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What Runs Where on Athena - Simulation and Modeling

Bioinformatics

AFNI

Description: collection of programs for viewing and analyzing 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 is locate at /mit/seven/doc/AFNI98; there is also a central information site and a resource site
See also: clustalw, GENSCAN, NetPBM Utilities, xv |

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 Biopythoncommands
There is a documentation site
See also: BLAST, CLC Sequence Viewer, clustalw, COPASI, Cytoscape, emboss, Geneious, GENSCAN, hmmer, Integrative Genomics Viewer, meme/mast, Osprey, phylip, primer3, python, R, SnapGene, UGENE |

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 Website. This installation contains the standalone and Web client versions from NCBI
TO RUN:
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 documentation, a Wiki and a Web page
See also: Biopython, CLC Sequence Viewer, clustalw, emboss, Geneious, GENSCAN, hmmer, Integrative Genomics Viewer, meme/mast, phylip, primer3, R,SnapGene, UGENE |

CLC 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% *clcseqview6 & *
There is a local pdf manual and Website
See also: Biopython, BLAST, clustalw, emboss, Geneious, GENSCAN, hmmer, Integrative Genomics Viewer, meme/mast, Net Entrez, phylip,SnapGene,UGENE |

clustalw

Description: general purpose multiple sequence alignment program for DNA or proteins
TO RUN:
athena% *clustalw *(command-line version)
athena% clustalx & (GUI version)
There is a Web page
See also: AFNI, Biopython, BLAST, CLC Sequence Viewer, emboss, Geneious, GENSCAN, hmmer, Integrative Genomics Viewer, meme/mast, phylip, primer3, R,SnapGene, UGENE
*Note: *This application is no longer installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
sudo to root and install from the clustalw *and clustalx * Ubuntu packages using aptitude or synaptic |

COPASI

Description: software application for simulation and analysis of biochemical networks and their dynamics
TO RUN:
athena% add copasi
athena% *CopasiUI & *(GUI interface)
athena% *CopasiSE *_options file _(command line interface)
There is a Web page and online manual
See also: Biopython, Cytoscape, NEURON, Osprey |

Cytoscape

Description: Open Source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data
TO RUN:
athena% add cytoscape
athena%* runcyto*
There is a Web page, documentation and local online manual
See also: Biopython, COPASI, Gephi, NEURON, Osprey
Note: There are some limitations in using Cytoscape on Athena. See the *MISCELLANEOUS:*section of README.athena for details |

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
TO RUN:
athena% *runJemboss.sh *(to run GUI)
athena% command __options file(s) _(command{_} is one of the emboss commands; see docs for list)
There is documentation at the development site and a Web page
See also: Biopython, BLAST, CLC Sequence Viewer, clustalw, Geneious, GENSCAN, hmmer, Integrative Genomics Viewer, meme/mast, phylip, primer3, R,SnapGene, UGENE
*Note: *This application is no longer installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
sudo to root and install from the emboss and jemboss Ubuntu packages using aptitude or synaptic |

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 Sequence Viewer, clustalw, emboss, GENSCAN, hmmer, Integrative Genomics Viewer, meme/mast, Net Entrez, phylip,SnapGene,UGENE
Note: *The version of {}Geneious* on Athena is the free, restricted version, not the more advanced Pro version |

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 Sequence Viewer, clustalw, emboss, Geneious, hmmer, Integrative Genomics Viewer, meme/mast, phylip,SnapGene, UGENE |

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% *hmmfetch *_options database name _
athena% *hmmalign *_options hmmfile seqfile _
athena% *hmmsearch *_options hmmfile seqfile _
athena% *hmmbuild *_options hmmfile seqfile _
(other commands exist; see man hmmer for documentation)
There is documentation and a Web page
See also: Biopython, BLAST, CLC Sequence Viewer, clustalw, emboss, Geneious, GENSCAN, Integrative Genomics Viewer, meme/mast, phylip, primer3, R, UGENE |

Integrative Genomics Viewer

Description:* visualization tool for interactive exploration of large integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. The Athena installation includes {}IGV Tools*, a set of utilities for preprocessing data files, which can be invoked either from within the IGV GUI, or separately
TO RUN:
athena% *add igv *
athena% *igv *(to run main igv GUI)
athena% igvtools_gui (to run igv tools GUI)
athena% igvtools command options files (to run igv tools from the command line, where command is one of toTDF, count, index, sort, formatexp, version)
There is a Web page and IGV Tools Web page and author documentation. There is also an FAQ, and a tutorial here and here
See also: Biopython, BLAST, CLC Sequence Viewer, clustalw, emboss, Geneious, GENSCAN, hmmer, meme/mast, phylip, primer3,SnapGene, UGENE |

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% *setup meme *
athena% *meme *_dataset options _
athena% *mast *options motif-file sequence-file
athena% {_}utility-command __options date-files _(see documentation for usage instructions)
There is local documentation; there is also a Web page with author documentation
See also: Biopython, BLAST, CLC Sequence Viewer, clustalw, emboss, Geneious, GENSCAN, hmmer, Integrative Genomics Viewer, phylip, primer3,SnapGene, UGENE |

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% *nrniv -python *(to run command-line Python version)
athena% *neurondemo *(to run a demo)
Look below /mit/neuron/bin to see launch commands for various components and utilities; local tutorials are available. There is an author Web page and pointers to additional documentation with 7.4 documentation
See also: COPASI, Cytoscape, Osprey |

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, COPASI, Cytoscape, NEURON |

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% phylip_ 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. drawtree and drawgram additionally require a font file in the current directory
There is documentation and a Web page
See also: Biopython, BLAST, CLC Sequence Viewer, clustalw, emboss, Geneious, GENSCAN, hmmer, Integrative Genomics Viewer, meme/mast, primer3, UGENE
Note: this application is no longer installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
sudo to root and install from the phylip Ubuntu package using aptitude or synaptic |

primer3

Description: program for designing Polymerase Chain Reaction primers. It can also design hybridization probes and sequencing primers
TO RUN:
athena% *primer3_core < *inputdata
There is an author page and documentation
See also: Biopython, BLAST, clustalw, emboss, hmmer, Integrative Genomics Viewer, meme/mast, phylip, UGENE
*Note: *This application is no longer installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
sudo to root and install from the *primer3 *Ubuntu package using aptitude or synaptic |

