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Usage of hdf2v3 and hdf2file

hdf2v3/hdf2file [-f display_file] [-fs solver_file] [-s basic_filename ׀ -m] time-step_number    

hdf2v3 and hdf2file are AMROC's native visualization tools. hdf2v3 relies on the Visual3-library and is intended for the comfortable graphical visualization of two- and especially three- dimensional results. hdf2file is a conversion tool with a similar parameter-interface that can produce new HDF-files, ASCII-tabulars and input for IBM's Data Explorer. hdf2file is intended to be used for one-dimensional results, to generate lower-dimensional cuts, to create HDF-files for derived quantities and as an interface to very advanced visualization tools.

Up to now, hdf2v3 and hdf2file are limited to HDF-files with cell-centered data that have been produced by finite-volume scheme for Euler equations.

If the visualizers are started without -s or -m Euler equations for a single ideal gas are assumed. Specific physical values for the gas are read from the file chem.dat.

'Keys' select possible quantities. Hit the 'key' in the 3D-window in case of hdf2v3 or select multiple 'keys' in display_file in case of hdf2file.

Before using hdf2v3 you should go over the installation notes for Visual3 below.

The following keys are supported in the standard mode for a single ideal gas:
  i - Distribution s - Levels
  d - Density u - Velocity u
  v - Velocity v w - Velocity w
  e - Total Energy l - ׀Velocity׀
  f - Flow Vectors D - Schl.-Plot Density
  U - Schl.-Plot Velocity u V - Schl.-Plot Velocity v
  W - Schl.-Plot Velocity w E - Schl.-Plot Total Energy
  L - Schl.-Plot ׀Velocity׀ x - Vorticity of w and v
  y - Vorticity of u and w z - Vorticity of v and u
  t - Temperature p - Pressure
  n - Entropy c - Speed of Sound
  m - Machnumber T - Schl.-Plot Temperature
  P - Schl.-Plot Pressure N - Schl.-Plot Entropy
  C - Schl.-Plot Sound-Speed M - Schl.-Plot Machnumber
     
-f Name of parameter file for visualizer. Default values are display.in for hdf2v3 and display_file.in for hdf2file  

-fs Name of parameter file that contains the topological data and the basic filenames of the HDF-files to be read in. Default is solver.in.

-s basic_filename A single HDF-file with a given basic filename is displayed. The following keys are supported in the scalar mode:
  i - Distribution s - Levels
  f - Function F - Schl.-Plot Function

-m Multi-component Euler equations for arbitrary thermally perfect gases are choosen. Physical values for the different gases are read from the file chem.dat. The following keys are supported in this mode:
  i - Distribution s - Levels
  d - Density u - Velocity u
  v - Velocity v w - Velocity w
  e - Total Energy l - ׀Velocity׀
  f - Flow Vectors D - Schl.-Plot Density
  U - Schl.-Plot Velocity u V - Schl.-Plot Velocity v
  W - Schl.-Plot Velocity w E - Schl.-Plot Total Energy
  L - Schl.-Plot ׀Velocity׀ x - Vorticity of w and v
  y - Vorticity of u and w z - Vorticity of v and u
  t - Temperature p - Pressure
  g - Gamma c - Speed of Sound
  T - Schl.-Plot Temperature P - Schl.-Plot Pressure
  G - Schl.-Plot Gamma C - Schl.-Plot Sound-Speed
  0 - Mass fraction Gas 1 1 - Mass fraction Gas 2
  2 - Mass fraction Gas 3 3 - Mass fraction Gas 4
  4 - Mass fraction Gas 5 5 - Mass fraction Gas 6
  6 - Mass fraction Gas 7 7 - Mass fraction Gas 8
  8 - Mass fraction Gas 9 9 - Mass fraction Gas 10

time-step_number During computation a unique integer-valued number is assigned to each time-step. The format for HDF-files is [basic_filename]_[time-step_number].hdf.  


