MIT Athena Computing Environment: What Runs Where: Simulation and Modeling Detail
Keywords: athena, what runs where, athena help, simulation, modeling

What Runs Where
| Major Applications |
### Full Table:
| Help/Information Screen Accessories Communication Text Software Graphics Software Audio Software Numerical/Math Soft Languages/Debuggers Programming Libraries Simulation & Modeling Courseware Miscellaneous Utilities |
Help
| What's new? Tips for Using Athena Software Academic Computing locker configuration Web browser Java plugin issues Note on changing window managers |
| # What Runs Where on Athena: Simulation and Modeling On this page: Bioinformatics | Circuit Design | Field Simulations | Finite Element Analysis | Geographic Information Systems | Molecular Modeling and Dynamics | Other Simulations | Virtualization
| Bioinformatics |
Title and description: AFNI Description: collection of programs for viewing and analysing functional magnetic resonance images of the brain. Supplied with many associated command-line utility functions To run: athena% add seven athena% afni data-directory (main application) athena% command options files (utilities) Please see documentation for usage of utility commands Local documentation starts here; there is also a central information site and a resource site See also: clustalw, GENSCAN, NetPBM Utilities, xv
Title and description: Biopython Description: collection of Python tools for computational molecular biology- allows processing of biological sequences and databases To run in interactive mode: athena% add seven athena% biopython followed by commands from the Biopython package, for example: >>> from Bio.Seq import Seq >>> new_seq = Seq('GATC') >>> new_seq[0:2] To run as a stand-alone application, you can write python scripts that contain Biopython commands There is a documentation site and tutorial See also: BLAST, CLC Free Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, hmmer, meme/mast, Osprey, phylip, primer3, python
Title and description: BLAST Description: BLAST (Basic Local Alignment Search Tool) is an application for finding regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. BLAST can be run standalone, as an NCBI Web client, via a local BLAST server and via a Web form at the NCBI Web site. This installation contains the standalone and Web client versions from NCBI To run: athena% add blast athena% blastcl3 -i query options > outfile (Web client: to run query query, with output in outfile) athena% formatdb -i data options (standalone: to index a database data) athena% program options -d data -i query > outfile (standalone: use program to run query query against database data, output in outfile) There is local documentation, NCBI tutorial, Wiki and a Web page See also: Biopython, CLC Free Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, hmmer, meme/mast, phylip, primer3
Title and description: CLC Free Sequence Viewer Description: tool for bioinformatics analysis including: alignment creation and editing, interactive restriction site analysis, phylogenetics, integrated GenBank searches, DNA to protein translation and other features To run: athena% add clcbio athena% clcseqview4 & (to run 4.6.1 release, Linux) athena% clcfreewb3 & (to run prior 3.2.2 CLC Free Workbench release, Sun) There is a local 4.6.1 pdf manual, local 3.2.2 pdf manual, local 3.2.2 introductory notes and Web site See also: Biopython, BLAST, clustalw, emboss, Geneious, GENSCAN, hmmer, meme/mast, Net Entrez, phylip Note: This application has been renamed from CLC Free Workbench to CLC Free Sequence Viewer, but the new version no longer runs on Suns
Title and description: clustalw Description: general purpose multiple sequence alignment program for DNA or proteins To run: athena% add clustalw athena% clustalw There is local documentation here, here and here; also a Web page See also: AFNI, Biopython, BLAST, CLC Free Sequence Viewer , emboss, Geneious, GENSCAN, hmmer, meme/mast, phylip, primer3
Title and description: emboss Description: the European Molecular Biology Suite is a large collection of tools for molecular analysis of genomic data. It can handle data in a variety of formats and allows transparent retrieval of sequence data from the Web. A GUI Java-based interface, jemboss, is also available. emboss is configured to use clustalw, hmmer, meme and primer3 as helper applications. Most programs in the optional EMBASSY suite have also been installed. Graphics output is possible via Plplot libraries included in the installation To run: Athena machine: athena% setup emboss athena% jemboss (to run GUI) athena% command options file(s) (command is one of the emboss commands; see docs for list) Red Hat Linux machine running OpenAFS client: $ csh $ attach emboss $ source /mit/emboss/.attachrc athena% jemboss (to run GUI) athena% command options file(s) (command is one of the emboss commands; see docs for list) There is local documentation, a tutorial and quick reference, documentation at the development site and a Web page See also: Biopython, BLAST, CLC Free Sequence Viewer , clustalw, Geneious, GENSCAN, hmmer, meme/mast, phylip, primer3
Title and description: Geneious Description: integrated bioinformatics tool suite for manipulating, finding, sharing and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information and publications To run: athena% add geneious athena% geneious & There is a local pdf manual, and Web site See also: Biopython, BLAST, CLC Free Sequence Viewer , clustalw, emboss, GENSCAN, hmmer, meme/mast, Net Entrez, phylip