SnapGene

Description: SnapGene allows users to plan, visualize, and document molecular biology procedures. Select the DNA fragments that you wish to fuse, and SnapGene will design the primers. It simplifies the planning of a Gibson Assembly reaction, and automates the primer design. SnapGene automatically records the steps in a cloning project. Each time you edit a sequence or simulate cloning or PCR or mutagenesis, the procedure is automatically logged in a graphical history
TO RUN:
athena% add snapgene
athena%* snapgene* &
There is a manual and home page
See also: Biopython, BLAST, CLC Sequence Viewer, clustalw, emboss, Geneious, GENSCAN, Integrative Genomics Viewer, meme/mast, UGENE |

UGENE

Description: bioinformatics application that integrates multiple well-known biological tools and algorithms, providing both graphical and command-line interfaces. The required tools and algorithms can be arranged in a workflow scheme using UGENE Workflow Designer
TO RUN:
athena% add ugene
athena% *ugene -ui & *(to run GUI)
athena% ugene *_options _(to run command-line version; type {}ugene --help* or man ugene to see available options)
There is a local pdf manual, Web site, online forums and quickstart
See also: Biopython, BLAST, CLC Sequence Viewer, clustalw, emboss, Geneious, GENSCAN, hmmer, Integrative Genomics Viewer, meme/mast, phylip, primer3, SnapGene |

Finite Element Analysis

Abaqus

Description: Abaqus is a software suite for finite element analysis and computer-aided engineering. There are 5 core products:
1. Abaqus/CAE is a software application used for both the modeling and analysis of mechanical components and assemblies (pre-processing) and visualizing the finite element analysis result. A subset of Abaqus/CAE including only the post-processing module can be launched independently in the Abaqus/Viewer product
2. Abaqus/Standard, a general-purpose Finite-Element analyzer that employs implicit integration scheme (traditional)
3. Abaqus/Explicit, a special-purpose Finite-Element analyzer that employs explicit integration scheme to solve highly nonlinear systems with many complex contacts under transient loads
4. Abaqus/CFD, a Computational Fluid Dynamics software application which provides advanced computational fluid dynamics capabilities with extensive support for preprocessing and postprocessing provided in Abaqus/CAE
5. Abaqus Multiphysics, the ability to extend an Abaqus structural FEA model with additional physics interactions
TO RUN:
athena% add abaqus
athena% abaqus options (to run command-line version, using options)
athena% *abaqus help *(to get information about options)
athena% *abaqus doc *(to view documentation in a web browser)
athena% abaqus cae & (to run GUI)
Please see README.athena for additional important information
There is a wikipedia article and home page
*See also: *CalculiX, Elmer, FreeFem++, Gmsh/GetDP, OpenFOAM, Stanford University Unstructured |

CalculiX

Description: 3d structural analysis finite-element program, incorporating a pre- and post-processor (Graphix, cgx) and solution engine (CrunchiX, ccx_2.7_MT). The cfd computation application isaac is also installed. A vda to fdb conversion utility* vda2fbd* and meshing utility ng_vol are also in the locker
TO RUN:
athena% *add calculix *
athena % export OMP_NUM_THREADS=cores (cores is the number of cores in your CPU, bash shell)
athena % setenv OMP_NUM_THREADS cores (cores is the number of cores in your CPU, C shell)
athena% ccx_2.7_MT_ file_ (to run_ ccx_2.7_MT 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% vda2fbd **{}file.vda __{*}>*_ file.fbd (to convert {}file.vda_ to file.fbd)
athena% *ng_vol *file_ (to run mesher on file_)
athena% isaac < **{}file.dat _(to run {}isaac on input data file {}file.dat_)
There is an online ccx manual, cgx manual, cgx tutorial and an author Web page; there is also a discussion group
For isaac, there is a Web page and online manual
*See also: *Abaqus, Elmer, FreeCAD, FreeFem++, Gmsh/GetDP, LibreCAD, Mathematica (IMTEK Mathematica supplement), OpenFOAM |

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 and ShowMesh documentation
EasyMesh is used by some of the demos in the IMTEK Mathematica supplement added to our Mathematica installation
See also: Gmsh/GetDP, Mathematica (IMTEK Mathematica supplement), tetgen, triangle |

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% ElmerGUI & (to run the main GUI)
athena% ElmerGrid options (to run the mesh generator)
athena% ElmerSolver (to run solver on model file file.sif, where this file is in the current directory)
There is a Web page and Elmer community portal
See also: Abaqus, CalculiX, Dakota, FreeFem++, Gerris Flow Solver, Gmsh/GetDP, Mathematica (IMTEK Mathematica supplement), oof, OpenFOAM, OpenModelica, Stanford University Unstructured, TAO/PETSc
Note: This application is no longer installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
sudo to root and run the following commands:
root@host# apt-add-repository ppa:elmer-csc-ubuntu/elmer-csc-ppa
root@host#* apt-get update*
root@host# apt-get install elmerfem-csc
You may also wish to install ParaView to visualize simulation results
This application is technical and complex and generally requires multiple solutions steps involving a number of distinct programs. You will need to read the documentation and work through some of the tutorials to learn how to use it |

FreeFem++

Description: finite-element method solver for partial differential equations that incorporates an internal scripting language. It can output graphics directly
TO RUN:
athena% FreeFem++_ file.edp (to run FreeFem++ on model file {}file.edp_)
There is an online manual and an author Web page
*See also: *Abaqus, CalculiX, Elmer, Gerris Flow Solver,Gmsh/GetDP, Mathematica (IMTEK Mathematica supplement), OpenFOAM, Stanford University Unstructured
Note: This application is no longer installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
sudo to root and install from the freefem++ Ubuntu package using aptitude or synaptic |