Parameters in display_file of hdf2v3 [display.in]

Possible parameters and default values (in brackets [ ]):

Type[1] = 1 Vertex-centered display mode. The originally cell-centered data is interpolated onto the neighboring vertices. Various Visual3-options, e.g. isosurfaces, require vertex-centered data.
  = 6 Cell-centered display mode. Optimal for debugging and faster than vertex-centered.

UseEquiv[0] = 1 Vertex equivalencies between vertices of the geometric grid are calculated
  and are handed over to Visual3. If this option is not used and Edgeoutlineon is in the script section is in effect white lines will be drawn at the borders of each subgrid. The drawing of these lines can be suppressed completely by adding Edgeoutlineoff to the script section.
  = 0 Don't find vertex equivalencies.

DisplayMinLevel[0] = l Min. level to be displayed.  
     
DisplayMaxLevel[0] = l Max. level to be displayed.  

PlotGrid(1...l)[0] = 0 Do not plot the subgrids on a particular level.  
  = 1 Plot the subgrids on a particular level.  

ShowMin(1/2/3)[geometric min. from solver_file]
ShowMax(1/2/3)[geometric max. from solver_file]
  A restricted rectangular area may be choosen in geometric coordinates from the computational domain. This option is useful to speed up the visualizer in case of large simulations.
     
ShowCut(1/2/3)[Not set]   Calculate a lower-dimensional cutting plane that is orthogonal to x(=1)-, y(=2)- or z(=3)-axis.

Symmetry(1/2/3)[0] = 0 Do not use symmetry in x(=1)-, y(=2)- or z(=3)-direction.  
  = 1 Doubles domain by assuming symmetry at the upper bound.  
  = -1 Doubles domain by assuming symmetry at the lower bound.  
  Symmetry in multiple directions can be selected.  
     
Periodic(1/2/3)[0] = 0 Do not use periodicity in x(=1)-, y(=2)- or z(=3)-direction.  
  = 1 Doubles domain by assuming periodicity at the upper bound.  
  = -1 Doubles domain by assuming periodicity at the lower bound.  
  Periodicity in multiple directions can be selected.  

A special script section can be used to automatically set Visual3 in a predefined state. The syntax is

ScriptBegin {    
Commands...
   
}    

The commands are defined in visualizer/include/HDFToV3/FileEventhandler.h. In visualizer/include/HDFToV3/Eventhandler.h a queue is set up that in principle does nothing else than passing parameters to V3_SETSTATE() whenever Visual3 calls this function during its X-event-loop. See the Visual3 Advanced Programmer's Guide for further details and possible parameters, if you want to use this functionality of hdf2v3 extensively.


Parameters in display_file of hdf2file [display_file.in]

Possible parameters and default values (in brackets [ ]):

Type[6] = 1 Vertex-centered display mode. The originally cell-centered data is interpolated onto the neighboring vertices. Like Visual3, IBM's Data explorer can calculate for instance isosurfaces only in this mode.
  = 6 Cell-centered display mode. Optimal for debugging and faster than vertex-centered.

FileName[None] Basic filename for generated files. If no name is selected the ouput goes to standard output.  

FileType[0] = 0 Browse through all cells and write an ASCII-tabular with highest level data. This type is intended to create one-dimensional output. With LinePoint(1/2/3) and LineVector(1/2/3) it can used to create plotting line-lots through higher dimensional data (set Type=1 for this option). The cells are not ordered and the tabular may not be appropriate for some plotting tools.The format is:
 
