OVERGRID Version 2.2

Author: William M. Chan

Date: May, 2007.

Notes:

• Transforms, zoom box, direct entity picking coded by Steven M. Nash
• Compatible with Chimera Grid Tools version 2.0

Introduction

• interactive visualization, manipulation, processing and diagnostic of geometry and grids
• performing overset surface and volume grid generation
• preparation of grid boundary conditions
• preparation of inputs for the PEGASUS 5 and GEN_X/DCF domain connectivity codes, and for the OVERFLOW and OVERFLOW-2 flow solvers
• creating components hierarchy, preparing inputs and viewing animations for multiple component dynamics.
• visualization/animation of flow solutions for single and multiple time frames
• preparation of inputs for debris transport analyses
• visualization of prismatic near-body grid and AMR Cartesian grids

The programming languages used by the GUI are listed below. It is assumed that the necessary libraries are available on the local machine.

 C        - main program and driver for graphics
Tcl/Tk    - window management, widgets creation
OpenGL    - graphics display
Fortran90 - geometry/grid input routines

For users without Tcl/Tk, look under

    http://www.tcl.tk/

   Tcl/Tk 8.0p2, 8.0.3, 8.0.4, 8.0.5
   Tcl/Tk 8.1.1
   Tcl/Tk 8.2.2, 8.2.3
   Tcl/Tk 8.3.0, 8.3.1, 8.3.2, 8.3.3, 8.3.4, 8.3.5
   Tcl/Tk 8.4.0, 8.4.1, 8.4.2, 8.4.3, 8.4.4, 8.4.5, 8.4.6, 8.4.7,
          8.4.8, 8.4.9, 8.4.10, 8.4.11, 8.4.12, 8.4.13

This code is in beta test mode so there may still be some undiscovered bugs and it is under frequent modifications and improvements. OVERGRID is used by invoking a C-shell script called overgrid which then calls the C executable og and the Tcl/Tk script og.tcl. OVERGRID also has its own Makefile which should be modified based on the instructions under the Installation section below. The user is urged to go through the tutorial under chimerax.x/gui/tutorial for details on the capabilities and usage of the modules of OVERGRID.

Installation of Tcl/Tk on Linux/Unix machines

1. Down load tcl8.4.13.tar.gz and tk8.4.13.tar.gz from the web-site given above.
2. Expand the tcl file first.
3. Go to the unix subdirectory and type ./configure to generate a Makefile for your particular operating system and hardware.
4. Type make to create the tcl library called libtcl8.4.so or libtcl8.4.a.
5. Repeat the same procedure for the tk directory to create a library called libtk8.4.so or libtk8.4.a.

Installation of OVERGRID on Linux/Unix machines

1. The following 3 variables should be modified in the overgrid Makefile:

     Modify the INCLUDES variable to point to where tcl.h and tk.h are located.
     These should be $TCLINSTALLDIR/generic and $TKINSTALLDIR/generic.
   
     Modify the LIBDIRS variable to point to where libtcl8.4.so (or libtcl8.4.a) and
     libtk8.4.so (or libtk8.4.a) are located.
     These should be $TCLINSTALLDIR/unix and $TKINSTALLDIR/unix.
   
     Modify the tcl/tk library names in the LIBS variable. Use -ltk8.4 if the
     library is called libtk8.4.so, or use -ltk if it is called libtk.so.
     Follow a similar procedure for tcl.
     

2. If the tcl/tk libraries are installed in non-standard places, the following environment variables have to be set in .cshrc:

    
     setenv LD_LIBRARY_PATH $TCLINSTALLDIR/unix:$TKINSTALLDIR/unix
     setenv TCL_LIBRARY $TCLINSTALLDIR/library
     setenv TK_LIBRARY $TKINSTALLDIR/library
     

3. Users on Linux machines have to pay special attention to all variables in the Makefile, e.g. compilers names and flags, directory names, etc. For PGI compilers, '-Mnomain' should be added to the LFLAGS definition to avoid the multiple 'main' error; '-byteswapio' could be added to FFLAGS and CFLAGS to read IEEE data. For certains Linux installations, the user may have to add -L/usr/X11R6/lib to the definition of LIBDIRS.