Title and description: GENSCAN Description: tool for predicting the locations and exon-intron structures of genes in genomic sequences To run: athena% add seven athena% genscan /mit/seven/share/HumanIso.smat sequence-file options (vertebrates) athena% genscan /mit/seven/share/Maize.smat sequence-file options (maize) athena% genscan /mit/seven/share/Arabidopsis.smat sequence-file options (arabidopsis) Local documentation starts here See also: AFNI, Biopython, BLAST, CLC Free Sequence Viewer , clustalw, emboss, Geneious, hmmer, meme/mast, phylip
Title and description: hmmer Description: set of tools that profile hidden Markov models for protein sequence analysis. This can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus To run: athena% add hmmer athena% hmmfetch options database name athena% hmmalign options hmmfile seqfile athena% hmmsearch options hmmfile seqfile athena% hmmbuild options hmmfile seqfile (see man pages for these and other commands in /mit/hmmer_v2.3.2/man/man1) There is local documentation and a Web page See also: Biopython, BLAST, CLC Free Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, meme/mast, phylip, primer3
Title and description: meme/mast Description: meme is a tool for discovering motifs in a group of related DNA or protein sequences. mast is a tool for searching molecular sequence databases for sequences that contain one or more of a group of known motifs. A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences To run: athena% add meme athena% meme dataset options athena% mast motif-file options There is local documentation for meme and mast; there is also a Web page See also: Biopython, BLAST, CLC Free Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, hmmer, phylip, primer3
Title and description: NEURON Description: simulator of neurons and networks of neurons, with an extensible library of biophysical mechanisms To run: athena% add neuron athena% nrngui (to run GUI) athena% neurondemo (to run a demo) Look below /mit/neuron/bin to see launch commands for various components and utilities; local tutorials and documentation are available. There is an author Web page and pointers to additional documentation See also: Osprey
Title and description: Osprey Description: tool for graphically representing biological interaction networks, drawing on data from various interaction databases. Osprey is integrated with the BioGRID To run: athena% add osprey athena% osprey & There is an author page with documentation See also: Biopython, NEURON Note: Sun version not supported by authors and has some format/sizing problems; windows may need to be enlarged manually to see all dialog buttons (in particular, initital launch "Select database.." dialog); help browser won't launch on help invocation
Title and description: phylip Description: phylip (Phylogeny Inference Package) is a collection of separate programs for inferring phylogenies (evolutionary trees). It can infer phylogenies by parsimony, compatibility, distance matrix methods and likelihood. It can also compute consensus trees, compute distances between trees, draw trees, resample data sets by bootstrapping or jackknifing, edit trees and compute distance matrices. It can handle data that are nucleotide sequences, protein sequences, gene frequencies, restriction sites, restriction fragments, distances, discrete characters and continuous characters. To run: athena% add phylip athena% command file(s) (command is one of the phylip commands; see docs for list) generally a data file named intree or infile is expected as input in the current directory; output is produced in files outtree and outfile in the same directory. drawree and drawgram additionally require a font file in the current directory; a number are supplied with the distribution, and a suitable one can be copied from the /mit/phylip_v3.66/fonts directory to the current directory and renamed to fontfile There is local documentation and a Web page See also: Biopython, BLAST, CLC Free Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, hmmer, meme/mast, primer3
Title and description: primer3 Description: program for designing Polymerase Chain Reaction primers. It can also design hybridization probes and sequencing primers To run: athena% add primer3 athena% primer3_core < inputdata There is an author page and local documentation See also: Biopython, BLAST, clustalw, emboss, hmmer, meme/mast, phylip
| Circuit Design |
Title and description: awaves, hspice Description: optimizing analog circuit simulator for steady-state, transient and frequency domains Licenses: 100 floating licenses To run: athena% add hspice athena% awaves (for X interface, Sun only) athena% hspice file.sp > outputfile (batch mode) See also: Electric VLSI, gEDA, hfss, Magic, xcircuit Note: this application is not maintained by IS&T. If you have problems running it please contact Myron Freeman (fletch1@eecs.mit.edu), x3-4650, 3-0930 in the EECS department
| Field Simulation |
Title and description: hfss Description: 3d high frequency Maxwell equation solver; used for design of on-chip embedded passives, PCB interconnects, antennas, RF/microwave components and high-frequency packages Licenses: limited number of floating licenses To run: athena% add ansoft athena% hfss & There is a vendor page See also: awaves, hspice, ePhysics, maxwell Note: this application is not maintained by IS&T. If you have problems running it please contact Myron Freeman (fletch1 at eecs.mit.edu), x3-4650, 3-0930 in the EECS department