Gerris Flow Solver

Description: solver and visualization tool for the solution of partial differential equations describing fluid flow
TO RUN:
athena% gerris2D_ options file.gfs_ (to generate 2d simulation based on model description file file.gfs)
athena% gerris3D_ {}options file.gfs_ (to generate 3d simulation based on model description file file.gfs)
A variety of data conversion and display utilities, some of them external to Gerris, can be used to convert output data formats and visualize results. See documentation for details
There is a home page, object hierarchy, introductory tutorial, basic tutorial and examples. See also the Wikipedia article
*See also: *Elmer, FreeFem++, Mathematica (IMTEK Mathematica supplement), OpenFOAM, Stanford University Unstructured
Note: This application is not installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
sudo to root and install from the gerris *or gerris-mpi* Ubuntu package using aptitude or synaptic |

Gmsh/GetDP

Description: Gmsh is a 3d finite-element mesh generator with built-in pre- and post-processing capabilities, incorporating a GUI. GetDP is a finite-element solver integrated with Gmsh. It uses mixed elements to discretize de Rahm-type complexes in one, two and three dimensions
TO RUN:
athena% setup gmsh
athena% gmsh & *(to run {}gmsh* GUI)
athena% gmsh **{}input files* {_}options _(to run gmsh *in command-line mode)
athena% getdp **{}input files* {_}options _(to run getdp *standalone)
There is Gmsh documentation and a web page, GetDP documentation and a web page, wiki examples. See also the README.athena for important additional information
See also: Abaqus, CalculiX,EasyMesh, Elmer, FreeFem++, OpenFOAM, Stanford University Unstructured, tetgen, triangle |

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. OpenFOAM is supplied with pre- and post-processing environments. The interfaces to the pre- and post-processing are themselves OpenFOAM utilities
TO RUN:
athena% bash (if not already running bash shell)
athena$ . /opt/openfoam240/etc/bashrc
athena$ program __options file_(s)_
Many utilities and solvers can be run directly from the command line.
There is a home page with html documentation, and a Wiki
*See also: *Abaqus, CalculiX, Elmer, FreeFem++, Gerris Flow Solver,Gmsh/GetDP, Mathematica (IMTEK Mathematica supplement), Stanford University Unstructured
This application is technical and complex and generally requires multiple solutions steps involving a number of distinct programs. You need to read the documentation and work through some of the tutorials to learn how to use it. |

tetgen

Description: 3d tetrahedral mesh generator and Delaunay triangulator. These meshes can be used in finite-element and finite-volume simulations. tetview 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% tetgen **{}options infile _(to run {}tetgen on input data file {}infile_)
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,Gmsh/GetDP, Mathematica (IMTEK Mathematica supplement), triangle |

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% 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,Gmsh/GetDP, Mathematica (IMTEK Mathematica supplement), tetgen
Note: This application is not installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
sudo to root and install from the triangle-bin Ubuntu package using aptitude or synaptic |

Geographic Information Systems

ArcExplorer

Description: lightweight Java-based client for viewing GIS maps and related data
TO RUN:
athena% add arcims
athena% aejava
Documentation is here |

Molecular Modeling and Dynamics

AIMAll

Description: software package for performing quantitative and visual QTAIM (Quantum Theory of Atoms in Molecules) analyses of molecular systems starting from molecular wavefunction data. AIMQB is the primary program for setting up and running computations. AIMStudio is a 3D graphics program for visualizing AIMALL data
TO RUN:
athena% add aimall
athena%* aimqb.ish (to launch {}AIMQB* in GUI mode)
athena% aimqb.ish -nogui name.wfn (to run a job from the command line using job description file name.wfn)
athena% aimstudio.ish (to launch AIMStudio)
There is a README, AIMQB manual and home page
See also: CPMD, Espresso, GAMESS, Gaussian, molekel, Multiwfn, NAMD, ORCA, Psi4, Q-Chem (MPICH), Q-Chem (OpenMPI) |

Avogadro

Description: extensible molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related fields
TO RUN:
athena% avogadro &
There is a home page with documentation and tutorial
See also: babel, Cambridge Structural Database, CPMD, Discovery Studio Visualizer, Jmol, molekel, molscript, molSimplify, Net Entrez, rasmol, VMD |

babel

Description: converts molecular description files between a variety of formats
TO RUN:
athena% babel -iinput type input file -ooutput type output file
athena% babel -H (for options and supported formats)
See also: Avogadro, Cambridge Structural Database, Discovery Studio Visualizer, Jmol, molekel, molscript, molSimplify, Net Entrez, rasmol, VMD |

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
  • Mogul (mogul): knowledge base for molecular geometry
  • IsoStar (run_isostar): knowledge base of intermolecular interactions
  • Gold (gold): genetic algorithm for docking flexible ligands into protein binding sites
  • Hermes (hermes): 3d visualizer with emphasis on functionality for the analysis of protein-ligand interactions
  • SuperStar (superstar): produces maps of interaction sites in proteins or around small molecules
  • enCIFer (encifer): validator for Crystallographic Information Files (CIF)TO RUN:
    athena% *setup cambsd *
    athena% *cq & *(to run ConQuest)
    athena% *mercury & *(to run Mercury)
    athena% *mogul *(to run Mogul)
    athena% *run_isostar *(to run IsoStar)
    athena%* gold *(to run GOLD)
    athena% hermes & (to run Hermes; SuperStar is usually run from within Hermes by selecting Calculate -> SuperStar)
    athena% encifer (to run enCIFer)
    There is now a Web version (MIT only)
    There are local manuals for Mercury, Mogul, IsoStar, ConQuest, Hermes, SuperStar; also a CSD home page and MIT Library support site
    See also: Avogadro, Deep View, Discovery Studio Visualizer, molscript, molSimplify, rasmol, Star Biochem, VMD, XCrySDen
    Note: only the* IsoStar* client is installed, not the server component |

    CPMD

    Description: computational molecular chemistry application; specifically, a parallelized plane wave/pseudopotential implementationof Density Functional Theory, particularly designed for ab-initio molecular dynamics computations
    TO RUN:
    athena% add cpmd
    athena% mpirun -n cores __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; cores is the number of cores in your CPU)
    athena% mpirun -n cores __cpmd2cube.x *options _{*}files (to convert volume data generated by CPMD to realspace 3d-gridded data in .cube format; {}cores_ is the number of cores in your CPU)
    There is an online manual and author site
    See also: AIMAll, Avogadro,Espresso, GAMESS, Gaussian, molden, molSimplify, Multiwfn, ORCA, Psi4, Q-Chem (MPICH), Q-Chem (OpenMPI), VMD |