4. Users on SGI should be careful with compatibility between -32, -n32, -64 objects. Users on systems with IRIX 6.5 should use -n32 or -64 objects by modifying the CFLAGS and FFLAGS appropriately in the Makefile. Also, check the file type of the library files libtcl8.4.so and libtk8.4.so to ensure the object types are compatible with that of og.

5. Type make to compile og.c and produce the og executable

6. Modify the EXECDIR variable in the overgrid script file to point to the directory where og and og.tcl are located.

7. Move the overgrid script file to a directory in the user's path, e.g. ~/bin.

8. The following modules in the chimerax.x/src directory are used by overgrid: grided, srap, progrd, seamcr, seamcrt, surgrd, sblock, wkcut, hypgen, and boxgr. Single and double precision versions of the executables should be stored in separate directories. Loading a single or double precision file into overgrid will automatically trigger the use of executables in the appropriate directory specified by the user (see next item below and on-line help under PREFERENCES in the Controls Window).

9. Create a preferences file called .overgridrc in the user's home directory. This file should contain the following 3 lines:

          < directory_path_for_single_precision_executables >
          < directory_path_for_double_precision_executables >
          < background_color >
     

   where the first 2 lines must point to different locations, and < background_color > = 0/1 (black/white). This file can also be created from inside OVERGRID by clicking on the PREFERENCES button, filling in the appropriate entries, and saving the contents to disk. The `endianess' of these executables must match that of any grid files read into overgrid if operations are to be performed on these grid files with these executables.

Installation of OVERGRID on Mac OS-X Intel machines

       setenv IFORTLIB /opt/intel/fc/$intelversion/lib

          where $intelversion is the version number of the libraries (e.g., 9.1.030)

       source /opt/intel/fc/$intelversion/bin/ifortvars.csh
       source /opt/intel/cc/$intelversion/bin/iccvars.csh
   

1. Down load tcl8.4.13.tar.gz and tk8.4.13.tar.gz from the web-site given above.
2. Put these files in a directory (let's call it $PKG from now).
3. Expand the tcl8.4.13 directory, cd to the macosx subdirectory, and type make.
4. Expand the tk8.4.13 directory, cd to the macosx subdirectory, and type make.
5. This will generate a directory called build in $PKG which contains two subdirectories, one called tcl, one called tk.

For self-installed tcl/tk,

         setenv TCL_FRWK $PKG/build/tcl/Tcl.framework
         setenv TK_FRWK  $PKG/build/tk/Tk.framework
   

         setenv TCL_FRWK /System/Library/Frameworks/Tcl.framework
         setenv TK_FRWK  /System/Library/Frameworks/Tk.framework
   

         setenv TOGL_DIR $CGT/gui/macosx
         setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:${TOGL_DIR}

             where $CGT is the full path to the chimera2.0 directory
   

Installation of OVERGRID on Windows machines

 Executables for OVERGRID and single precision executables for other CGT
     modules will be provided in a directory called cgt.
 Download and install ActiveTcl for Windows from
     http://www.activestate.com/Products/ActiveTcl/
 Install ActiveTcl using the default install path.
 Put the cgt directory in disk C:.
 Set the environment variables TCL_LIBRARY and TK_LIBRARY as
     (Control Panel -> System -> Advanced -> Environment variables)
        TCL_LIBRARAY = C:\Tcl\lib\tcl8.4
        TK_LIBRARAY  = C:\Tcl\lib\tk8.4
 Under system environment variables, add the following to the PATH variable
        C:\cgt\gui;C:\cgt\bin

Platform specific problems

• Linux - with certain combinations of Linux kernels and graphics drivers, remote display from/to a Linux box to/from a remote machine may not work. Even for local display, it is usually risky to use the latest graphics drivers.