Title and description: maxwell Description: 2d and 3d electromagnetic field simulation Licenses: limited number of floating licenses To run: athena% add ansoft athena% maxwell3d & (for 3d field simulator) athena% maxwell2d & (for 2d field simulator) There is a vendor page To create new 3d projects: click on File -> New, and accept the default name added by the application or edit it to one of your choosing To run existing 3d projects: click on File -> Open To create new 2d projects: click on Projects -> New, enter a name for the project in the Name field of the popup window that appears, and set the type to Maxwell 2d Version 11 To run existing 2d projects, click on Projects, select the desired project by name and click on Open See also: Elmer, ePhysics, FreeFem++, hfss, OpenFOAM Note: You will get significantly better performance if you set both your project directory and your temporary file location to be on the local hard drive before a data run (/var/tmp for example). Please note that this location is for temporary storage and that you will need to copy any output files you want to save back to persistent storage, such as your AFS home directory. This application is not maintained by IS&T. If you have problems running it please contact Myron Freeman (fletch1 at eecs.mit.edu), x3-4650, 3-0930 in the EECS department
| Finite Element Analysis |
Title and description: adina Description: Finite Element design package, used mostly in Mechanical Engineering. At the present time only students enrolled in certain courses using adina should expect to be able to use it on Athena. Please contact your instructor or course TA for assistance Licenses: limited number of floating licenses To run: Please contact a course TA or instructor in a course using Adina for assistance See also: CalculiX, Pro-Engineer Note: this application is not maintained by IS&T. If you have problems running it please contact Prof. Klaus-Jurgen Bathe (kjb@mit.edu, x3-6445) in Mechanical Engineering or call Adina R&D Inc. at 617-926-5199
Title and description: CalculiX Description: 3d structural analysis finite-element program, incorporating a pre- and post-processor (Graphix, cgx) and solution engine (CrunchiX, ccx_1.6). A vda to fdb conversion utility is also in the locker To run: athena% add calculix athena% ccx_1.6 file (to run ccx_1.6 on model file file.inp) athena% cgx model.frd (to view model in file model.frd; use left mouse button outside drawing rectangle for popup menu) athena% cgx -b model.fbd (to preprocess model in file model.fbd; use left mouse button outside drawing rectangle for popup menu) athena% vda2fdb file.vda > file.fbd (to convert file.vda to file.fbd) There is an online ccx manual, cgx manual, cgx tutorial and an author Web page; there is also a discussion group See also: adina, Elmer, FreeFem++, Mathematica (IMTEK Mathematica supplement), OpenFOAM
Title and description: EasyMesh Description: 2d Delaunay mesh generator that supports a variety of features, including materials containing holes, domains composed of more than one material and Laplacian smoothing. Output can be generated in a variety of file formats. ShowMesh is a viewer for displaying meshes created by EasyMesh To run: athena% add easymesh athena% easymesh infile options (to run EasyMesh on input data file infile) athena% showmesh infile (to run ShowMesh on input data file infile) There is EasyMesh documentation, ShowMesh documentation and an author Web page EasyMesh is used by some of the demos in the IMTEK Mathematica supplement added to our Mathematica installation See also: Mathematica, tetgen, triangle
Title and description: Elmer Description: multiphysics/finite-element application capable of solving problems that can be described by partial differential equations in fields such as fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics. It includes a front end, solver and post-processor, and can import data from a variety of commercial finite-element applications To run: athena% add elmer athena% ElmerFront (to run front end) athena% ElmerSolver (to run solver on model file file.sif, where this file is in the current directory) athena% ElmerPost (to run post-processor; needs to read data in file.ep generated by solver) There is local pdf documentation and a Web page See also: CalculiX, FreeFem++, Mathematica (IMTEK Mathematica supplement, maxwell, OpenFOAM
Title and description: FreeFem++ Description: 2d finite-element method solver for partial differential equations that incorporates an internal scripting language. The distribution comes with an IDE and can output graphics directly To run: athena% add freefempp athena% FreeFem++ file.edp (to run FreeFem++ on model file file.edp) athena% FreeFem++-ide & (to launch the IDE) There is an online manual and an author Web page See also: CalculiX, Elmer, Mathematica (IMTEK Mathematica supplement), maxwell, OpenFOAM
Title and description: OpenFOAM Description: OpenFOAM is primarily a C++ library used to create executables, known as applications. The applications fall into two categories: solvers, that are each designed to solve a specific problem in continuum mechanics; and utilities, that are designed to perform tasks that involve data manipulation. The OpenFOAM distribution contains numerous solvers and utilities covering a wide range of problems. New solvers and utilities can be created by its users with some prerequisite knowledge of the underlying method, physics and programming techniques involved. Information relating to these subjects is in the Programmer's Guide. OpenFOAM is supplied with pre- and post-processing environments. The interfaces to the pre- and post-processing are themselves OpenFOAM utilities To run: athena% setup openfoam athena% FoamX (to run GUI setup interface) athena% paraFoam root case (to run postprocessor/display utility on a specific case rooted at root) Many utilities and solvers can be run directly from the command line. There is a local User Guide, a home page with html documentation, and a Wiki See also: CalculiX, Elmer, FreeFem++, Mathematica (IMTEK Mathematica supplement), maxwell