    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 Website
    See also: Cambridge Structural Database, DINO, Discovery Studio Visualizer, Jmol, molden, molekel, molscript, Net Entrez, PyMOL, rasmol, Star Biochem, VMD, XCrySDen |

    DINO

    Description: realtime 3D visualization program for structural biology data. There are five data-types supported: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar fields (electron densities and electrostatic potentials), topographs (surface topography scans) and geom (geometric primitives such as lines). Supported input file formats are PDB (coordinates), X-PLOR/CNS (coordinates, electron densities and trajectories), CHARMM (coordinates, trajectories and scalar fields), CCP4 (electron densities), UHBD (electrostatic potentials), DELPHI/GRASP (electrostatic potentials), MSMS (surfaces), MSP (surfaces), GRASP (surfaces), MEAD (coordinates and electrostatic potentials) and greyscale TIFF (surface topographs). Output can be written as PNG, PostScript and POV-Ray
    TO RUN:
    athena% add dino
    athena% dino
    There is a local manual
    See also: Deep View, Discovery Studio Visualizer, Jmol, molden, molekel, molscript, PyMOL, rasmol, Star Biochem, VMD, XCrySDen |

    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% DiscoveryStudio2017R2 &
    There is a vendor site; also a datasheet
    See also: Avogadro, babel, Cambridge Structural Database, Deep View, DINO, Jmol, molekel, molscript, molSimplify, PyMOL, rasmol, Star Biochem, VMD, XCrySDen |

    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% setup espresso
    and in the terminal that opens:
    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% mpirun -np **{}cores* pw.x options < file.in __>*_ file.out_ (to run parallel commands on coresCPU cores in file.in, generating file.out)
    athena% pwgui & *(to run {}pwgui* interface)
    athena% cd /mit/espresso_v6.1; . set-examples (to set up for running examples)
    There is an Espresso Website, User Guide and other documentation
    See also README.athena
    See also: AIMAll, CPMD, GAMESS, Gaussian, Multiwfn, NAMD, ORCA, Psi4, Q-Chem (MPICH), Q-Chem (OpenMPI), XCrySDen |

    GAMESS, MacMolPlt

    Description: general ab initio quantum chemistry package. MacMolPlt is a graphics viewer for GAMESS files
    TO RUN:
    athena% add gamess
    on a public debathena machine, run the following script once as root, each time you start a new login session:
    root@host:~# /mit/gamess/setsharedmem
    commands below should be run using your usual non-root username:
    athena% rungms gamess-in cpus >& gamess-in.log (terminal using C shell, input data file gamess-in.inp, cpus is the number of CPU cores, output in gamess-in.log)
    athena% *gmshelp *(for abbreviated help)
    athena% *gmshelp *control-group (for abbreviated help on commands in control-group)
    athena% mbldr data (to make data.lis from data.mb)
    athena%* wxmacmolplt (to run the {}MacMolPlt* GUI)
    Local GAMESS pdf documentation is here; please read the README.athena for additional important information. Tutorials are here and there is a GAMESS home page
    There is local MacMolPlt documentation and a home page
    See also: AIMAll, CPMD, Espresso, Gaussian, molden, molekel, Multiwfn, NAMD, ORCA, Psi4, Q-Chem (MPICH), Q-Chem (OpenMPI), VMD/NAMD
    Note: our rungms script does not use the version command line parameter (the second one in GAMESS documentation). On private debathena machines, it's possible to permanently configure the memory setting needed by GAMESS without having to run the setsharedmemscript. See the README.athena for details |

    Gaussian, Gaussview

    Description: computational molecular chemistry application. Gaussian is the command-line computational engine. Gaussview is a 3d molecular structure visualizer add-on 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)
    There is a local Gaussian manual and Gaussview manual
    See also: ***AIMAll,* Cambridge Structural Database, CPMD, Espresso, GAMESS, molden, molekel, Multiwfn, NAMD, ORCA, Q-Chem (MPICH), Q-Chem (OpenMPI), VMD/NAMD
    Note: We do not have access to Gaussian 09 or later due to a licensing issue with the vendor. We do not know if or when this will be resolved |

    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% jmol &
    There is an author site with demonstration pages
    See also: ***Avogadro,* babel, Cambridge Structural Database, Deep View, DINO, Discovery Studio Visualizer, molekel, molscript, molSimplify, PyMOL, rasmol, Star Biochem, VMD/NAMD, XCrySDen |

    molden

    Description: molden is a chemistry application for displaying molecular density computed from 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, DINO, GAMESS, Gaussian, molekel, platon, povray, Psi4 |

    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...)
    TO RUN:
    athena% add molekel
    athena% molekel
    There is 5.x online documentation, msms documentation also a Molekel home page
    *See also: *AIMAll, Avogadro, babel, Cambridge Structural Database, Deep View, DINO, Discovery Studio Visualizer, GAMESS, Gaussian, Jmol, molden, molscript, molSimplify, Multiwfn, ORCA, Psi4, PyMOL, Q-Chem (MPICH), Q-Chem (OpenMPI), rasmol, Star Biochem, VMD, XCrySDen |

    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% setenv LD_LIBRARY_PATH */afs/athena/software/molscript_v2.1.2/lib*
    athena% cd /var/tmp/examples
    athena% make
    There is a molscript home page
    See also: ***Avogadro, *babel, Cambridge Structural Database, Deep View, DINO, Discovery Studio Visualizer, Jmol, molekel, molSimplify, Net Entrez, platon, PyMOL, rasmol, Star Biochem, VMD |

    molSimplify

    Description: utility that incorporates geometric manipulation routines necessary for the generation of transition metal complexes, automated setup and completion of electronic structure calculations, post-processing and data analysis
    TO RUN:
    athena% *add molsimplity *(version 1.0)
    athena% *setup molsimplity *(version 1.3)
    athena%* molsimplify* &
    There is a home page and local 1.0 documentation, tutorials
    *See also: *Avogadro, babel, Cambridge Structural Database, CPMD, Discovery Studio Visualizer, Jmol, molekel, molscript, rasmol, VMD |