Execution

   overgrid
or
   overgrid < FILENAMES >

Input File Types

The following file name extensions are used by OVERGRID to identify the CAD file type:

    CATIAV5 - .CATPart, .CATProduct
    FELISA  - .dat
    OpenCASCADE - .BRep
    Parasolid   - .xmt_txt
    Pro/ENGINEER - .prt, .asm, .prt.n, .asm.n where n can be any integer
    SolidWorks - .sldprt, .sldasm
    UniGraphics -.prt

The following structured grid and unstructured triangulation file types are currently readable by OVERGRID:

1. PLOT3D grid (unformatted/formatted, big/little endian, single grid/multiple grid, 3-D/2-D, with/without iblanks, single/double precision). The format is automatically determined by OVERGRID. The filename can be any string. If a filename contains the strings ".tri", ".i.tri", or ".fst", it will first be considered as a triangulation file. If read fails, an attempt will be made to read it as a PLOT3D file. OVERGRID can currently read and write both big and little endian PLOT3D files. However, for the execution of CGT batch modules like SRAP and HYPGEN to work successfully, the endian type of the file still has to match the endian type of the CGT batch module executables.
2. CART3D triangulation (unformatted/formatted). The format is automatically determined but the filename must contain the string ".tri" (un-intersected components) or the string ".i.tri" (intersected components).
3. FAST unstructured triangulation (unformatted/formatted). The format is automatically determined but the filename must contain the string ".fst".

• read/write .tri, .i.tri or .fst files
• view triangulation in wireframe or shaded modes
• perform TRIGED functions
• interrogate vertex or face index info by modifying constant vertex/face widgets in Entity Highlight and Selection window
• construct surface curves in the SEAMCR module
• generate hyperbolic surface grids using triangulation as reference surface in the SURGRD module
• project surface or curve entities onto triangulated reference surface in the PROGRD module
• used in components definition and animation

 PLOT3D File Format 
     write(2) ngrid
     write(2) (nj(n),nk(n),nl(n),n=1,ngrid)
     do n=1,ngrid
        write(2) (((x(j,k,l),j=1,nj(n)),k=1,nk(n)),l=1,nl(n)),
    &            (((y(j,k,l),j=1,nj(n)),k=1,nk(n)),l=1,nl(n)),
    &            (((z(j,k,l),j=1,nj(n)),k=1,nk(n)),l=1,nl(n)),
    &            (((ib(j,k,l),j=1,nj(n)),k=1,nk(n)),l=1,nl(n))
     enddo

     where ngrid    = number of grids
           nj,nk,nl = j,k,l dimensions of each grid
           x,y,z    = vertex coordinates
           ib       = vertex iblank value (optional)

     For single grid format, ngrid is omitted.

 CART3D Surface Triangulation File Format 
     write(2) nvert,nface
     write(2) (x(i),y(i),z(i),i=1,nvert)
     write(2) (iface(i,1),iface(i,2),iface(i,3),i=1,nface)
     write(2) (icomp(i),i=1,nface)

     where nvert  = number of vertices
           nface  = number of faces
           x,y,z  = coordinates of vertex i
           iface  = vertex indices of face i (vertex numbering begins with 1)
           icomp  = ID tag of face i (integer)

 FAST Surface Triangulation File Format 
     write(2) nvert,nface,ntet
     write(2) (x(i),i=1,nvert),(y(i),i=1,nvert),(z(i),i=1,nvert),
  &           (iface(i,1),iface(i,2),iface(i,3),i=1,nface),
  &           (icomp(i),i=1,nface)

     where ntet = 0

Help and Tutorial

Transforms

   Left mouse (up/down motion)    - rotate about screen X axis
   Left mouse (side motion)       - rotate about object Z axis
   Middle mouse                   - zoom
   Right mouse                    - translate
   Alt + Left mouse (side motion) - rotate about screen Y axis

1. With mouse button depressed, the transforms continue when the mouse motion stops in PLOT3D. In OVERGRID, the transforms stop when the mouse motion stops.
2. There is no acceleration with mouse motion in OVERGRID.

Entity Highlight and Selection

Highlighting can be applied to a single entity (using the Entity # widget at the upper left corner of the "Entity Highlight and Selection" window). Highlighting is used when the user needs to flag a single entity for performing operations such as grided functions.

Selection can be applied to multiple entities. After an entity is highlighted, it can be selected by clicking on the Select button. Another entity can then be highlighted and selected subsequently. All entities that belong to a certain type (volumes, surfaces or curves) can be selected at once by pressing the appropriate Select All button. Selection is used when the user needs to flag multiple entities for performing further operations. The `Clear All' button clears all selections.

Selection of an unblanked entity can also be achieved by holding down the Ctrl key and clicking on the entity in the Graphics Display window with one of the mouse buttons.

Ctrl + left mouse button   - surface entity
Ctrl + middle mouse button - curve entity
Ctrl + right mouse button  - point entity

Selection/unselection of a group of entities can be achieved by drawing a drag box with

Shift + middle mouse buttom  - select entities within or partially within box
Shift + right mouse buttom  - unselect entities within or partially within box

Blank, Unblank, and Delete

Index Notation

Current limitations

Entity Names

Drag box and Overlays

GRIDED

• Swap J/K, K/L, L/J indices
• Reverse J, K, and/or L index
• Mirror about x, y, or z=0
• Scale by specified factor in x, y, and z
• Translate by specified amount in x, y, and z
• Rotate about x, y, or z Cartesian axis, or user-defined axis
• Extract a subset
• Extrapolate a number of planes by given stretching ratio at J/K/L boundaries
• Split an entity into 2 along a J, K or L constant slice
• Concatenate 2 entities in J, K or L
• Auto-concatenate multiple surface entities recursively in arbitrary orientations
• Swap entity ID's between 2 entities
• Resequence all entity ID's
• Generate surface/volume of revolution from curve/surface entity
• Smooth surface entity
• Create curve between intersector surface entity and intersectee surface entities

1. The Swap, Reverse, Mirror, Scale, Translate and Rotate functions can be used on one or multiple entities. The Extract and Extrapolate functions can only be used on a single entity at a time. The Concat function operates on two selected entities only, i.e. the user must select the first and then the second entity to be concatenated. The order of selection is important. Use the tangent vector display to determine which should be selected first. The Auto-concat function operates on two or more surface or curve entities. Auto-concat does not work on volume entities currently.
2. The Extract function operates on a highlighted subset of an entity.
3. The old entity is replaced by the new entity for Swap J/K, Swap K/L, Swap J/L, Reverse, Mirror, Scale, Translate and Rotate. The old entity is retained and the new entity/entities is/are created for Extract, Extrapolate, Concatenate, Split, Auto-concatenate and Smooth.
4. The UNDO button will erase the effects of the last operation only. UNDO's with scale, translate, rotate may be subjected to round-off errors, i.e. entities after the UNDO may not be bitwise identical to the original under these operations.

SRAP

1. It is assumed that the user is familiar with the terminology used for SRAP. See srap.html for explanation of usage.
2. The current end spacings of the segment are displayed in Da_c and Db_c. The new end spacings of segment can be specified under Da_n and Db_n.

PROGRD

Reference surface             : yellow
Unprojected active entities   : green
Projected active entities     : red

DIAGNOS

The grid quality functions supported for structured surface and volume entities include:

• stretching ratio in J, K, or L
• turning angle in J or K
• truncation error estimate
• average cell size at vertex
• iblanks statistics
• orphan points analysis
• Jacobians statistics (volume entities only)
• surface grid topology display and reset (surface entities only)

• vertex valence (number of faces sharing the vertex)
• minimum and maximum angle at vertex
• curvature function at vertex

• Iblanks analysis
• Orphan points analysis
• Jacobians analysis
• Surface topology analysis and reset

TRIGED

• Swap edge between two adjacent faces
• Reverse normals of all faces
• Mirror about x, y, or z=0
• Scale by specified factor in x, y, and z
• Translate by specified amount in x, y, and z
• Rotate about x, y, or z Cartesian axis, or user-defined axis
• Remove unused vertices
• Extract all faces on one side of x, y, or z=constant plane
• Extract all faces belonging to specified components
• Change face tags for all triangles with a given tag
• Assign different face tags to different regions based on disjointedness and sharp edge criteria

SEAMCR

For multiple panel networks, it can be used for

• automatic extraction of seam curves
• creation of surface curves by intersection with x, y, or z constant plane
• generation of spider web surface grids around the seam corners (where 3 or more seam curves meet)
• trimming and redistribution of seam curves based on global spacing and local turning angle. See seamcr.html for more details.

• automatic extraction of sharp edges
• intersection with x, y, or z constant plane
• stencil walk between 2 given vertices along existing edges
• construction of direct surface path between 2 given vertices

SURGRD

1. Once the SURGRD button is depressed from the main menu, the colors of all entities will change: all surfaces will become gray and will be assumed to be part of the reference surface; all curves will be colored individually and are available for selection as reference curves.
2. After generating one set of surface grids, the user must hit UNDO or exit the overgrid session before trying to generate something else with SURGRD. This limitation will be removed in the future.
3. Use the SAVE button to store surface grids generated and the input parameter file produced.
4. It is assumed that the user is familiar with the terminology used for SURGRD. See surgrd.html for explanation of usage.

SBLOCK

WKCUT

HYPGEN

BOXGR

TOPOLOGY AND BC

COMPONENTS

A configuration is defined to be the complete collection of objects in a simulation. Each configuration is made up of a collection of components. Each component can be a structured grid, a set of triangles, or a container. A container is used to group a set of lower level components and is not linked to any geometry or grids. Each component can be positioned initially by applying a sequence of transforms (rotate, translate, mirror). This mechanism is used to place duplicated components into their proper initial positions. For example, the 3 blades of a rotor can all be read from an input file with all 3 in the same location. The second and third blades can be placed into their proper positions by a rotation transform.

Also, each component is allowed to have one parent or none at all. A component inherits the motion of its immediate parent. Each component can have no motion relative to the inertial reference frame or to its parent component, or be allowed to move relative to other components under Prescribed Rotation motion, Prescribed Translation motion, Table-Lookup motion or Aero6dof motion.

This tool can be used to

• Assign a name to a component, specify its type, parent, transforms, and the structured grids and triangle tags that it is associated with. This information can be written to or read from a Configuration XML file. An additional option allows the output of the components file (Components.list) to be read by the CART3D suite of tools (WRITE CART).
• Prescribe and animate motion for components. Specified velocities are assumed to be non-dimensionalized and consistent with the grid/geometry units provided. Analytic expressions in the time variable 't' and the constant 'pi' are allowed in the translational velocity components and the rotation speed, e.g. rotation speed = 2.0 * sin ( 0.5 * pi * t ).
• Read or write the prescribed motion from and to a Scenario XML file.
• Animate motion for table-lookup components with optional contact dynamics (see below for table input format).
• Prepare inputs to Aero6dof motion - motion that is driven by aerodynamic forces and moments, with optional external applied loads and constraints.

Format for Table-Lookup Motion

 Component_ID  T  xc  yc  zc  e1  e2  e3  e4

where

 Component_ID = integer that stores the component ID tag
 T            = time
 xc,yc,zc     = coordinates of component center of mass at time T
 e1,e2,e3,e4  = Euler parameters of component at time T

An optional contacts log file can also be read to indicate the times, locations and local surface normals of contact points. The format for this file is

 ID_1  ID_2  T  xc  yc  zc  nx  ny  nz  diam

where

 ID_1, ID_2 = component ID tags of component pair in contact
 T          = time of contact
 xc,yc,zc   = coordinates of contact point
 nx,ny,nz   = local surface normal at point of contact
 diam       = tolerance for contact detection

Non-dimensionalization of Component Inertial Properties and Loads

Non-dimensional variables are indicated with an asterisk.

Length scale              = L
Free stream fluid density = rho_0
Free stream sound speed   = c_0

mass              m* = m/(rho_0 L^3), 
moment of inertia I* = I/(rho_0 L^5)
applied force     F* = F/(rho_0 c_0^2 L^2)
applied moment    M* = M/(rho_0 c_0^2 L^3)

PEGASUS 5

GEN_X

CALCULATORS

1. Freestream conditions calculator based on standard atmosphere

     Input : altitude, speed, reference length in dimensional units
     Output: Mach number, Reynolds number, pressure, temperature, density, sound speed,
             viscosity, mean free path

2. Mass properties calculator for triangulated objects
   
     Input : surface triangulation, density (constant)
     Output: mass, volume, surface area, center of mass, principal moments and axes of
             inertia, Euler parameters for transformation from inertial to principal
             axes coordinates

3. 6-dof units conversion

     Input : mass properties, gravity, applied forces/moments, etc. in dimensional units
     Output: corresponding parameters in non-dimensional units suitable for input to
             OVERFLOW-2 flow solver

OVERFLOW

OVERFLOW-2

SOLUTION VIEWER

                                         Grid frame       Solution frame
Steady state cases                           1                  1      
Steady/unsteady cases at different times     1               multiple
Moving/adaptive grid cases                multiple           multiple

The next step is to pick single or multiple frame for grid and q and read the files. The PLAY button will automatically cycle through the frames if multiple frames are read. The REC button will play and save each frame to a png image file, and the collection of png files can then be processed into a movie using an external program such as ffmpeg. Function options are available to plot all q variables in the q files, including those from turbulence models and species partial densities, common functions such as Mach number and velocity vectors. A log option is allowed for showing scalar functions. The function display can be made to appear in grid wireframes or contours.

After quitting this module, the grid and solution frames are released from memory. These have to be read in again for further viewing.

WARNING: there is currently no check for negative densities.

DEBRIS TRACING

Currently, the initial positions are restricted to constant L surfaces. A convenient way to prescribe the initial positions is to click on the `Use highlighted' button to copy a highlighted subset (lower right window) into the J,K,L range entries for initial positions. For a uniform distribution, the initial velocity direction is the local surface normal direction if only one entry is prescribed. If more than one entry is prescribed, the initial velocity direction is varied over a hemisphere with axis aligned with the local normal. Display of initial positions and velocity vector directions can be toggled via the appropriate checkbuttons.

Clicking the DEBRIS button will execute the code (assumed to be in user's path or in the CGT bin directory) and display the trajectories in the graphics window. The impact points on L=1 surfaces are colored by the impact speed. Note that when `Minimal output' is selected, there is no information to determine impact points. In this case, all trajectories are assumed to end in impact points. Work is in progress to add various options and filters for viewing the trajectories.

An input file for the DPREP input preparation batch code is automatically written to ogdprep.i. This can be used to generate the DEBRIS code input file in batch mode.

HYBRID GRID VIEWER

1. Display prism cut cells as wireframes, colored by same color or by component ID of triangles on surface triangulation

2. Display prism cut cells as shaded polygons which will reveal gaps between the trimmed prism cells

3. Highlight the cut cell polygons that belong to fringe cells which will show whether these are surrounded by any donor cells.

4. Display neighboring strands that straddle the cut plane.

5. Display the surface triangle face index for each intersection polygon. Each intersection polygon comes from a prism cell which belongs to a prism stack that can be traced down to a surface triangle. This option provides a map of the prism stacks and shows where they terminate on the cut plane and if they terminate at a fringe cell.

On the same display, the user can read in AMR Cartesian grids (in PLOT3D format for now) and display the different levels at the specified cut plane. Options are available to color by level, display wireframe grid lines or display just the grid bounding box outline. Having the prism cut and Cartesian cut in the same display provides a valuable tool for checking the AMR grid generator and for debugging interpolation stencil problems.

To be implemented

• Configuration scripts
• Elliptic grid smoothing capability
• Better arrowheads for direction vectors for curves

References

Chan, W. M., CAD Interface, Strand Grid Technology, and Other New Developments in Chimera Grid Tools 2.0, Proceedings of the 8th Symposium on Overset Composite Grids and Solution Technology, Houston, Texas, October, 2006.

Chan, W. M., The OVERGRID Interface for Computational Simulations on Overset Grids , AIAA Paper 2002-3188, 32nd AIAA Fluid Dynamics Conference, St. Louis, Missouri, June, 2002.

Chan,, W. M., Meakin, R. L. and Potsdam, M. P., CHSSI Software for Geometrically Complex Unsteady Aerodynamic Applications, AIAA Paper 2001-0593, January, 2001.

Murman, S., Chan, W. M., Aftosmis, M. J., Meakin, R. L., An Interface for Specifying Rigid-Body Motions for CFD Applications, AIAA Paper 2003-1237, 41st Aerospace Sciences Meeting and Exhibit, January, 2003.

Chan, W. M., Innovative Software Streamlines Overset Grid Generation , NAS News, Vol. 3, No. 3, May-June, 1998.

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Questions and Comments