ESM4714
Scientific Visual Data Analysis and Multimedia
Exercise #7: AVS-Introduction

NCSA has an excellent AVS tutotial that was created by John Shalf
who was a former Virginia Tech student who took this course in 1993.

1. Logon onto mercury -> pluto.smvc.vt.edu at the VT-CAVE classroom (SMVC).

2. Mount your optical disk (see procedure for mounting scsi devices).
3. Go to the ESM4714/examples directory.

4. Locate files D.fld (density), P.fld (pressure), and T.fld (Temperature), in the directory /optical/ESM4714/examples/ragab/viz_method/gas/fields/. The field file D.fld is listed below as an example.

    
   # AVS Field File
   #
   # 3D Density
   ndim=3            #number of dimensions in the field
   dim1=73           #dimension of axis 1
   dim2=129          #dimension of axis 2
   dim3=73           #dimension of axis 3
   nspace=3          #number of physical coordinates
   veclen=1          #number of elements at each point
   data=integer      #data type (byte, integer, float, double)
   variable 1 file = /optical/examples/ragab/viz_method/gas/D.file filetype=ascii
   
   NOTE: you may have to change the path in the last statement
         if you are not using your optical disk.
   

   where ndim=3 defines a 3D field, dim1, dim2, dim3 are the original dimensions of the Ragab data set, nspace=3 defines the number of physical coordinates, veclen=1 defines the vector length or number of elements assign to a property at each of the coordinate points (for a vector such as a velocity veclen=3 which corresponds to the three x,y,z components of velocity), the data type is integer, and the field type is uniform, and finally the path to where the original ascii integer data file was stored.

5. Create the same type of field file for the brown data set and call it C.fld and put it in the brown directory.

   #AVS Field File
   # 3D Concentration
   #
   ndim=3
   dim1=64
   dim2=64
   dim3=44
   nspace=3
   veclen=1
   data=integer
   field=uniform
   variable 1 file = /optical/example/brown/brown.ascii.start filetype=ascii
   
   NOTE: you may have to change the path in the last statement
         if you are not using your optical disk.
   

6. Execute AVS: viz?% avs --> a window should appear on the left of the screen.

7. Choose (click left mouse button) the window 'network editor' --> a larger window will appear on the right with modules at the top.

   - Choose the "readfield" and "generate colormap" modules from the "Data Input" section of the module library by dragging (holding down the left mouse button and moving simultaneously) these modules into the empty window below. Continue this process by also dragging modules "field to byte" from "filters", also drag "arbitrary slicer" and "volume bound" from "Mappers" and finally drag the module "geometry viewer" from "Display Output" where you can place these modules in a pattern similar to that shown below.

   

   - To connect modules, move the pointer into a color tabbed region on the perimeter of the module: red is for output to an image module and blue is for data. For example the blue region of the "read field" module is connected with the blue region of the "field to byte" by holding down the middle mouse button on either of the two tabs until a thin blue line appears and is seclected by moving the mouse until the thin blue line changes to white and the mouse button is released and then the white line become the final inforamtion path. Continue to connect the remaining modules: blue to blue, red to read, and yellow to yellow, etc.

8. Data is read by the "read field" module by selecting the small square in the "read field" module with the left mouse button and a window appears at the left from which a file is selected with the right mouse button and directories are also selcted with the right button touching the top most "/" in the window. Experiment with the various controls until the usage becomes clear. Most of the choices are intuatitive.

9. You can observe the flow of data from module to module. When the data enters the last module ("geometry viewer") an image appears in a window which should look familiar.

   

10. Sometimes the image in the window is too big. To shrink the image to fit inside the window, press the shift key followed by the holding the middle mouse button down and dragging the mouse pointer from the top of the viewing window to the bottom until you get the desired image size. Now let go of the shift key and grab the edge of the image with the middle mouse button and rotate the image into desired orientation.

11. Experiment with moving the arbitrary slice. Choose the slicer controls by clicking on the small square on the right side of the "arbitrary slicer" module: the slicer controls will appear in the window on the left. If you decrease the resolution in the plane the slice moves faster but the images is more coarse.

12. Try other features such as the "isosurface" module.

Like NCSA, Virginia Tech also installed AVS on the VT-CAVE computer. VT-CAVE has also installed a real-time AVS to CAVE link called GROTTO viewer (AVS cave_viewer network module) that was created at the Naval Research Laboratory's Virtual Laboratory.

Below we provide a brief description on how to used AVS in the VT-CAVE.

Procedure: Viewing the brown.ascii.start data set in the CAVE

1. Logon onto the VT-CAVE (contact R.D. Kriz for procedure to get a CAVE account)

2. If you have an optical disk, mount your optical disk (see procedure for mounting scsi devices).

3. Contact the CAVE Sysadmin and have them install the .grottorc file in your home directory.

4. Find and change directory to grotto_viewer setup on rkriz's home directory. To setup a similar grotto_viewer in your home directory contact rkriz@vt.edu.

   cave% cd ~rkriz/NRL_grotto/grotto_viewer

5. Start up AVS.

   cave% avs -size 1024x768

6. Proceed to build the same network as described in the previous procedure in steps 8 thru 9. From the read field module locate and select the same C.fld file you created on your optical disk in step 6. After you confirm that the network module is functioning correctly, follow the procedure below to view the results in the CAVE.

7. In the upper left corner of the AVS Network Editor window select Module Tools and just below that select Read Module(s). Another window will appear from which you can select the file named grotto_viewer. You will notice that when selected grotto_viewer appears as a module in the Data Output section of the Network Editor.

8. Drag the grotto_viewer module into the network programing area and connect it to the other modules as you did with the geometry viewer module ---- a new window will appear near the center of the CRT screen. Drag and move this window to a convenient location by holding down the alt+f7 keys with the mouse cursor located over the window and hold down the left mouse button and drag the window a new location.

   NOTE: The middle mouse button rotates image and the right mouse button zooms in and out. The window generated by the geometry viewer module uses the standard AVS mouse format.

Example 2: AVS used to view molecular dynamics simulations.

AVS is used closely with supercomputer simulations. For a summer project in 1995, Michael Yilma (NSF Summer Undergraduate Research Program), created a Tutorial on Molecular Dynamics which used AVS to view the motion of small group of atoms. Since the number of atoms was small the calculations can be done on a PC computer. The tutorial was designed so that all information could be downloaded and simulations done on a remote site computer and the results of the simulation transfered to workstations in the SMVC and visualized with AVS.