Title and description: tetgen Description: 3d tetrahedral mesh generator and Delaunay triangulator. These meshes can be used in finite-element and finite-volume simulations. tetview (Linux only) is a 3d viewer for viewing meshes created by tetgen as well as other objects and triangular and tetrahedral meshes in other formats To run: athena% add tetgen athena% tetgen options infile (to run tetgen on input data file infile) athena% tetview options infile (to run tetview on input data file infile; Linux only) There is a pdf manual and author site tetgen is used by some of the demos in the IMTEK Mathematica supplement added to our Mathematica installation See also: EasyMesh, Mathematica, triangle
Title and description: triangle Description: 2d mesh generator and Delaunay triangulator that supports a variety of file formats. showme is a viewer for meshes generated by triangle To run: athena% add triang athena% triangle options infile (to run triangle on input data file infile) athena% showme options infile (to run showme on input data file infile) There is triangle documentation, showme documentation triangle is used by some of the demos in the IMTEK Mathematica supplement added to our Mathematica installation See also: EasyMesh, Mathematica, tetgen
| Geographic Information Systems |
Title and description: ArcExplorer Description: lightweight Java-based client for viewing GIS maps and related data To run: athena% add arcims athena% aejava Documentation is here See also: ArcInfo/ArcView Note: this application was formerly in the arcej locker. It is now supplied with other administrative utilities in the arcims locker
Title and description: ArcInfo/ArcView Description: ArcInfo is a sophisticated GIS programming environment that allows for automating, displaying, manipulating and analyzing spatial data and making maps. ArcView is a viewing and data manipulation application that allows display and analysis of GIS data. Both of these come with many add-on and extension modules Licenses: large number of floating licenses To run: athena% add arcinfo athena% arcinfo athena% add arcview athena% arcview There is a local Web page. A wide range of ESRI products, including ArcView and ArcInfo, are available for installation on MIT-owned machines under our site license. Information is here See also: ArcExplorer, FWTools Note: ArcView does not work well with non-default Athena window managers and may crash if you attempt to use a different one
| Molecular Modeling and Dynamics |
Title and description: babel Description: converts molecular description files between a variety of formats To run: athena% add xdrawchem athena% babel -iinput type input file -ooutput type output file athena% babel -H (for options and supported formats) See also: Discovery Studio Visualizer, Jmol, Mercury, molekel, molscript, Net Entrez, rasmol, VMD Note: An older version is in the babel-chem locker. It has similar functionality but command options are not identical
Title and description: Cambridge Structural Database Description: database of bibliographic, chemical and crystallographic information for organic molecules and metal-organic compounds. It is distributed with a number of client applications: Conquest (cq): search and information retrieval utility Mercury (mercury): structure visualization application Vista (vista): statistical analysis and display of geometric data PreQuest (prequest): database creation in CSD format Mogul (mogul): knowledge base for molecular geometry IsoStar (run_isostar): knowledge base of intermolecular interactions To run: athena% add cambsd athena% cq & (to run ConQuest) athena% mercury & (to run Mercury) athena% vista -j jobname (to run Vista) athena% prequest (to run PreQuest) athena% mogul (to run Mogul) athena% run_isostar (to run IsoStar) There are local pdf manuals, release notes, tutorials, Mercury README, pages for Mercury, Mogul, IsoStar and ConQuest; also a CSD home page and MIT Library support site See also: Deep View, Discovery Studio Visualizer, Mercury, molscript, rasmol, Star Biochem, VMD, XCrySDen Note: This release will no longer run correctly on Linux Athena 9.4 machines mercury in this locker supersedes the version in the hg locker as it is newer and integrated with the CSD; IsoStar is not fully supported at the moment and functionality related to this may be partly or completely broken on Athena 10 machines, you may get licensing errors unless the lines in your /etc/hosts file starting with 127.0.0.1 and 127.0.1.1 have only fully qualified host names, i.e. 127.0.1.1 zippy zippy.mit.edu may cause denials, but 127.0.1.1 zippy.mit.edu should be OK. You will need to be root to edit this file
Title and description: ChemDraw (old; current versions not available for UNIX) Description: GUI "drag and drop" interface for building and manipulating chemical formulas To run: athena% add chemdraw athena% chemdraw & There is an online user's Guide in pdf format- see /mit/chemdraw_v3.1/cdu3_1.pdf See also: XDrawChem Note: X server needs to be in 8 bit mode to run this application. Login with Other Options, select restart X in 8 bit mode
Title and description: CPMD Description: computational molecular chemistry application; specifically, a parallelized plane wave/pseudopotential inplementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics computations To run: athena% add cpmd athena% cpmd.x file.inp [pseudopotential-path] >file.out (to run commands in file.inp, generating file.out using pseudopotential in pseudopotential-path directory; if omitted, looks for pseudopotential file(s) in current directory) There is an online manual, source code file tree and author site See also: Espresso, Gaussian, molden, VMD, Xaim