    Multiwfn

    Description: open source multifunctional wavefunction analyser
    TO RUN:
    athena% add multiwfn
    athena%* multiwfn *infile _(to run multiwfn using input date in {}infile_)
    There is a local manual and home page
    See also: ***AIMall, *CPMD, Espresso, GAMESS, Gaussian, molekel, NAMD, ORCA, Psi4, Q-Chem (MPICH), Q-Chem (OpenMPI) |

    ORCA

    Description: general-purpose computational quantum chemistry application with emphasis on spectroscopic properties of open-shell molecules. The version on Athena is configured to be able to do parallel computation on up to the number of CPU cores in the computer it is currently running on. The locker also contains NBO, a program for calculating bonding orbitals with maximum electron density. NBO can be invoked by ORCA or can be run separately via the gennbo script. The m2a utlility has also been installed. m2a converts input data files from molden format to AIM .wfm files, and optionally saves NBO .47 data file
    TO RUN:
    athena% add -f orca-chem
    athena%* orca file.inp >file.out & *(run orca on input file file.inp, output in file.out)
    athena% gennbo job (to run NBO for job specified in file job.47, output in job.nbo; _the job file should have a .47 _extension but do not type this in the launch command line)
    athena% m2a inputfile (to run m2a on inputfile, creates output files in various formats)
    There is an ORCA online manual, NBO manual, additional information in the README.athena file and an ORCA home page, NBO home page
    See also: ***AIMAll,* CPMD, Espresso, GAMESS, Gaussian, molekel, Multiwfn, NAMD, Psi4, Q-Chem (MPICH), Q-Chem (OpenMPI), VMD/NAMD |

    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 .povformat, 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: Cambridge Structural Database, molden, molscript, povray, rasmol |

    Psi4

    Description: open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties
    TO RUN:
    athena%* add psi4*
    athena% *psi4 *options inputfile outputfile (to run computation for input data in inputfile, output in outputfile)
    There is an online manual, paper, user forum and home page
    *See also: *AIMAll, CPMD, Espresso, GAMESS, molden, molekel, Multiwfn, NAMD, ORCA, Q-Chem (MPICH), Q-Chem (OpenMPI) |

    PyMOL

    Description: tool for displaying, manipulating and modeling 3d molecular images
    TO RUN:
    athena% add -f pymol
    athena% pymol
    There is local documentation and tutorials, a wiki, a support site, video tutorial and website
    See also: Cambridge Structural Database, Deep View, DINO, Discovery Studio Visualizer, FreeWRL, geomview, Jmol, molekel, molscript, Net Entrez, rasmol, Star Biochem, VMD, XCrySDen
    Note: an Open Source version of PyMOL is also in the Athena release. The locker version is an enhanced proprietary release and you need to add the locker with the -f switch to access it. PyMOL will not work correctly and is likely to crash if run remotely |

    Q-Chem (OpenMPI), IQmol

    Description: ab-initio quantum chemistry program for accurate prediction of molecular structures, reactivities and vibrational, electronic and NMR spectra. This version incorporates OpenMPI parallel processing which can be used on Athena to do parallel processing on all cores of the local machine's CPU. IQmol is an open-source molecular editor and visualization package integrated with Q-Chem. It includes a molecular editor, surface generation (orbitals and densitis) and animations (vibrational modes and reaction pathways)
    TO RUN:
    athena%* setup qchem*
    athena%* qchem options file.in >file.out & *(run Q-Chem with OpenMPI on input file file.in, output in file.out)
    athena% iqmol (to launch IQmol)
    There is a Q-Chem manual, IQmol documentation, additional information in the README.athenafile and a Q-Chem home page
    See also: AIMAll, CPMD, Espresso, GAMESS, Gaussian, molekel, Multiwfn, NAMD, ORCA, Psi4, Q-Chem (MPICH) |

    Q-Chem (MPICH), IQmol

    Description: ab-initio quantum chemistry program for accurate prediction of molecular structures, reactivities and vibrational, electronic and NMR spectra. This version incorporates MPICH parallel processing which can be used on Athena to do parallel processing on all cores of the local machine's CPU. IQmol is an open-source molecular editor and visualization package integrated with Q-Chem. It includes a molecular editor, surface generation (orbitals and densitis) and animations (vibrational modes and reaction pathways)
    TO RUN:
    athena%* setup qchemmpich*
    athena%* qchem options file.in >file.out & *(run Q-Chem with MPICH on input file file.in, output in file.out)
    athena% iqmol (to launch IQmol)
    There is a Q-Chem manual, IQmol documentation, additional information in the README.athenafile and a Q-Chem home page
    See also: ***AIMAll,* CPMD, Espresso, GAMESS, Gaussian, molekel, Multiwfn, NAMD, ORCA, Psi4, Q-Chem (OpenMPI) |

    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% rasmol -format description_file
    See also: Avogadro, babel, Cambridge Structural Database, Deep View, DINO, Discovery Studio Visualizer, FreeWRL, geomview, Jmol, molekel, molscript, molSimplify, Net Entrez, pymol, Star Biochem, VMD, XCrySDen
    Note: this application is no longer installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
    sudo to root and install from the rasmol Ubuntu package using aptitude or synaptic |

    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, DINO, Discovery Studio Visualizer, Jmol, molekel, molscript, PyMOL, rasmol, VMD, XCrySDen |

