/* visualization_output.mdl" */

/* This MDL statement block specifies the content, format, and 
timing of simulation data to be output for 3-D visualization. */

VIZ_DATA_OUTPUT {
  MODE = DX    /* 3-D rendering requires use of an external 
rendering software package, and is a complex issue in and of 
itself.  The choice of MODE here primarily determines the 
format of the output data, aimed at a particular choice of 
rendering software (see book Chapter 4, note 6 for rendering 
software URLs).  At present the choices include: DX (IBM 
DataExplorer), RENDERMAN (Pixar RenderMan or Blue Moon 
Rendering Tools), IRIT, RAYSHADE, or POVRAY.  The preferred 
format (from an MCell perspective) is DX because: (1) the 
output data can be organized hierarchically, similar to the 
way that the MCell objects are organized; (2) the output data 
can be much more compact than for the other choices; (3) DX is 
actually a high-dimensional data analysis and manipulation 
tool in addition to a renderer.  It has a graphical user 
interface that is a powerful visual programming environment, 
and can be extremely useful for designing and modifying MCell 
structures. */
  STATE_VALUES {    /* These are arbitrary values that are 
assigned to surfaces and molecules.  If output for rendering 
purposes, they can be used to assign colors and other surface 
properties, and/or to selectively render only a subset of the 
data.  Particular physical objects instantiated within a 
metaobject hierarchy can be selected by a top-down list of 
object names separated by periods.  If the last (lower_most) 
named object is itself a metaobject, all of its own subobjects 
are included in the MDL operation. */
    nmj.nerve_layer = 1
    nmj.lamina_layer = 2
    nmj.muscle_layer.top = 3
    nmj.muscle_layer.middle = 4
    nmj.muscle_layer.bottom = 5
    nmj.sampling_boxes = 6    /* All 5 subobjects (boxes) that are 
part of "nmj.sampling_boxes" will be included and will 
receive a value of 6." */
    AChR.R0 = 1    /* Names for molecules defined implicitly by 
reaction mechanism states are used as described in the 
ADD_EFFECTOR block in "nerve_membrane.mdl". */
    AChR.AR1 = 2
    AChR.AR2 = 2    /* Since the two single-bound AChR states are 
statistically identical in this example, they are given the 
same state value. */
    AChR.A2R3 = 3
    AChR.A2R4 = 4
    AChE.E = 5
    AChE.AE = 6
    AChE.AcE = 7
    AChE.AAcE = 8
    ChR.R0 = 9
    ChR.AR1 = 10
    ChR.AR2 = 11
    ACh = 12    /* Explicitly defined molecule name (DEFINE_LIGAND 
block in "rat_nmj.main.mdl"). */
    Ch = 13
  }
/* Visualization output data is written into different files 
containing surface and molecule positions and states, and these 
sets of files must be output for each desired time-step iteration.  
To organize the output files according to the MCell objects that 
they contain, different objects can be assigned different prefixes 
for the associated sets of visualization output file names. */
  MOLECULE_FILE_PREFIX = "viz"    /* All output files for 
molecules that are not effector sites will have the prefix 
"viz". */
  OBJECT_FILE_PREFIXES {
    nmj = "viz"    /* All surfaces and effector sites included in 
"nmj" (which in this example includes all instantiated 
objects) will be output to data files that have the prefix 
"viz".  For DX rendering this method is efficient and 
convenient.  For other rendering modes, it is generally 
desirable to subdivide the objects, e.g.:
    nmj.nerve_layer = "viz.nerve"
    nmj.lamina_layer = "viz.basal_lamina"
    nmj.muscle_layer.top = "viz.postsynaptic.top"
    nmj.muscle_layer.middle = "viz.postsynaptic.middle"
    nmj.muscle_layer.bottom = "viz.postsynaptic.bottom"
    nmj.sampling_boxes = "viz.sampling_boxes"
    */
  }
/* For the most part, surface and effector site positions do not 
change during a simulation, and therefore do not need to be output 
repeatedly for imaging purposes.  It is also generally true that 
changing molecule positions and states only need to be visualized 
for a subset of simulation time-step iterations.  A snapshot of 
the simulation at the end of one particular iteration constitutes 
one frame of an animation, and the following statement block 
specifies what visualization data should be output for one or more 
iteration frames. */
  ITERATION_FRAME_DATA {
    SURFACE_POSITIONS = [0]    /* Output surface position data 
files only after iteration 0, i.e., after surfaces and 
molecules are initialized but before any movements or 
transitions occur. */
    SURFACE_STATES = [0]    /* Output surface states data files 
only after iteration 0. */
    EFFECTOR_POSITIONS = [0]    /* Output effector site position 
data files only after iteration 0. */
    EFFECTOR_STATES = [0,[2 TO 598 STEP 2],[600 TO 2600 STEP 
100],5000,10000,14000]    /* Output effector states into 
data files after each of the listed iteration numbers. */
    LIGAND_POSITIONS = [0,[2 TO 598 STEP 2],[600 TO 2600 STEP 
100],5000,10000,14000]    /* Output positions of molecules 
into data files after each of the listed iteration numbers. 
*/
    LIGAND_STATES = [0,[2 TO 598 STEP 2],[600 TO 2600 STEP 
100],5000,10000,14000]    /* Output states of molecules into 
data files after each of the listed iteration numbers. */
  }
/* A shortcut to output of all position and state data (very 
inefficient for large simulation structures) can be used in place 
of ITERATION_FRAME_DATA, e.g.:
  ITERATION_LIST = [0,[2 TO 598 STEP 2],[600 TO 2600 STEP 
100],5000,10000,14000]
*/
}