Title and description: Deep View Description: tool for structural analysis and display of molecular chemistry models of proteins. It can read molecular density maps and interface to a variety of tools that generate them; output in POV-Ray format is possible, allowing for the generation of ray-traced images To run: athena% add deepview athena% spdbv & athena% ppov10 -w width -h height file.pov (rendered image output, file.pov made by spdbv output via File -> Save -> Pov-Ray3 Scene in ~/SPDBV/PPOV) There is documentation and a tutorial at the author's Web site See also: Cambridge Structural Database, Discovery Studio Visualizer, Jmol, Mercury, molden, molekel, molscript, Net Entrez, pymol, rasmol, Star Biochem, VMD, XCrySDen
Title and description: Discovery Studio Visualizer Description: application that allows visualizing, analyzing and sharing biological and chemical data. Data can be viewed in multiple ways, including visually, from sequences and from data tables To run: athena% add dsvisualizer athena% DSVisualizer20 There is a vendor site and local help See also: babel, Cambridge Structural Database, Deep View, Jmol, Mercury, molekel, molscript, pymol, rasmol, Star Biochem, VMD, XCrySDen
Title and description: Espresso Description: computational molecular chemistry applications: programs for quantum-mechanical simulations of extended or isolated systems based on density functional theory, periodic boundary conditions, plane-waves and norm-conserving or ultrasoft pseudopotentials To run: athena% attach espresso athena% source /mit/espresso/conf.csh (C shell) athena% . /mit/espresso/conf.sh (Bourne/bash shell) athena% pw.x options < file.in > file.out (to run commands in file.in, generating file.out) (and similarly for other commands like ph.x etc.) athena% pwgui & (to run pwgui interface) There is an Espresso Web site To run examples: copy subtree /mit/espresso_v4.0.3/i386_rhel4/espresso-4.0.3/examples to a writable location, cd to a directory like example01 and run ./run_example See also: CPMD, Gaussian
Title and description: Gaussian, Gaussview Description: computational molecular chemistry application. Gaussian is the command-line computational engine. Gaussview is a GUI front-end to Gaussian To run: athena% setup gaussian (for default 03-D01 version) followed by: athena% g03 <file.com (to run Gaussian from a command file file.com) athena% gv & (for Gaussview interface) See also: CPMD, Espresso, Mercury, molden, Xaim
Title and description: Jmol Description: 3d molecular viewing application written in Java that can read a variety of molecular file description formats. Can be integrated as a component into other Java applications. can also export snapshot images directly, and render images using POV-Ray To run: athena% add jmol athena% jmol For a sample: athena% jmol /mit/jmol/1crn.pdb There is an author site with demonstration pages See also: babel, Deep View, Discovery Studio Visualizer, Mercury, molekel, molscript, pymol, rasmol, Star Biochem, VMD, XCrySDen
Title and description: Mercury Description: Mercury is a 3d crystal structure visualization and exploration tool To run: athena% add hg athena% mercury & There is local online documentation and a ReadMe; see also the Mercury Web page See also: babel, Cambridge Structural Database, Deep View, Discovery Studio Visualizer, Gaussian, Jmol, molekel, molscript, platon, pymol, rasmol, Star Biochem, VMD, XCrySDen Note: mercury in this locker is superseded by the version in the cambsd locker as the latter is newer and integrated with the CSD
Title and description: molden Description: molden is a chemistry application for displaying molecular density computed fron various ab-initio packages. It can output image description files in .pov format, suitable for input to the POV-Ray ray tracer To run: athena% add molden athena% molden options file athena% gmolden options file (OpenGL-enabled version) athena% mpfit.molden options file (mpfit-enabled version) athena% moldenogl file.ogl (utility for displaying molden-format .ogl files) There is an online user's Guide; see also the molden Web page See also: CPMD, Deep View, Gaussian, molekel, platon, povray
Title and description: molekel Description: Molecular graphics visualization package for displaying 3d images of molecular model and electronic structure data. Reads molecule description files in a variety of standard formats (pdb, xyz) and output data from molecular chemistry computation packages (Gaussian, adf, zindo, molden...) Versions: there is version skew (Linux version is newer) To run: athena% add molekel athena% molekel To run 4.3 samples from a command-line launch, do something like: athena% molekel -pdb /mit/molekel_v4.3/distrib/molekel/examples/outputs/oligo.pdb There is 5.x online documentation, msms documentation, 4.3 online html documentation, and a local 4.3 pdf manual; also a Molekel home page See also: babel, Deep View, Discovery Studio Visualizer, Jmol, Mercury, molden, molscript, pymol, rasmol, Star Biochem, VMD, XCrySDen
Title and description: molscript Description: application for creating schematic or detailed molecular graphics images from molecular 3D coordinates, usually, but not exclusively, protein structures To run: athena% add molscript athena% molscript options -in input file -out output file athena% molauto file.pdb | molscript -gl (to generate interactive 3d image) To build examples: athena% cp -r /afs/athena/software/molscript_v2.1.2/examples /var/tmp athena% cd /var/tmp/examples athena% make There is a molscript home page See also: babel, Cambridge Structural Database, Deep View, Discovery Studio Visualizer, Jmol, Mercury, molekel, Net Entrez, platon, pymol, rasmol, Star Biochem, VMD