    VMD/NAMD

    Description: VMD is an 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. NAMD is a parallel molecular dynamics code based on Charm++. NAMD uses VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM and X-PLOR. It can be used on Athena but with limited performance as current Athena machines don't have access to parallel computing resources on the network; however parallel processing is possible on multiple cores in the local CPU; as of this writing, the maximum number of cores is four.
    TO RUN:
    athena% add vmd
    athena% vmd *(to run {}VMD*)
    athena% namd2 **{}options* configfile _(to run {}NAMD* with input data specified in {}configfile_)
    athena% cd /mit/vmd_v1.9.3; . run-alanin-demo.bash *(to run a simple {}NAMD* demo from a bash shell)
    athena% cd /mit/vmd_v1.9.3; . run-apoa1-demo.bash *(to run a longer {}NAMD* demo from a bash shell)
    There are VMD 1.9.3 release notes, User's Guide and a tutorial and NAMD 2.12 release notes,User's Guide and tutorial
    See also: AIMAll, Avogadro, babel, Cambridge structural Database, CPMD, Deep View, DINO, Discovery Studio Visualizer, Espresso, GAMESS, Gaussian, Jmol, molekel, molscript, molSimplify, Multiwfn, Net Entrez, ORCA, Psi4, PyMOL, Q-Chem (MPICH), Q-Chem (OpenMPI), rasmol, Star Biochem, XCrySDen |

    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, DINO, Discovery Studio Visualizer, Espresso, Jmol, molekel, PyMOL, rasmol, Star Biochem, VMD |

    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% xdrawchem
    There is online documentation and an author home page
    Note: This application is no longer installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
    sudo to root and install from the xdrawchem Ubuntu package using aptitude or synaptic |

Other Simulations

Alloy

Description:* *MIT-developed language for describing structures and a tool for exploring them. An Alloy model is a collection of constraints that describes (implicitly) a set of structures, for example: all the possible security configurations of a web application,or all the possible topologies of a switching network. Alloy’s tool, the Alloy Analyzer, is a solver that takes the constraints of a model and finds structures that satisfy them
TO RUN:
athena% add alloy
athena% alloy
For tests and samples, select File -> Open Sample Models and choose one of the models from the file selection dialog that opens
There is online documentation and more at the Alloy Website
*See also: *Coq, sketch, spin, TLA Toolbox |

AVL, XFOIL

Description: AVL is a program for the aerodynamic and flight-dynamic analysis of rigid aircraft of arbitrary configuration. XFOIL is an interactive program for the design and analysis of subsonic isolated airfoils
TO RUN:
athena% add aeroutil
athena% avl **{}parameter_file* (to run {}AVL*)
athena% xfoil (to run XFOIL)
There isAVL documentation and a Web page; also XFOIL documentation and a Web page
See also: Stanford University Unstructured |

CHEMKIN PRO

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 chemkinpro
athena% *chemkinpro *(to run CHEMKIN PRO GUI interface)
CHEMKIN PRO manuals are here; there is a CHEMKIN PRO home page
See also: FORTE, RMG |

Coq

Description:* Coq is a formal proof management system based on a formal internal language. There are two implementations (*coqtop, which is command-line based and coqide, which incorporates a GUI). Proof General is an XEmacs-based interface to proof assistants (including Coq)
TO RUN:
athena% coqtop (for command-line version)
athena% *coqide & *(for GUI version)
athena% proofgeneral & *(to run {}Proof General*)
There are Coq and Proof General Websites with Coq and Proof General documentation; there is also a Coq Getting Started document
If you install the coq-doc Ubuntu package, documentation for the version of Coq in the current debathena release will be available in pdf _and {}html_ formats below file:///usr/share/doc/coq-doc-pdf *and *file:///usr/share/doc/coq-doc-html repectively
See also: Alloy, sketch, spin, TLA Toolbox |

Dakota

Description:* *Dakota's parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. The Dakota toolkit provides a flexible, extensible interface between such simulation codes and its iterative systems analysis methods, which include:

  • optimization with gradient and nongradient-based methods
  • uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods
  • parameter estimation using nonlinear least squares (deterministic) or Bayesian inference (stochastic)
  • sensitivity/variance analysis with design of experiments and parameter study methodsThese capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty
    TO RUN:
    athena%* add dakota*
    athena% *dakota *_options args _(to run command-line version)
    athena% DakotaUI & (to run GUI)
    There is a local manual and author site documentation. See also the README.athena file
    See also: AMPL, Elmer, ipopt, lpsolve, snopt, Stanford University Unstructured, TAO/PETSc |

    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% *electric & *
    There is an Electric home page, online manual and a GNU Electric information page
    See also: dia, eagle, gEDA, gerbv, Magic, ngspice, Qucs, SmartSim, xcircuit
    Note: This application is no longer installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
    sudo to root and install it from the electric Ubuntu package using aptitude or synaptic |

    FORTE

    Description: FORTE is a computational fluid dynamics (CFD) package that enable multi-component surrogate fuel models to work with comprehensive spray fluid dynamics. It incorporates CHEMKIN-PRO's solver technology
    TO RUN:
    athena% add forte
    athena%* forte *(to run FORTE GUI interface)
    FORTE manuals are here and there is a web page
    See also: CHEMKIN PRO, RMG |

    gEDA

    Description: suite of electronic design tools, currently offering schematic capture and simulation tools. There are numerous tools in the suite. All can, and some must be invoked independently from the command line. 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)
  • pcb (PCB layout editor)
  • vvp (Icarus Verilog simulation runtime engine)TO RUN:
    athena% *gnetlist *_options files(s) _
    athena% *gsch2pcb *_options files(s) _
    To run other components, consult the documentation. There is a gEDA home page and a documentation Wiki
    See also: eagle, Electric VLSI, Magic, ngspice, Qucs, SmartSim
    Note: ngspice is also part of the gEDA suite |

    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
    TO RUN:
    athena% glpsol -m **{}sample.mod* >*_ sample.sol_ (to solve a MathProg model sample.mod, with results in sample.sol)
    To create executable binaries, add the following line to your code:
    #include <glpk.h>
    and compile as:
    athena% gcc -o **{}sample sample.c* -lglpk -lgmp -lm *(C source file sample.c, dynamic linking)
    athena% gcc -o **{}sample sample.c* /usr/lib/libglpk.a /usr/lib/x86_64-linux-gnu/libgmp.a -lm -lz -lltdl -ldl *(C source file sample.c, static linking, 64 bit systems)
    athena% gcc -o **{}sample sample.c* /usr/lib/libglpk.a /usr/lib/i386-linux-gnu/libgmp.a -lm -lz -lltdl -ldl *(C source file sample.c, static linking, 32 bit systems)
    For dynamic linking, you may or may not need to include the -lgmp link, depending on your code
    There is a GLPK home page; local docs are at file:///usr/share/doc/glpk-doc on debathena machines
    See also: AMPL, ipopt, lpsolve, snopt |

