP 1e-5]]
            ALL_DATA     @ [3e-6, 4e-6]
            ORIENTATIONS @ [4e-6, 5e-6]
        }
    }
    MESHES
    {
        NAME_LIST { "world.*" }
        NAME_LIST { world.big_object.box1 }
        NAME_LIST { world2.rs8 }
        TIME_POINTS
        {
            ALL_DATA @ [2e-6]
            GEOMETRY @ [3e-6, 4e-6]
            REGION_DATA  @ [4e-6, 5e-6]
        }
    }
}

// ===================================================================
// All output blocks below here have been created by taking the corresponding
// output blocks from above and replacing the MODE with 'MODE = NONE'.
// ===================================================================

/* 51. ASCII-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/51 - ASCII old/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    ITERATION_FRAME_DATA
    {
        ALL_DATA           = [1]
        EFFECTOR_POSITIONS = [[1 TO 100 STEP 10], 102, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        EFFECTOR_STATES    = [[1 TO 100 STEP 10], 103, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        MOLECULE_POSITIONS = [[1 TO 100 STEP 10], 104, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        MOLECULE_STATES    = [11, 105]
    }
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 52. ASCII-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/52 - ASCII old/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    ITERATION_LIST = [[1 TO 100 STEP 10], [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 53. ASCII-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/53 - ASCII old/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    TIME_LIST = [[1e-6 TO 1e-4 STEP 1e-5], [1.01e-4 TO 1e-3 STEP 1e-4], [1.001e-3 TO 1e-2 STEP 1e-3]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 54. ASCII-mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/54 - ASCII new/"
VIZ_OUTPUT
{
    MODE = NONE
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        ITERATION_NUMBERS
        {
            ALL_DATA     @ [2, 3]
            POSITIONS    @ [[0 TO 100 STEP 10]]
            ORIENTATIONS @ [3, 4]
        }
    }
}

/* 55. ASCII-mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/55 - ASCII new/"
VIZ_OUTPUT
{
    MODE = NONE
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        TIME_POINTS
        {
            ALL_DATA     @ [2e-6, 3e-6]
            POSITIONS    @ [[0 TO 1e-4 STEP 1e-5]]
            ORIENTATIONS @ [3e-6, 4e-6]
        }
    }
}

/* 61. RK-mode viz output, VIZ_DATA_OUTPUT notation [secretly ASCII] */
thisvizdir = vizdir & "/61 - RK old ASCII/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    ITERATION_LIST = [[1 TO 100 STEP 10], [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 62. RK-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/62 - RK old/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    ITERATION_LIST = [[1 TO 100 STEP 10], [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 63. RK-mode viz output, VIZ_OUTPUT notation [secretly ASCI] */
thisvizdir = vizdir & "/63 - RK new ASCII/"
VIZ_OUTPUT
{
    MODE = NONE
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        ITERATION_NUMBERS
        {
            ALL_DATA     @ [2, 3]
            POSITIONS    @ [[0 TO 100 STEP 10]]
            ORIENTATIONS @ [3, 4]
        }
    }
}

/* 64. RK-mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/64 - RK new/"
VIZ_OUTPUT
{
    MODE = NONE
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        TIME_POINTS
        {
            ALL_DATA     @ [2e-6, 3e-6]
            POSITIONS    @ [[0 TO 1e-4 STEP 1e-5]]
            ORIENTATIONS @ [3e-6, 4e-6]
        }
    }
}

/* 71. DX-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/71 - DX old/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    OBJECT_FILE_PREFIXES
    {
        world  = thisvizdir & "objects_a"
        world2 = thisvizdir & "objects_b"
    }
    ITERATION_FRAME_DATA
    {
        EFFECTOR_POSITIONS = [[1 TO 100 STEP 10], 111, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        EFFECTOR_STATES    = [1, [2 TO 100 STEP 10], 112, [102 TO 1000 STEP 100], [1002 TO 10000 STEP 1000]]
        MOLECULE_POSITIONS = [1, [3 TO 100 STEP 10], 113, [103 TO 1000 STEP 100], [1003 TO 10000 STEP 1000]]
        MOLECULE_STATES    = [11, 25, 104]
        SURFACE_POSITIONS  = [1, 2]
        SURFACE_STATES     = [1, 3]
    }
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
        world.big_object.box1     = 5
        world.big_object.box1[r2] = 9
        world.big_object.box1[r3] = 1
        world.big_object.box1[r4] = 2
    }
}

/* 72. DX-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/72 - DX old/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    OBJECT_FILE_PREFIXES
    {
        world  = thisvizdir & "objects_a"
        world2 = thisvizdir & "objects_b"
    }
    ITERATION_LIST = [[1 TO 100 STEP 10], [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
    STATE_VALUES
    {
        s_g_5                    = 4
        s_v_3                    = 3
        world.big_object.box1[r2] = 9
        world.big_object.box1[r3] = 1
        world.big_object.box1[r4] = 2
    }
}