Title and description: platon Description: platon is a crystallographic computational chemistry tool incorporating a variety of computations and image generation formats. It can output image description files in .pov format, suitable for input to the POV-Ray ray tracer, and in rasmol format for the rasmol viewer To run: athena% add platon athena% platon options datafile There is local online documentation. See also the platon Web page See also: Mercury, molden, molscript, povray, rasmol
Title and description: pymol Description: tool for displaying and manipulating 3d molecular images To run: athena% add pymol athena% pymol There is online html documentation, a pdf reference manual and a pdf user manual; also a Web site See also: Deep View, Discovery Studio Visualizer, FreeWRL, geomview, Jmol, Mercury, molekel, molscript, Net Entrez, rasmol, Star Biochem, VMD, XCrySDen
Title and description: rasmol Description: 3d imaging tool for displaying 3d molecular images that can be rotated in space. Reads molecule description files in standard formats such as Brookhaven Protein Databank (pdb) which is the default, as well as others (alchemy, mdl) To run: athena% add rasmol athena% rasmol -format description_file (the launch window accepts rasmol commands after startup) For samples, do: athena% rasmol /mit/rasmol/data/3cro.pdb athena% rasmol -alchemy /mit/rasmol/data/asprin.alc There is local online html documentation, a pdf manual and a pdf quick reference See also: babel, Cambridge Structural Database, Deep View, Discovery Studio Visualizer, FreeWRL, geomview, Jmol, Mercury, molekel, molscript, Net Entrez, pymol, Star Biochem, VMD, XCrySDen
Title and description: Star Biochem Description: Java-based 3d biomolecule viewer developed at MIT for use in courses and designed for easy, intuitive analysis commands. Accessible here through Java3D-enabled browsers See also: Deep View, Cambridge Structural Database, Discovery Studio Visualizer, Jmol, Mercury, molekel, molscript, pymol, rasmol, VMD, XCrySDen
Title and description: VMD Description: application designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies etc. It can also view more general molecules in standard representations (such as pdb and other standard molecular description files). It provides a wide variety of methods for visualizing and rendering molecules, and can also be used to animate and analyze the trajectory of molecular dynamics simulations To run: athena% add vmd athena% vmd Sample data files are in the /afs/athena.mit.edu/software/vmd_v1.8.6/distrib/vmd-1.8.6/proteins directory There is a 1.8 Quick Help page, online User's Guide and a VMD home page; 1.8.6 documentation and tutorials start here See also: babel, Cambridge structural Database, CPMD, Deep View, Discovery Studio Visualizer, Jmol, Mercury, molekel, molscript, Net Entrez, pymol, rasmol, Star Biochem, XCrySDen
Title and description: Xaim Description: computational molecular chemistry application; provides a GUI interface to programs that 1. locate critical points in the electronic charge density distribution and determine various properties at those points (extreme) and 2. plot molecular distribution functions of various quantities (molecular orbitals, electronic density, kinetic energy density...) (flopo). Can take input from the output of computation performed by Gaussian To run: athena% add xaim athena% Xaim & There is local documentation and an author home page See also: CPMD, Gaussian
Title and description: XCrySDen Description: crystalline and molecular structure visualization program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated To run: athena% setup xcrysden athena% xcrysden There is local online documentation and an author home page See also: Cambridge Structural Database, Deep View, Discovery Studio Visualizer, Jmol, Mercury, molekel, pymol, rasmol, Star Biochem, VMD
Title and description: XDrawChem Description: 2d molecule drawing program similar to ChemDraw in functionality. Can input and output a variety of chemical structure formats using openbabel translator also installed in locker. Can also read structures from a database on the Internet. To run: athena% add xdrawchem athena% xdrawchem There is online documentation and an author home page See also: ChemDraw
| Other Simulations |
Title and description: CHEMKIN Description: package to investigate problems in elementary gas-phase chemical kinetics. Can be used via a GUI interface or in batch mode To run: athena% add chemkin athena% chemkin (to run GUI interface) Release 4.1.1 manuals are here; also 4.1.1 help pages to build the 3.7 version examples without running the GUI (you will need 5-6 meg. of free disk space in your home directory): athena% add chemkin_v3.7 athena% source /mit/chemkin_v3.7/cshrc athena% cd ~/reaction/chemkin37/samples athena% buildsamples See also: ePhysics
Title and description: Electric VLSI Description: VLSI circuit design and simulation application written in Java that incorporates many features and optional add-ons. Design features include custom IC layouts (ASICs), schematic drawing and hardware description language specifications To run: athena% add electric athena% electric & There is an Electric home page, online manual, GNU Electric information page and background information See also: dia, eagle, gEDA, gerbv, hspice, Magic, xcircuit
Title and description: ePhysics Description: interactive software package for analyzing thermal and structural deformation and stress Licenses: limited number of floating licenses To run: athena% add ansoft athena% ephysics & There is a vendor page See also: CHEMKIN, hfss, maxwell Note: this application is not maintained by IS&T. If you have problems running it please contact Myron Freeman (fletch1 at eecs.mit.edu), x3-4650, 3-0930 in the EECS department