    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, MATLAB and R
    TO RUN:
    athena% *add ipopt *
    athena% *setenv PKG_CONFIG_PATH /mit/ipopt/lib/pkgconfig *(C shell)
    athena% *export PKG_CONFIG_PATH=/mit/ipopt/lib/pkgconfig *(bash shell)
    athena% gcc -O3 -o **{}sample __-I/mit/ipopt/include/coin_ *sample.c `pkg-config --libs ipopt` -lstdc++ *(C source file {}sample.c_)
    athena% g++ -O3 -o **{}sample __-I/mit/ipopt/include/coin_ *sample.cpp [istdraft:other.cpp] **`pkg-config --libs ipopt` *(C++ source file(s) {}sample.cpp_, other.cpp)
    athena% gfortran -O3 -o **{}sample __-I/mit/ipopt/include/coin_ *sample.f *`pkg-config --libs ipopt`* -lstdc++** *(FORTRAN source file {}sample.f_)
    athena% *add ampl *(to run within AMPL)
    athena% ampl
    ampl: model mymodel.mod;
    ampl: data mymodel.dat;
    ampl: option solver ipopt;
    ampl: solve;
    There is an ipopt Website, online documentation and API documentation; see also README.athena for use within R
    See also: AMPL, Dakota, GNU Linear Programming Kit, lpsolve, snopt, TAO/PETSc |

    JFLAP

    Description: package of graphical tools for learning concepts of Formal Languages and Automata Theory. Capabilities include simulators for Regular Languages, Context-free Languages, Recursively Enumerable Languages (including Turing Machines) and L-Systems
    TO RUN:
    athena% add jflap
    athena% jflap &
    There is a home page with tutorial documentation and a wiki |

    LabVIEW

    Description: system-design platform and development environment for a visual programming language called "G", a dataflow programming language. Execution is determined by the structure of a graphical block diagram (the LabVIEW source code) on which the programmer connects different function-nodes by drawing wires. These wires propagate variables and any node can execute as soon as all its input data become available. G is inherently capable of parallel execution. LabVIEW is commonly used for data acquisition, instrument control, and industrial automation
    TO RUN:
    athena% *add labview *
    athena% *labview & *(to run main GUI)
    athena% LVCompare <path to firstVI> <path to secondVI> (to compare twoVirtual Instruments)
    athena% *LVMerge *<path to baseVI> <path to theirVI> <path to yourVI> <path to destVI> (to merge a checked out VI, a revision and a modified revision to a merged revision)
    There is vendor documentation, a web site, aand community site. There are also local pdf manuals
    See also: matlab |

    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.csh (C shell)
    athena% *source /mit/lpsolve/set-environment.bash *(bash shell)
    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, Dakota, GNU Linear Programming Kit, ipopt, matlab, snopt, TAO/PETSc |

    Magic

    Description: interactive editor for VLSI layouts. IRSIM is an event-driven logic level simulator for MOS circuits
    TO RUN:
    athena% magic *_options _& (to launch {}magic*)
    athena% irsim **{}options* {_}files _(to launch {}IRSIM*)
    There are Magic and IRSIM home pages; see file:///usr/share/doc/magic/html/commands.html for Magic documentation, and man irsimfor IRSIM
    See also: dia, eagle, Electric VLSI, gEDA, gerbv, ngspice, Qucs, SmartSim, xcircuit
    Note: this application is no longer installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
    sudo to root and install from the magic *and {}irsim* Ubuntu packages using aptitude or synaptic |

    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. Harminvis a program for performing harmonic inversion of discrete-time, finite-length signals
    TO RUN:
    athena% add -f meep_v1.3 (to run new Meep 1.3 release, does not apply to MPB or Harminv)
    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
    See also: matlab |

    ngspice

    Description:* *mixed-level/mixed-signal circuit simulator based on Spice, Cider and Xspice
    TO RUN:
    athena% *ngspice *options infile (to run ngspice using circuit design data in infile)
    athena% *ngspice *(to run ngspice interactively from a command prompt)
    Other components are available; see man page for each for explanation and usage:

  • ngmultidec
  • ngnutmeg
  • ngsconvertAuthor site is here
    See also: eagle, Electric VLSI, gEDA, Magic
    Note: This application is part of the gEDA suite and is no longer installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
    sudo to root and install from the ngspice and ngspice-doc Ubuntu packages using aptitude or synaptic |

    oof

    Description: oof is a tool designed to help materials scientists calculate macroscopic properties from images of real or simulated microstructures. the current release is called oof2, to distinguish it from an earlier release with significantly different functionality
    TO RUN:
    athena% setup oof
    athena% oof2 options infile (to run oof2 on data in infile)
    Author site is here, and documentation starts here. There is also a what's new in 2.1 page.
    See also: Elmer |

    OpenModelica

    Description:* language and development environment that allows specification of mathematical models of complex natural or man-made systems; has built-in plotting capabilities. There are a number of components that can be run from the command line or invoked internally from the Modelica shell (*OMShell). There is documentation
    TO RUN:
    athena% OMShell (primary shell interface)
    From within the shell, a typical command sequence to read in a Modelica simulation file, run the simulation and plot the results looks something like this:
    >> loadFile("/var/tmp/helloworld.mo")
    >> simulate(HelloWorld, stopTime=2)
    >> plot(x)
    Other components that can also be launched from the command line include:

  • OMShell-terminal (terminal shell)
  • OMEdit (connection editor)
  • OMNotebook (basic notebook interface, with built-in tutorial)
  • OMOptim (optimization tool)
  • OMPlot (plotting system)
  • omc (compiler, translates Modelica code to C)See also: Elmer, euler, Julia, Mathematica, matlab, SAGE, Stanford University Unstructured
    Note: This application is not installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
    sudo to root and follow the author's installation instructions for setting up a Ubuntu repository |

