Partial list of file formats and their details VisIt supports

Revision as of 18:21, 26 June 2009 by Jsmeredith (talk | contribs) (test categories for science domains)

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Detailed list of all file formats

Application Code Formats

These are formats that were originally designed primarily for and are part of some specific application code. That is, the code that writes these files is typically part of the application itself and is not a stand-alone product of its own. Nonetheless, these formats may use some lower level library such as HDF5, or they may use raw ASCII.

Plug-in Name Format Name Typical File Names Description Links
ANSYS ANSYS input *.inp ANSYS is a computer-aided engineering suite of tools. ANSYS home page
AUXFile AUX files *.aux Diagnostic data for the National Ignition Facility (NIF). NIF home page
Cale CALE output *.pdb *.cale CALE is a hydrodynamics code.
CCM STAR-CD output *.ccm The CCM plugin reads data from the STAR-CD CFD code. STAR-CD home page
Cosmos Cosmos output *.cosmos Cosmos++ is a "massively parallel, multi-dimensional, fully covariant, modern object-oriented (C++) magnetohydrodynamics code written to support structured and unstructured adaptively refined meshes, and for both Newtonian and general relativistic astrophysical applications."
CosmosPP *.cosmospp *.cosmos++
CTRL TB-LMTO control file *.ctrl CTRL files are the control files for TB-LMTO software, which uses the linear muffin-tin orbital (LMTO) method. This reader supports the STRUC, CLASS, SITE, ALAT, and PLAT file categories. STUTTGART TB-LMTO program
DDCMD DDCMD *.ddcmd ddcMD is a parallel domain-decomposition molecular dynamics code from LLNL.
Dune deprecated
Dyna3D Dyna3D output files *.dyn Dyna3D is a finite element engineering code from LLNL. Dyna3D home page
Enzo Enzo HDF4, HDF5, and HDF5 packed-AMR output *.boundary *.hierarchy Output from the scientific simulation code Enzo. Enzo is "an adaptive mesh refinement (AMR), grid-based hybrid code (hydro + N-Body) which is designed to do simulations of cosmological structure formation." Enzo home page Enzo portal
FLASH FLASH HDF5 output FLASH is the code from the ASC / Alliances Center for Astrophysical Thermonuclear Flashes. FLASH home page
Fluent Fluent case/data files *.cas FLUENT is a popular commercial CFD code, now owned by ANSYS. FLUENT home page
Gadget Gadget files *.gadget GADGET is a parallel cosmological N-body/SPH simulation code.
GGCM GGCM 3df files *.3df The centerpiece of the NSF/GEM program is the development of a Geospace General Circulation Model (GGCM), to be used as a research tool as well as a prototype for space weather forecasting models. Open Geospace General Circulation Model
GTC GTC HDF5 output "The gyrokinetic toroidal code (GTC) is a massively parallel, particle-in-cell code for simulations of turbulence and transport in fusion plasmas such as ITER." GTC home page
H5Nimrod NIMROD HDF5 output .h5nimrod The H5Nimrod plugin was developed at Lawrence Berkeley National Laboratory to read NIMROD's HDF5 output file format. H5Nimrod information
KullLite KULL lite format *.pdb *.mkf KULL is "LLNL's ASCI inertial confinement fusion simulation code"
LAMMPS (coming in 1.12) LAMMPS Atom-style dump *.dump LAMMPS is the "Large-scale Atomic/Molecular Massively Parallel Simulator". This reader supports both the output dump in "Atom" style and the format used by the read_data input script command. LAMMPS dump documentation LAMMPS home page
LAMMPS read_data input *.eam *.meam *.rigid
M3D M3D files *.m3d M3D is a parallel multilevel 3D plasma simulation code.
Mili Mili files *.mili *.m Mili is an engineering code from LLNL. Note that you might have to run a file preparation utility before reading these files.
Miranda Miranda files *.mir *.raw Miranda is a research hydrodynamics code from LLNL.
MFIX MFIX restart file *.res "MFIX (Multiphase Flow with Interphase eXchanges) is a general-purpose computer code developed at the National Energy Technology Laboratory (NETL) for describing the hydrodynamics, heat transfer and chemical reactions in fluid-solids systems." MFIX home page
MM5 MM5 *.mm5 MM5 is a limited-area, nonhydrostatic, terrain-following sigma-coordinate model designed to simulate or predict mesoscale atmospheric circulation. MM5 Community Model
NASTRAN NASTRAN ASCII bulk data format *.nas *.f06 "MSC Nastran is a powerful general purpose finite element analysis solution for small to complex assemblies." Nastran home page
Nek3D deprecated
Nek5000 NEK5000 field files *.nek3d *.nek2d *.nek5k *.nek5000 *.nek NEK5000 is a spectral element CFD solver developed at Argonne National Laboratory. Note that this reader requires a meta-data file that you open in VisIt, and which points to the field files. NEK5000 home page
OVERFLOW OVERFLOW output files *.dat *.save OVERFLOW is an overset flow solver for structured grids from NASA. Wikipedia OVERFLOW entry OVERFLOW code page
PATRAN PATRAN Neutral *.neu PATRAN neutral file, which is an ASCII file containing the definition for an unstructured mesh. PATRAN Home Page
PFLOTRAN PFLOTRAN HDF5 output pflotran.h5 PFLOTRAN is massively parallel groundwater simulation code. PFLOTRAN home page
Pixie Pixie HDF5 output *.h5 Pixie is a single-block, rectilinear mesh file using HDF5. Pixie files are generated by software at Los Alamos (may be related to Polar Ionospheric X-Ray Imaging Experiment (PIXIE)). VisIt's Pixie reader was written with a high degree of generality in mind. It makes few assumptions regarding the names and/or locations of HDF5 objects in the file and can often be used successfully to read arbitrary, HDF5 arrays of data.
S3D S3D NetCDF output S3D is a combustion simulation from Sandia National Laboratories.
SAS SAS output *.sasgeom *.sasdata *.sas SAS is a nuclear reactor modeling code from Argonne National Laboratory. Nuclear engineering codes at ANL
Tetrad TETRAD HDF5 file *.h5 *.hdf5 TETRAD is a reservoir simulation from Idaho National Lab (formerly INEEL).
UNIC UNIC HDF5 output *.h5 UNIC is a neutronics code from Argonne as part of the Simulation-based High-efficiency Advanced Reactor Prototyping (SHARP) Framework.
VASP VASP charge density grid CHGCAR* VAMP/VASP is the Vienna Ab-initio Simulation Package for performing quantum-mechanical molecular dynamics.VASP outputs a variety of different files; this reader supports several of them. VASP home page
VASP output ion positions, velocities, forces OUTCAR*
VASP ion positions and velocities POSCAR*
ZeusMP Zeus-MP *.zeus This database reader plugin reads HDF4 files from ZEUS-MP, which is a parallel addition to the ZEUS line of community application codes developed by the Laboratory for Computational Astrophysics. Zeus-MP home page