x_1 [y_1] [z_1] key_1 ... key_n
.....
x_m [y_o] [z_p] key_1 ... key_n
  = 1 Same as FileType=0, but the cells are ordered by the coordinates. This format should be appropriate for most plotting tools.
  = 2 Browse through all cells and create a regular ASCII-tabular with extends determined RegularData(1/2/3). Data from finer levels is assigned to the nearest cells. This type is intended to be used to create three-dimensional plots from two-dimensional with simple plotting tools, e.g. Gnuplot.
  = 3 Creates unstructured binary data for IBM Data Explorer.
  = 4 Creates unstructured ASCII data for IBM Data Explorer.
  = 5 Creates unstructured binary data for IBM Data Explorer that can be read into Data Explorer via an external filter.
  = 6 Creates HDF data. If a cut through the data is selected the dimension of the output is NOT reduced.
  = 7 Creates HDF data. If a cut through the data is selected, the output is of lower dimension than the input data.
  = 8 Creates structured Tecplot data in ASCII format. Use PointOutput = 1 to switch from output type f=block to f=point.
  = 9 Reserved for structured Tecplot data in binary format. Not implemented yet.
  = 10 Creates unstructured VTK ASCII format suitable for Visit. Ending .vtk
  = 11 Creates unstructured VTK binary format suitable for Visit. Ending .vtk.
  = 12 Creates unstructured VTK ASCII format suitable for Paraview. Ending .vtu
  = 13 Creates unstructured VTK binary format suitable for Paraview. Ending .vtu
  = 15 Creates structured SILO binary format suitable for Visit. Ending .silo. Requires parameter SILO_DIR for vtf/configure.

Keys A list of 'keys' (seperated by commas or white-spaces) defining the quantities that have to be calculated. FileTypes 3-5 only use the first key, if a list supplied. All other FileTypes allow multiple keys during a single run of the converter.

DisplayMinLevel[0] = l Min. level to be used.  
   
DisplayMaxLevel[0] = l Max. level to be used.  

ShowMin(1/2/3)[geometric min. from solver_file]
ShowMax(1/2/3)[geometric max. from solver_file]
  A restricted rectangular area may be choosen in geometric coordinates from the computational domain. This option is useful to speed up the visualizer in case of large simulations.
     
ShowCut(1/2/3)[Not set]   Calculate a lower-dimensional cutting plane that is orthogonal to x(=1)-, y(=2)- or z(=3)-axis.

Symmetry(1/2/3)[0] = 0 Do not use symmetry in x(=1)-, y(=2)- or z(=3)-direction.  
  = 1 Doubles domain by assuming symmetry at the upper bound.  
  = -1 Doubles domain by assuming symmetry at the lower bound.  
  Symmetry in multiple directions can be selected.  
     
Periodic(1/2/3)[0] = 0 Do not use periodicity in x(=1)-, y(=2)- or z(=3)-direction.  
  = 1 Doubles domain by assuming periodicity at the upper bound.  
  = -1 Doubles domain by assuming periodicity at the lower bound.  
  Periodicity in multiple directions can be selected.  

LinePoint(1/2/3)
LineVector(1/2/3)
For FileType=0/1. Defines a straight line. Only vertices that are hit by this line will be plotted (set Type=1 for this option).  

RegularData(1/2/3) For FileType=2.  

Installation of Visual3 for hdf2v3

The Visual3-library has a minor flaw! Visual3 is aborted with a core-dump without any warning during startup, if no own valid definitions for its X-Window-fonts are supplied. This usually happens when the program tries to open its first window. The following definitions should be added permanently to .Xresources or .Xdefaults:

Visual*small: 6x10
Visual*medium: 8x13
Visual*med2: -adobe-courier-bold-r-normal--17-120-100-100-m-100-iso8859-1
Visual*large: -adobe-courier-bold-r-normal--25-180-100-100-m-150-iso8859-1

Use xfontsel to ensure that fonts defined in Visual*med2 and Visual*large are really available on your local system.

If you are using a Linux system with an 8-bit color depth Xserver you must set the environment variable MESA_RGB_VISUAL to PseudoColor 8 before running Visual3. But the display will look much better, if 12 or more bits/pixel are used in a TrueColor mode so that no dithering is required. If you have a graphics card with enough VRAM it is recommended to start the Xserver in 12, 15 or 24 bits TrueColor mode. Note that Visual3 does NOT support 16 bit.



-- RalfDeiterding - 12 Dec 2004

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