    Qucs

    Description:* *integrated circuit simulator that can emulate a wide variey of circuit types
    TO RUN:
    athena%* add qucs*
    athena% qucs &
    There is local documentation and author site wiki, tutorial and documentation
    Author site is here
    See also: eagle, Electric VLSI, gEDA, Magic |

    RMG

    Description: RMG is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react
    TO RUN:
    athena% setup rmgchem
    in the window that opens:
    rmgchem$ source activate rmg_env
    rmgchem$ rmg.py input.py (where input.py is a job input data file)
    to deactivate:
    rmgchem$ source deactivate rmg_env
    There is local and author site documentation, and an RMG home page
    See also: ***CHEMKIN PRO,* FORTE |

    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 --help *(to get help on command-line options)
    athena% *sketch *options file.sk (to generate code for sketch in input script file.sk)
    For samples, look in the /mit/sketch_v1.7.4/examples directory. There is a local manual
    See also: Alloy, Coq, spin, TLA Toolbox |

    SmartSim

    Description:* *digital logic circuit design and simulation package
    TO RUN:
    athena%* add smartsim*
    athena%* smartsim*
    There is local documentation and a tutorial
    Author site is here
    See also: eagle, Electric VLSI, gEDA, Magic |

    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, Dakota, GNU Linear Programming Kit, ipopt, lpsolve, matlab, TAO/PETSc |

    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% *ispin & *(for GUI interface version)
    For tests and samples, look in the /mit/spin_v6.4.7/Examples directory
    There is local online documentation and more at the spin Website
    See also: Alloy, Coq, sketch, TLA Toolbox
    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 commercial compiler preprocessors tend to have trouble with the syntax |

    Stanford University Unstructured

    Description:* *The Stanford University Unstructured (SU2) suite is an open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE constrained optimization problems. The toolset is designed with computational fluid dynamics and aerodynamic shape optimization in mind, but it is extensible to treat arbitrary sets of governing equations such as potential flow, electrodynamics, chemically reacting flows, and many others
    TO RUN:
    athena% setup su2
    thena%* parallel_computation.py -f{}_ config_file {}-n n *(to run a parallel computation on {}n{_}processors (max 4); see documentation for details)
    athena%* {}su2_program __config_file{} (see documentation for {}su2_program* naming and usage)
    athena% python_script* options file (see documentation for {}python_script* naming and usage)
    There is a Web page, online documentation and local README.athena and paper
    See also: ***Abaqus, *AVL,XFOIL, Dakota, Elmer, FreeFem++, Gerris Flow Solver,Gmsh/GetDP, OpenFOAM, OpenModelica, TAO/PETSc |

    TAO/PETSc

    Description: PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It supports MPI, shared memory pthreads, and NVIDIA GPUs, as well as hybrid MPI-shared memory pthreads or MPI-GPU parallelism. The version on Athena does not support GPU computation. TAO is software for solving large-scale optimization problems. It uses an object-oriented design to create a flexible toolkit with strong emphasis on the reuse of external tools (it is designed to run on top of PETSc). The design enables bi-directional connection to lower level linear algebra support (for example, parallel sparse matrix data structures) as well as higher level application frameworks. It has algorithms for unconstrained and bound-constrained optimization. petsc4py is a Python binding for PETSc
    TO RUN:
    athena% setup tao-petsc
    Copy one of the tutorials subtrees in the tree below /mit/tao-petsc/current to a location where you have write permission and use the makefiles to compile examples and run the code. You can modify these build and run examples to use with your own code. An outline for the rosenbrock1.c example in /mit/tao-petsc_v3.7/petsc/src/tao/unconstrained/examples/tutorials:
    compile:
    g++ -o rosenbrock1.o -c -O3 -I/mit/tao-petsc_v3.7/include rosenbrock1.c
    g++ -O3 -o rosenbrock1 rosenbrock1.o -L/mit/tao-petsc_v3.7/lib -lpetsc -lmpi
    run:
    ./rosenbrock1 -tao_monitor -tao_view > rosenbrock1.out
    There is a local TAO manual, PETSc manual, documentation starting point and PETSc Web page. See also the README.athena file
    See also: AMPL, Dakota, Elmer, ipopt, lpsolve, snopt, Stanford University Unstructured
    These are very complex command-line applications and involve compiling binaries that make calls to TAO and PETSc routines. You will need to study the documentation and examples contained in the tao-petsc_v3.7 locker in order to learn how to use them |

    TensorFlow, Torch

    Description: TensorFlow is an open source software library for numerical computation using data flow graphs applied to machine intelligence. Torch is a scientific computing framework with support for machine learning algorithms
    TO RUN:
    athena% *setup mach-learn_v110217 *(to run new TensorFlow 1.4, Torch 7 releases)
    athena% *setup mach-learn *(to run older TensorFlow 0.12, Torch 7 releases)
    To activate TensorFlow:
    mach-learn% *source /mit/mach-learn_v110217/tensorflow/bin/activate *(1.4 release)
    mach-learn% *source /mit/mach-learn/tensorflow/bin/activate *(0.12 release)
    To run TensorFlow commands interactively:
    (tensorflow)mach-learn% *python3 *(1.4 release)
    (tensorflow)mach-learn% *python *(0.12 release)
    >>> import tensorflow as tf
    To deactivate TensorFlow:
    (tensorflow)mach-learn%* deactivate*
    To activate Torch:
    mach-learn%* . /mit/mach-learn_v110217/torch/install/bin/torch-activate *(newer release 7)
    mach-learn%* . /mit/mach-learn/torch/install/bin/torch-activate *(older release 7)
    To launch Torch interpreter:
    mach-learn% th
    There is TensorFlow getting started, basic usage and tutorials and Torch getting started, cheat sheet and tutorials
    Also: TensorFlow home page, Torch home page
    *See also: * Mathematica. matlab |

    TLA Toolbox

    Description: IDE for TLA+ tools. TLA+ is a formal specification language used to design, model, document, and verify concurrent systems. The toolbox GUI is based on a customized version of Eclipse
    TO RUN:
    athena% add tla
    athena%* toolbox* &
    There is a Toolbox information page and a Web page
    See also: Alloy, Coq, sketch, spin |

IS&T Contributions

Documentation and information provided by IS&T staff members


Last Modified:

March 24, 2021

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