Application Toolkit Formats

These are similar to application code formats except that instead of being part of one specific application code, they are instead part of a broader framework or toolkit for writing application codes. Again, the code that writes files in these formats is not a stand-alone product on its own. Instead, it is part of the associated toolkit.

Plug-in Name Format Name Typical File Names Description Links
Boxlib2D Boxlib data file Header *.boxlib2d The Boxlib library is an adaptive mesh refinement (AMR) framework developed at CCSE. This plugin reads the 2D and 3D versions of the file. CCSE home page at LBL
Boxlib3D Header *.boxlib3d
CEAucd CEA data *.inp Unstructured data from CEA.
Chombo Chombo HDF5 file *.h5 *.hdf5 The Chombo package provides a set of tools for implementing finite difference methods for the solution of partial differential equations on block-structured adaptively refined rectangular grids. Chombo home page
Claw CLAWPACK files CLAWPACK is the Conservation Law Package, an AMR code from University of Washington.
ITAPS_C ITAPS files varies by ITAPS implementation ITAPS is the Interoperable Technologies for Advanced Petascale Simulations interface specification. ITAPS is not so much a file format as it is an interface specification for data exchange. There are several impelementations of this interface including MOAB, FMDB, and GRUMMP. Each implementation writes ITAPS data to its own, unique file format. For this reason, a given installation of VisIt may have support for any and/or all of these ITAPS implementations, each with a different name such as ITAPS_MOAB, ITAPS_FMDB or ITAPS_GRUMMP. ITAPS Home page
OpenFOAM OpenFOAM controlDict The OpenFOAM (Open Field Operation and Manipulation) CFD Toolbox can simulate anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics, electromagnetics and the pricing of financial options. OpenFOAM is freely available and open source, licensed under the GNU General Public License. OpenFOAM Home Page
SAMRAI SAMRAI HDF5 files *.samrai SAMRAI is the Structured Adaptive Mesh Refinement Application Infrastructure library from Lawrence Livermore National Laboratory. SAMRAI home page
Spheral Spheral++ output *.sv *.spheral Spheral++ is a steerable parallel environment for performing coupled hydrodynamical and gravitational numerical simulations. Spheral++ SourceForge page
Vista deprecated