Title and description: gEDA Description: suite of electronic design tools, currently offering schematic capture and simulation tools. There are numerous tools in the suite, and major ones are accessible through a common interface called geda (however, not all of them are currently installed). All can, and some must be invoked independently from the command line; you can see their names by looking in the /mit/geda/arch/sun4x_510/bin and /mit/geda/arch/i386_rhel4/bin directories. Major available components include: gattrib (attribute editor) gerbv (Gerber circuit board viewer) gnetlist (netlister- textual representation of a schematic) gnucap (GNU circuit analysis package) gschem (schematic editor) gsch2pcb (interfaces gEDA schematics to PCB layout files) gtkwave (digital waveform viewer) iverilog (Icarus Verilog compiler) ngspice (SPICE simulator) pcb (PCB layout editor) vvp (Icarus Verilog simulation runtime engine) To run: athena% add geda athena% geda & athena% gnetlist options files(s) athena% gsch2pcb options files(s) To run other components, consult the documentation. There is a gEDA home page and some local documentation below here; also a documentation Wiki See also: eagle, hspice, Electric VLSI, Magic
Title and description: GNU Linear Programming Kit Description: set of routines packaged up into a library (libglpk.a) and a solver (glpsol) for solving linear programming (LP), mixed integer linear programming (MIP) and other related problems. The solver processes directives in a language called the "GNU MathProg modeling language" that is a subset of AMPL. The current release includes support for the GMP bignum library, which is included in the locker To run: athena% add glpk athena% glpsol -m sample.mod -y sample.sol (to solve a MathProg model sample.mod, with results in sample.sol) athena% gcc -o sample sample.c -I/mit/glpk/include -L/mit/glpk/lib -lglpk -lgmp -lm (C source file sample.c, dynamic linking) athena% gcc -o sample sample.c -I/mit/glpk/include /mit/glpk/libglpk.a /mit/glpk/libgmp.a -lm (C source file sample.c, static linking) For dynamic linking, you will need to add /mit/glpk/lib to the LD_LIBRARY_PATH environment variable at runtime; you may or may not need to include the -lgmp link, depending on your code There is a MathProg language guide, reference manual, data tables manual and GLPK home page; also a tutorial article at IBM See also: AMPL, ipopt, lpsolve, OPL Studio, snopt
Title and description: ipopt Description: application for solving general nonlinear programming problems. It is supplied as a library/API that you can link against (C/C++/FORTRAN code), and as a solver than can be invoked from within AMPL To run: athena% add ipopt athena% add -f gcc-4.0 athena% setenv LD_LIBRARY_PATH /mit/ipopt/lib athena% gcc -O3 -o sample -I/mit/ipopt/include/coin sample.c -L/mit/ipopt/lib -lipopt -lm \ -lgcc_s -lstdc++ -lgfortran (C source file sample.c) athena% g++ -O3 -o sample -I/mit/ipopt/include/coin sample.cpp [other.cpp] -L/mit/ipopt/lib \ -lipopt -lm -lgcc_s -lstdc++ (C++ source file(s) sample.cpp, other.cpp) athena% g77 -O3 -o sample -I/mit/ipopt/include/coin sample.f -L/mit/ipopt/lib -lipopt -lm \ -lstdc++ (FORTRAN source file sample.f) athena% add oplstudio (to run within AMPL) athena% ampl ampl: model mymodel.mod; ampl: data mymodel.dat; ampl: option solver ipopt; ampl: solve; There is an ipopt Web site, online tutorial manual See also: AMPL, GNU Linear Programming Kit, lpsolve, OPL Studio, snopt
Title and description: lpsolve Description: Mixed Integer Linear Programming solver; can run via a standalone solver, a library with accompanying API which can be used to produce C, C++ and Java code and as a plugin to mathematical applications like Matlab (the latter has been installed in the matlab locker). It comes with multiple converters to convert models written in other solver's modeling languages to its native format, and can be used as a solver within AMPL To run: athena% add lpsolve athena% source /mit/lpsolve/set-environment athena% lp_solve sample.lp (to use solver to solve a model sample.lp) athena% gcc -o sample sample.c -I/mit/lpsolve/include -L/mit/lpsolve/lib -llpsolve55 -lm (C source file sample.c) Please read this for other ways of invoking lpsolve There is an FAQ, version 5.5 changes, online manual, Matlab guide, Java guide and API index See also: AMPL, GNU Linear Programming Kit, ipopt, matlab, OPL Studio, snopt
Title and description: Magic Description: interactive editor for VLSI layouts. The IRSIM add-on is an event-driven logic level simulator for MOS circuits To run: athena% add magic-vlsi athena% magic options & (to launch magic) % irsim (to start IRSIM from the Tcl prompt within Magic) There is a Magic home page, local pdf manuals and local internal command descriptions See also: dia, eagle, Electric VLSI, gEDA, gerbv, hspice, xcircuit
Title and description: Meep, MPB, Harminv Description: related utilities for analysis of time-domain signals. Meep is a finite-difference time domain signal simulator. MPB (MIT Photonic-Bands) is an application for computing definite-frequency eigenstates of Maxwell's equations in periodic dielectric structures. Harminv is a program for performing harmonic inversion of discrete-time, finite-length signals To run: athena% add meep (for version 1.0.1 on Linux machines) athena% add sunmeep (for version 0.10 on Sun machines) athena% meep (to run Meep interactively) athena% meep options file.ctl (to run Meep from command file file.ctl) athena% mpb (to run MPB interactively) athena% mpb options file.ctl (to run MPB from command file file.ctl) athena% harminv options < input.dat (to run Harminv with input data in input.dat) There are home pages for Meep, MPB and Harminv with further links to documentation and tutorials; also some local MPB pages See also: matlab