/* 73. DX-mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/73 - DX old/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "molecules"
    OBJECT_FILE_PREFIXES
    {
        world  = thisvizdir & "objects_a"
        world2 = thisvizdir & "objects_b"
    }
    TIME_LIST = [[1e-6 TO 1e-4 STEP 1e-5], [1.01e-4 TO 1e-3 STEP 1e-4], [1.001e-3 TO 1e-2 STEP 1e-3]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
        world.big_object.box1[r2] = 9
        world.big_object.box1[r3] = 1
        world.big_object.box1[r4] = 2
    }
}

/* 74. DX-mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/74 - DX new/"
VIZ_OUTPUT
{
    MODE = NONE
    FILENAME = thisvizdir & "world"
    OBJECT_FILE_PREFIXES
    {
        world  = thisvizdir & "objects_a"
        world2 = thisvizdir & "objects_b"
    }
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        ITERATION_NUMBERS
        {
            ALL_DATA     @ [[0 TO 100 STEP 10]]
            POSITIONS    @ [2, 3]
            ORIENTATIONS @ [3, 4]
        }
    }
    MESHES
    {
        NAME_LIST { ALL_MESHES }
        ITERATION_NUMBERS
        {
            ALL_DATA @ [1]
            GEOMETRY @ [2, 3]
            REGION_DATA  @ [3, 4]
        }
    }
}

/* 75. DX-mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/75 - DX new/"
VIZ_OUTPUT
{
    MODE = NONE
    FILENAME = thisvizdir & "world"
    OBJECT_FILE_PREFIXES
    {
        world  = thisvizdir & "objects_a"
        world2 = thisvizdir & "objects_b"
    }
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        TIME_POINTS
        {
            ALL_DATA     @ [2e-6, 3e-6]
            POSITIONS    @ [[0 TO 1e-4 STEP 1e-5]]
            ORIENTATIONS @ [3e-6, 4e-6]
        }
    }
    MESHES
    {
        NAME_LIST { ALL_MESHES }
        TIME_POINTS
        {
            ALL_DATA @ [1e-6]
            GEOMETRY @ [2e-6, 3e-6]
            REGION_DATA  @ [3e-6, 4e-6]
        }
    }
}

/* 81. DREAMM mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/81 - DREAMM old/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "world"
    ITERATION_FRAME_DATA
    {
        ALL_DATA           = [1]
        EFFECTOR_POSITIONS = [[1 TO 100 STEP 10], 102, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        EFFECTOR_STATES    = [[1 TO 100 STEP 10], 103, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        MOLECULE_POSITIONS = [[1 TO 100 STEP 10], 104, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        MOLECULE_STATES    = [11, 105]
        MOLECULE_POSITIONS = [3]
        MOLECULE_STATES    = [5]
    }
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 82. DREAMM mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/82 - DREAMM old/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "world"
    ITERATION_LIST = [[1 TO 100 STEP 10], [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 83. DREAMM mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/83 - DREAMM old/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "world"
    TIME_LIST = [[1e-6 TO 1e-4 STEP 1e-5], [1.01e-4 TO 1e-3 STEP 1e-4], [1.001e-3 TO 1e-2 STEP 1e-3]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 84. DREAMM mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/84 - DREAMM new/"
VIZ_OUTPUT
{
    MODE = NONE
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        TIME_POINTS
        {
            ALL_DATA     @ [2e-6, 3e-6]
            POSITIONS    @ [[0 TO 1e-4 STEP 1e-5]]
            ORIENTATIONS @ [3e-6, 4e-6]
        }
    }
    MESHES
    {
        NAME_LIST { ALL_MESHES }
        TIME_POINTS
        {
            ALL_DATA @ [1e-6]
            GEOMETRY @ [2e-6, 3e-6]
            REGION_DATA  @ [3e-6, 4e-6]
        }
    }
}

/* 85. DREAMM mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/85 - DREAMM new/"
VIZ_OUTPUT
{
    MODE = NONE
    VIZ_MOLECULE_FORMAT = ASCII
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        TIME_POINTS
        {
            ALL_DATA     @ [2e-6, 3e-6]
            POSITIONS    @ [[0 TO 1e-4 STEP 1e-5]]
            ORIENTATIONS @ [3e-6, 4e-6]
        }
    }
    MESHES
    {
        NAME_LIST { ALL_MESHES }
        TIME_POINTS
        {
            ALL_DATA @ [1e-6]
            GEOMETRY @ [3e-6, 4e-6]
            REGION_DATA  @ [2e-6, 4e-6]
        }
    }
}

/* 86. DREAMM mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/86 - DREAMM new/"
VIZ_OUTPUT
{
    MODE = NONE
    VIZ_MESH_FORMAT = ASCII
    VIZ_MOLECULE_FORMAT = BINARY
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        ITERATION_NUMBERS
        {
            ALL_DATA     @ [2, 3]
            POSITIONS    @ [[0 TO 100 STEP 10]]
            ORIENTATIONS @ [3, 4]
        }
    }
    MESHES
    {
        NAME_LIST { ALL_MESHES }
        ITERATION_NUMBERS
        {
            ALL_DATA @ [1]
            GEOMETRY @ [2, 3]
            REGION_DATA  @ [3, 4]
        }
    }
}