General Scientific Data Formats

These formats are specifically designed to be scientific interchange formats for a variety of applications, storing data for one or more computational science domains. These formats are not specific to any application code or toolkit and typically have standalone I/O libraries.

Plug-in Name Format Name Typical File Names Description Links
CGNS CGNS The CFD General Notation System (CGNS) consists of a collection of conventions, and software implementing those conventions, for the storage and retrieval of CFD (computational fluid dynamics) data. CGNS home page CGNS User's Guide
Exodus Exodus NetCDF file *.ex *.e *.exo *.ex2 *.exii *.gen *.exodus *.nemesis Exodus is a format from Sandia National Laboratories for storing scientific data. ExodusII documentation
H5Part H5Part HDF5 files *.h5part H5Part is a high-performance parallel data interface to HDF5, largely targeted at particle-based simulations. The H5Part plugin was developed at Lawrence Berkeley National Laboratory. H5Part plugin info H5Part home page
HDF_UC FastBit HDF5 file *.h5 *.h5part FastBit, "An Efficient Compressed Bitmap Index Technology", is from LBL's Scientific Data Management Research Group. FastBit home page
NETCDF ADAPT output files *.nc *.cdf *.elev *.ncd ADAPT is an meteorological modeling code from NARAC/LLNL. Reading NETCDF in VisIt
CCSM files CCSM is the Community Climate System Model code initially from NCAR.
FVCOM files FVCOM is an unstructured climate code from UMASSD-WHOI.
LODI LODI is an atmosphere dispersion code from NARAC/LLNL.
BasicNETCDF For NetCDF files not from one of the above codes, this sub-format does its best to extract 1D, 2D, and 3D arrays with Cartesian grids. It will not understand unstructured grids or other data storage conventions.
PDB PACT/PDB *.pdb *.r0000 PACT is the Portable Application Code Toolkit from Lawrence Livermore National Laboratories, and PDB is its Portable Data Base I/O layer. Several variants with conventions for a few specific application codes using PDB are also supported through this reader. PACT home page
LEOS output
PF3D output
Silo Silo PDB and HDF5 files *.silo Silo is an LLNL data file format for storing rectilinear, curvilinear, unstructured, or point meshes in 2D and 3D. Scalar, vector, and material data can be defined on meshes. Data can be broken up into different files (multi-block) to increase parallel performance. Silo home page
TimeVaryingExodus time-varying Exodus file *.exII This is a format specialized for reading time-varying Exodus files. (see Exodus above)
XDMF XDMF XML and HDF5 data *.xmf *.xdmf XDMF is standardized method to exchange scientific data between High Performance Computing codes and tools. It uses XML to store light data and HDF5 to store heavy data. XDMF home page

Specialized Scientific Data Formats

These are scientific data formats that are designed for one limited type of data, often specific to a single scientific domain such as geographic or molecular data. They often have standalone I/O libraries if they are not ASCII-based.