Title and description: oof Description: oof is designed to help materials scientists calculate macroscopic properties from images of real or simulated microstructures. ppm2oof reads images in ppm (Portable Pixel Map) format and assigns material properties to features in the image. oof conducts virtual experiments on the data structures created by ppm2oof to determine the macroscopic properties of the microstructure. Currently it calculates stresses and strains; it may also perform thermal, electric and magnetic field calculations in the future To run: athena% add oof athena% oof options infile (to run oof on data in infile) athena% ppm2oof -file file.ppm (to convert file.ppm to file.goof suitable for input to oof) Author site is here, and documentation starts here
Title and description: OPL Studio Description: modeling environment for mathematical programming and combinational optimization in the OPL modeling language Licenses: we have 10 floating licenses To run: athena% add oplstudio athena% oplst & (to run release 3.7 GUI) athena% oplrun file.mod file.dat (to run release 6.1 command-line invocation on model file.mod using data in file.dat) There is 6.1 online pdf documentation and html documentation See also: AMPL, GNU Linear Programming Kit, ipopt, lpsolve, snopt Note: OPL Studio is on Athena by courtesy of a license funded by Sloan. It is available "as is", with no end-user support. We cannot guarantee uninterrupted operation, nor that it will remain on Athena after the current license expires on 1/31/10. Questions about this can be addressed to the 3partysw@mit.edu mailing list The GUI is only available in release 3.7. Newer releases only support the command-line invocation through the oplrun command
Title and description: sketch Description: software synthesis tool allowing for rapid development of tuned, bug-free algorithm implementations. The programmer develops a "sketch", or partial implementation, and a separate specification of the desired functionality. The synthesizer them completes the sketch to behave like the specification To run: athena% setup sketch athena% sketch options file.sk (to generate code for sketch in input script file.sk) For samples, look in the /mit/sketch_v1.2.1/examples directory There is documentation at the sketch Wiki site See also: spin
Title and description: snopt Description: general purpose system for constrained optimization. Minimizes a linear or nonlinear function subject to bounds on the variables and sparse linear or nonlinear constraints. It is suitable for large-scale linear and quadratic programming and for linearly constrained optimization, as well as for general nonlinear problems. Supplied as a library that you can link against to generate C/C++/FORTRAN code. It can also be used within matlab and as a solver in AMPL To run: athena% setup snopt Please read /mit/snopt/current/README.to-run for detailed usage instructions; there is also a snopt home page There is an online pdf manual and pointers to additional documentation in /mit/snopt/current/README.athena See also: AMPL, GNU Linear Programming Kit, ipopt, lpsolve, matlab, OPL Studio
Title and description: spin Description: spin is an on-the-fly LTL model checking system for proving properties of asynchronous software systems designs. xspin is a Tcl-based GUI front end to spin, with some added bells and whistles To run: athena% add spin athena% spin options data_file (for command line version) athena% xspin & (for GUI interface version) For tests and samples, look in the /mit/spin_v4.2.5/Test directory There is local online documentation and more at the spin Web site See also: sketch Note: spin in some modes generates C code that must be compiled into a binary that you subsequently run- generally gcc is the preferred compiler as vendor compiler preprocessors tend to have trouble with the syntax
| Virtualization |
Title and description: vmplayer (VMware) Description: player for VMware virtual machines To run: athena% vmplayer (to launch the player interface) athena% vmplayer file.vmx (to run a virtual machine whose VMware configuration file is file.vmx) VMware's player site has links to a variety of resources including documentation and a knowledge base Note: Users must supply virtual machines. These tend to be quite large and you may run into difficulties with disk space. One way you can make them accessible to the player is by copying them onto a USB flash drive of suitable capacity and plugging the drive into an Athena machine; however, running directly from a flash drive may reduce performance. Please note that users are responsible for complying with licenses for both the operating system as well as the software run on top of it in virtual machines; proprietary software vendors may disallow or impose limitations on use of their software on virtual machines. Free virtual machines are available in a variety of places on the internet- a good place to start is the VMware Virtual Appliance Marketplace. You can also build your own if you have access to suitable software, from VMware or other sources You may see a launch error message like: libhal.c 644: Error connecting to system bus... this is harmless and can safely be ignored

|  | Home | Getting Started | Getting Services | Getting Help | About IS&T | Accessibility Send a comment about this web page.

Number of queries to this page: