VisIt Data Formats

Data Formats

VisIt supports a wide variety of file formats that are used in computational analysis.

Data Formats
Format Name Extension Description
ANALYZE *img, *hdr Rectilinear grid of integer values containing MRI and fMRI data for human brains.
ANSYS *.inp The VisIt ANSYS reader reads in the ASCII version of the ANSYS mesh input file format.
AUXFile *.aux LLNL ASCII file format containing target and beam diagnostic data for National Ignition. Facility (NIF) lasers.
BOV *.bov Brick of values format where the database can be broken down into small bricks of ZLIB compressed scalar arrays.
Boxlib2D *.boxlib2d Structured AMR format for 2-D. Requires a .VisIt file to group multiple time states into a single time-varying database.
Boxlib3D *.boxlib3d Structured AMR format for 3-D. Requires a .VisIt file to group multiple time states into a single time-varying database.
CGNS *.cgns CFD General Notation System (CGNS) files contain platform-independent binary CFD (computational fluid dynamics) data for both unstructured and structured grids. For more information on CGNS, VisIt http://www.cgns.org.
CMAT *.cmat ASCII output of CMAT Fortran simulation
Cosmos *.cosmos Astronomical simulation data saved in HDF4 format.
CosmosPP *.cosmospp, *.cosmos++ Astronomical simulation data saved in HDF5 format.
Curve2D *.curve, *.ultra, *.ult ASCII text file containing two columns of X,Y pairs that describe a curve. Each curve is preceded by a "#" comment containing the name of the variable.
Dune *.dat ASCII file containing point meshes and variables written by Dune simulation code.
EnSight files *.case VisIt can read CEI EnSight data files.
Enzo *.boundary, *.hierarchy Stanford University AMR Astrophysics simulation output saved in HDF4 format.
Exodus *.ex, *.e, *.exo, *.ex2, *.exII, *.exii, *.gen, *.EX, *.E, *.EXO, *.EX2, *.EXII, *.GEN, *.exodus, *.EXODUS,*.nemesis, *.NEMESIS Sandia National Laboratory's file format for storing simulation data.
FLASH None AMR data stored in HDF5 file format produced by the FLASH code from the University of Chicago. The -default_format FLASH command line options must be specified to select this database reader plugin because the plugin is not associated with any file extensions.
GDAL *.adf, *.asc, *.bt, *.ddf, *.dem, *.ecw, *.gxf, *.jp2, *.map, *.mem, *.mpl, *.mpr, *.n1, *.nat, *.ntf, *.pix, *.rsw, *.sid, *.vrt, *.xpm GDAL is a translator library for raster geospatial data formats common in the Geographic Information Systems (GIS) field. VisIt's GDAL reader can read the formats that GDAL itself can read including popular GIS formats such as: ArcInfo binary grid and Digital Elevation Map (DEM). For a complete list of the file formats that VisIt can access through the GDAL reader plugin, refer to http://www.gdal.org/formats_list.html. Note that many of the formats that GDAL can read are actually image file formats. VisIt reads image file formats through its Image database reader plugin unless you tell the GDAL plugin to read image files by setting the VISIT_READ_IMAGES_WITH_GDAL environment variable.
Image *.BMP, *.JPEG, *.JPG, *.PNG, *.PNM, *.PPM, *.SDT, *.SPR, *.TIF, *.TIFF, *.bmp, *.imgvol, *.jpeg, *.jpg, *.png, *.pnm, *.ppm, *.sdt, *.spr, *.tif, *.tiff The Image database reader plugin can read in many popular image file formats, allowing you to plot images of experimental data or perform image analysis. In addition, the Image database reader plugin supports the creation of image volumes, which are comprised of a set of 2-D slice images that can be reassembled into a 3-D volume. An image volume file is a text file (ending in .imgvol) that contains the names of the images to be reassembled into a 3-D volume.
KullLite *.pdb, *.mkf Input mesh files for Kull simulation program. Data files are stored in PDB format.
Lines *.dat ASCII text format containing X,Y pairs or X,Y,Z triples.
Mili *.m, *.mili Popular LLNL engineering format used in Dyna3D, Nike3D simulation codes. Requires use of the VisIt -make mili utility to create a .mili file that can be opened.
NASTRAN *.nas, *.f06 NASTRAN is a popular commercial finite element tool. The VisIt NASTRAN reader plugin can import geometry from NASTRAN bulk data files.
NETCDF *.nc, *.cdf, *.elev Network Common Data Form (NetCDF) files are used to store scientific, array-oriented data in a machine-independent, binary format. NetCDF files often contain data from climate observations and results for climate simulations.
OVERFLOW *.dat, *.save Binary Fortran output files containing overlaid curvilinear meshes.
PATRAN *.neu PATRAN is a popular commercial finite element code. The VisIt PATRAN reader reads PATRAN neutral files, which are ASCII format files that contain unstructured geometry and simulation results.
PDB/Flash *.pdb, *.r0000 The PDB database plugin is an umbrella reader for multiple styles of files written in the PDB database format.

Flash files are read by this plugin. Equation of state databases in PDB format can also be read using this plugin. Finally, the PDB plugin supports reading wavelet-compressed data files generated with Pf3D simulation code.

Pixie *.h5 2-D and 3-D LANL simulation data saved in HDF5 format.
Plot2D *.p2d Structured data format for simulation data in Plot2D format.
Plot3D *.x, *.q Structured data format for simulation data in [Plot3D] format.
Point3D *.3d ASCII file format containing four columns of numbers: X,Y,Z points and a data value.
SAF *.saf Arbitrary simulation data stored in HDF5 file format by Sets and Fields (SAF) library.
SAMRAI *.samrai Structured AMR data stored in HDF5 file format. Requires a .VisIt file to group multiple time states into a single time-varying database.
SAR *.sar, *.SAR Specific Absorption Rate image volume files.
STL *.stl Stereolithographic file format containing triangle coordinates
Shapefile *.dbf, *.shp ESRI Shapefiles are commonly used in GIS applications to store vector data (boundaries, roads, building footprints, etc.).
Silo (*.pdb, *.silo) Popular LLNL file format based on PDB that supports scalar, vector fields, and materials stored on rectilinear, curvilinear, nstructured, or point meshes. Data can be split up into multiple domains.
Spheral *.sv, *.spheral Spheral files contain results of coupled hydrodynamical and gravitational simulations in ASCII form.
Tecplot *.plt *.tec, *.tp ASCII file format for the popular TecPlot plotting package.
Tetrad *.h5, *.hdf5 Tetrahedral meshes and variables stored in HDF5 file format.
TFT *.dat, *.tft ASCII output of TFT Fortran simulation.
Time Varying Exodus *.exII Same as Exodus
VTK *.vtk ASCII/Binary files containing data from multiple kinds of objects from Visualization Toolkit (VTK). For more information about VTK, VisIt http://www.kitware.com.
Vista *.vista Hierarchical file format based on Silo that stores data in HDF5 file format.
ViSUS *.idx, *.vis Research file format that allows dynamic decomposition of the file based on available processors and supports efficient reading of data (and subsets of data) from the file.
Wavefront OBJ *.obj Alias Wavefront Object file format. Contains 3-D models.
Xmdv *.okc ASCII file containing columns of data.

Reading in Data

File Menu in VisIt
File Menu in VisIt

File Open Menu in VisIt
File Open Menu in VisIt

VisIt uses the terminology of databases, instead of files, when it talks about reading in data. Normally a user thinks about just reading in data files, which is the first type of database. The second type of database would be a running computational simulation. A user can manage both types of databases using the same VisIt windows.

First launch VisIt and then select File->Open Data from the main menu. This will open "File Open" panel.

This panel gives the user the ability to load data in many different formats. The user will need to select the appropriate format for the data to load it, or allow VisIt to guess the format based on the extension. Allowing VisIt to guess the format can cause problems, since some files have the same extension, but different formats.

  1. The user selects File->Open from them main menu.
  2. Navigate to the correct directory where the data files reside.
  3. The user can select the correct file type from the list using the Open File as type.
  4. The user can select the desired file by double clicking or by clicking the OK button.

Above was the simple way to use File Open window. There are more advanced options that a user can utilize in the window.

Changing Hosts

VisIt's distributed nature allows it to run the compute engine on a large HPC machine while the user interface runs on a local workstation. This allows VisIt to visualize computational simulation data on the HPC machines without the need to move the data to a local workstation or visualization machine. It also allows VisIt to harness the local graphics card of the workstation for hardware acceleration. By default the host is: "localhost", which means the local machine that the user is running on. This can be changed to a remote computer, allowing the user to access remote data files. To access a remote computer, the user must provide the name in the Host text field. This can be done by either typing the remote computers name. Alternately, a remote computer can be selected from the list of recently visited hosts, by using the down-arrow at the right side of the Host text box.

Virtual Databases

VisIt artificially creates a virtual database out of a series of single time step databases that have related filenames. A virtual database allows the user to access time-varying data files without having to create a .VisIt file first. VisIt creates this virtual database automatically for the user. The user can turn off this feature by selecting the Off option in the File grouping pull-down menu in the File Selection Window.

Refreshing the File List

When computational simulations are running on the HPC system, they are writing out new data files to the disk system. The Refresh button on the File Open window causes VisIt to reread the current directory. This will allow VisIt to find any new data files recently written by the simulation. If the current database in VisIt is a virtual database, and that virtual database was changed by refreshing the file list, then VisIt will close and reopen the database. This allows information about any new time steps to be seen by VisIt.