Plug-in Name Format Name Typical File Names Description Links
BOW BOW files *.txt BOW files are compressed brick-of-wavelet files from LibGen, a suite of libraries developed at LLNL. LibGen home page
FITS FITS *.fit *.fits *.imh FITS stands for `Flexible Image Transport System' and is the standard astronomical data format endorsed by both NASA and the IAU. FITS is much more than an image format (such as JPG or GIF) and is primarily designed to store scientific data sets consisting of multi-dimensional arrays (1-D spectra, 2-D images or 3-D data cubes) and 2-dimensional tables containing rows and columns of data. FITS Home Page
GDAL GDAL files *.adf *.asc *.bt *.ddf *.dem *.ecw *.gxf *.jp2 *.map *.mem *.mpl *.mpr *.n1 *.nat *.ntf *.pix *.rsw *.sid *.vrt *.xpm GDAL is the Geospatial Data Abstraction Library.
MatrixMarket (coming in 2.0) MatrixMarket dense and sparse *.mtx MatrixMarket is a format for storing matrices in a variety of formats and data types. This reader supports the dense (array) and sparse (coordinate), real-valued forms. MatrixMarket home page
ProteinDataBank PDB files *.pdb Protein Databank (PDB) files contain molecular data describing the structures of biological macromolecules. RCSB Protein Data Bank
SAMI *.sami SAMI is a particular type of Silo file output by mesh generators such as TrueGrid and Pmesh for representing an unstructured mesh of hexahedra. It uses Silo's low-level array objects to output 3 floating point coordinate arrays and 8 integer connectivity arrays as well as some optional integer material information. TrueGrid
Silo home page
SAR SAR file *.sar This is a 3D regular grid format for Specific Absorption Rate from ARL.
Shapefile ESRI shapefile *.shp *.dhx *.dbf Shapefile is a vector data format for geographic information systems. Shapefile description
ViSUS ViSUS files *.idx *.vis ViSUS is a streaming format for large scientific data. ViSUS home page
VLI VLI connection *.vli Socket connection based reader, connecting to University of Tennessee's VLI multivariate data server.
XYZ XYZ file *.xyz The .xyz file format is a simple ASCII format used for describing atom positions, species, possibly variables, and possibly with multiple time steps. XYZ format information Wikipedia XYZ entry

Visualization Formats

These formats are geared towards storing data for visualization tools.

Plug-in Name Format Name Typical File Names Description Links
ANALYZE Analyze 7.5 Image *.img + *.hdr Analyze is a tool for 3D biomedical image visualization developed at the Mayo Clinic. This reader supports the .img/.hdr file pair format of Analyze 7.5. Analyze home page Analyze format description
BOV Brick Of Values *.bov BOV data are stored in two files. The first file is binary and it contains all of the data for an implied rectilinear grid stored as a brick of floats, doubles, etc. The second file is an ASCII header file that indicates the size of the data in the brick file as well as other attributes such as whether the brick is compressed. Getting Data Into VisIt Manual
EnSight EnSight Gold *.case Proprietary file format for 2D and 3D data. EnSight manuals (see ch. 2)
PLOT2D Plot3d files *.p2d *.g *.q Plot3d is a plotting program and file format from NASA. Plot2d is a specialized variant for 2D grids. Plot3d format
PLOT3D *.x *.q *.vp3d
Tecplot Tecplot ASCII and binary files *.tp *.plt *.tec Tecplot is another popular visualization tool. VisIt can read the ASCII and binary versions of the Tecplot file format, though VisIt's reader does not support all contents of all Tecplot files, such as custom labels or auxiliary data records. VisIt may also be more strict with regards to file formatting; Tecplot itself is very permissive in interpreting files. Tecplot home page
Vis5D Vis5D files *.v5d Vis5d is a free OpenGL-based volumetric visualization program for scientific data sets in 3+ dimensions. Vis5d+ home page
VTK VTK legacy format *.vtk The VTK legacy format is an ASCII-based format with straightforward structure, and an easy way to get a variety of mesh based data (structured, unstructured, particle, etc.) into VisIt with minimal complication. This format does support binary chunks for performance/size improvements, but this is still subject to the various limitations of the pure ASCII version, so those seeking large, portable, binary data containers might investigate formats based on scalable I/O libraries. VTK file format docs ASCII VTK Files
VTK XML format *.vts *.vtr *.vtu *.vti *.vtp The VTK XML formats were created to address some limitations of the original, legacy VTK formats. They are by definiton, more complex, though, so those seeking simple ways to get data into VisIt might find the legacy format more appealing.
Xmdv Xmdv *.okc File format used by XmdvTool, a public-domain software package for the interactive visual exploration of multivariate data sets. Xmdv file format description

Graphics Formats

These formats are designed for graphics uses such as digital content creation, computer aided design, or other graphics domains other than visualization.

Plug-in Name Format Name Typical File Names Description Links
Image JPEG *.jpg *.jpeg Various common image-based file formats.
PNG *.png
BMP *.bmp
PPM *.ppm
PNM *.pnm
TIFF *.tiff *.tif
SDT *.sdt + *.spr The SDT format is an image format developed for the Stimulate fMRI analysis software. Stimulate User's Guide
Image volume *.imgvol A sequence of images which are interpreted as a regular volumetric data set. The *.imgvol file is a text file containing the names of the files to assemble into the 3D volume. Optional lines at the top of the file may include: "Z_START: <val>", and/or "Z_STEP: <val>", which specify the placement and spacing of the slices.
RAW raw triangle mesh *.raw A RAW file contains triangle meshes, and is used by CAD programs, POV-Ray, etc. It is an ASCII text file that contains 1 triangle per line, and the line consists of 9 floating point numbers making up the coordinates.
STL Stereolithography CAD file *.stl STL (stereolithography) is an ASCII or binary file used in manufacturing. It is a list of the triangular surfaces that describe a computer generated solid model. This is the standard input for most rapid prototyping machines. STL Wikipedia entry
TSurf tsurf files *.ts_deg83 This is a triangle surface format used for representing terrain from USGS. Used by GOCAD software. GOCAD home page
WavefrontOBJ Wavefront Object *.obj Object files contain geometry that can be included in visualizations. The format was developed by Wavefront. file format info Wikipedia entry

General ASCII Data Formats

These formats allow for easy importing of simple ASCII data of various styles.

Plug-in Name Format Name Typical File Names Description Links
Curve2D 2D x/y pair ASCII data *.curve *.ultra *.u *.ult ASCII text file format containing pairs of x,y floating point values on each line. This file format is convenient for importing curve plots into VisIt. The curve format can store more than one curve provided you supply a variable name as a comment, beginning with "#". Getting Data into VisIt
Lines ASCII lines data Simple ASCII text connected points data format. Lines3D
PlainText Plain ASCII text files - The PlainText reader supports various ways of reading data from tab-delimited, comma-delimited, or whitespace-delimited text files, and interpreting them as 1D columns or 2D regular grids. It has various options for how to interpret and parse the ASCII data. PlainText reader instructions
Point3D ASCII 3D point data *.3D Point3D is a simple ASCII text format for 3D particles that have 1 scalar variable. This format can be useful for scripts or simple particle simulations that want an easy way to get particle data into VisIt. Reading point data

Debugging and Testing Formats

These formats are for testing VisIt and make good examples of how to write simple file reader plugins.

Plug-in Name Format Name Typical File Names Description Links
Hex - *.hex Example reader for unstructured hexahedral single-domain data.
Rect - *.rect Example reader for rectilinear, multi-domain data with ghost zone communication.
StreamGhostTest - - This is a plugin used for testing streaming ghost zone communication. It generates data instead of reading it from a file.

Special-purpose Formats

These formats are typically accessed in conjunction with another reader or specific features in VisIt, and are not intended to be used directly.

Plug-in Name Format Name Typical File Names Description Links
AugDecomp augmented decomposition data *.augd This is a format which specifies auxiliary material information as a addition to another file format (without materials).
ExtrudedVol extruded volume data *.exvol A file format designed to efficiently write out temporal-analysis results on the fly to minimize memory usage.
SimV1 In-situ connection - These readers are designed to read data from properly-instrumented running simulation code, for in-situ analysis and visualization.
SimV2 (coming in 2.0)
ZipWrapper compressed format wrapper *.gz *.bz2 *.zip Provides access to other formats stored inside compressed files by decompressing files on the fly as VisIt is processing them. This allows a majority of the files in a time series for example to remain compressed on disk while keeping only the most recently processed timesteps on disk uncompressed.

Unknown Formats -- Need More Information

Plug-in Name Format Name Typical File Names Description Links
CMAT *.cmat
TFT TFT file format *.dat *.tft (TFT is an ASCII text format for specifying X/Y curves.? Is TFT a code?)

Test categories for codes in first section