/* 87. DREAMM mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/87 - DREAMM new/"
VIZ_OUTPUT
{
    MODE = NONE
    VIZ_MESH_FORMAT = BINARY
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        ITERATION_NUMBERS
        {
            ALL_DATA     @ [2, 3]
            POSITIONS    @ [[0 TO 100 STEP 10]]
            ORIENTATIONS @ [3, 4]
        }
    }
    MESHES
    {
        NAME_LIST { ALL_MESHES }
        ITERATION_NUMBERS
        {
            ALL_DATA @ [1]
            GEOMETRY @ [2, 3]
            REGION_DATA  @ [3, 4]
        }
    }
}

/* 91. DREAMM grouped mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/91 - DREAMM grouped old/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "world"
    ITERATION_FRAME_DATA
    {
        ALL_DATA           = [1]
        EFFECTOR_POSITIONS = [[1 TO 100 STEP 10], 102, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        EFFECTOR_STATES    = [[1 TO 100 STEP 10], 103, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        MOLECULE_POSITIONS = [[1 TO 100 STEP 10], 104, [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
        MOLECULE_STATES    = [11, 105]
        MOLECULE_POSITIONS = [3]
        MOLECULE_STATES    = [5]
    }
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 92. DREAMM grouped mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/92 - DREAMM grouped old/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "world"
    ITERATION_LIST = [[1 TO 100 STEP 10], [101 TO 1000 STEP 100], [1001 TO 10000 STEP 1000]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 93. DREAMM grouped mode viz output, VIZ_DATA_OUTPUT notation */
thisvizdir = vizdir & "/93 - DREAMM grouped old/"
VIZ_DATA_OUTPUT
{
    MODE = NONE
    MOLECULE_FILE_PREFIX = thisvizdir & "world"
    TIME_LIST = [[1e-6 TO 1e-4 STEP 1e-5], [1.01e-4 TO 1e-3 STEP 1e-4], [1.001e-3 TO 1e-2 STEP 1e-3]]
    STATE_VALUES
    {
        s_g_5         = 4
        s_v_3         = 3
    }
}

/* 94. DREAMM grouped mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/94 - DREAMM grouped new/"
VIZ_OUTPUT
{
    MODE = NONE
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { ALL_MOLECULES }
        TIME_POINTS
        {
            ALL_DATA     @ [[0 TO 1e-4 STEP 1e-5]]
            POSITIONS    @ [2e-6, 3e-6]
            ORIENTATIONS @ [3e-6, 4e-6]
        }
    }
    MESHES
    {
        NAME_LIST { ALL_MESHES }
        TIME_POINTS
        {
            ALL_DATA @ [1e-6]
            GEOMETRY @ [2e-6, 3e-6]
            REGION_DATA  @ [3e-6, 4e-6]
        }
    }
}

/* 95. DREAMM grouped mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/95 - DREAMM grouped new/"
VIZ_OUTPUT
{
    MODE = NONE
    FILENAME = thisvizdir & "world2"
    MOLECULES
    {
        NAME_LIST { "s_*" c_s_0 }
        TIME_POINTS
        {
            ALL_DATA     @ [[0 TO 1e-4 STEP 1e-5]]
            POSITIONS    @ [2e-6, 3e-6]
            ORIENTATIONS @ [3e-6, 4e-6]
        }
    }
    MESHES
    {
        NAME_LIST { "world2.*" world.big_object.box1 }
        TIME_POINTS
        {
            ALL_DATA @ [1e-6]
            GEOMETRY @ [2e-6, 3e-6]
            REGION_DATA  @ [3e-6, 4e-6]
        }
    }
}

/* 96. DREAMM grouped mode viz output, VIZ_OUTPUT notation */
thisvizdir = vizdir & "/96 - DREAMM grouped new/"
VIZ_OUTPUT
{
    MODE = NONE
    FILENAME = thisvizdir & "world"
    MOLECULES
    {
        NAME_LIST { "m_*" }
        NAME_LIST { m_g_0=5 m_g_1=4 }
        TIME_POINTS
        {
            POSITIONS    @ [[0 TO 1e-4 STEP 1e-5]]
            ALL_DATA     @ [3e-6, 4e-6]
            ORIENTATIONS @ [4e-6, 5e-6]
        }
    }
    MESHES
    {
        NAME_LIST { "world.*" }
        NAME_LIST { world.big_object.box1 }
        NAME_LIST { world2.rs8 }
        TIME_POINTS
        {
            ALL_DATA @ [2e-6]
            GEOMETRY @ [3e-6, 4e-6]
            REGION_DATA  @ [4e-6, 5e-6]
        }
    }
}