NEMO - A Stellar Dynamics Toolbox

What is NEMO?

• Documentation
• Images and SnapShots (data archive)
• Papers
• Installation - Anonymous FTP Source Code
• Other Software
• N-body Data Interchange Format
• Local Information

Documentation

• The Users and Programmers Guide is an extensive (150 pages) manual. It's four major parts give a general introduction, a cookbook with many examples, a programmers guide and an appendix with many reference sections.
  NOTE: This manual is currently being rewritten for version 3.2. In the mean time you can download a snapshot of this new version.
• At the GH-2001 workshop we started a NEMO demo series, wrapped around A Gentle Introduction to NEMO.
• Example scripts to highlight certain procedures or packages in NEMO.
• The Survival Guide is intended for the casual usual, who is familiar with operating packages within UNIX. ( badly outdated )
• A summary of features . ( badly outdated )
• A Tutorial for the eager users who want to see what you can do, and try out features. ( under construction )
• NEMO manual pages: Good starting points are the manual pages programs(8NEMO), which lists programs thematically, and index(1NEMO), which lists them alphabetically.
  • programs (1NEMO).
  • functions (3NEMO) .
  • file formats (5NEMO) .
  • hardware (6NEMO) .
  • administrativia (8NEMO) .
  • local programs (lNEMO) .
  • whatis manual database.
• An AMSC664 lecture on some NEMO design (April 8, 2004) - see also AMSC664/Spring '04)

Images and Snapshots

Papers

• On Toolboxes and Telescopes , by Hut and Sussman, (1986) in: The Use of Supercomputers in Stellar Dynamics, Springer Verlag, p 193-198.
• An Environment for Experiments in Stellar Dynamics , by: Barnes, Hernquist, Hut and Teuben (1988) BAAS, 20, 706.
• A Laboratory for Gravitational Scattering Experiments by Hut, in: IAU colloq 109, pp. yyy.
• NEMO: A Stellar Dynamics Toolbox , by Teuben (1994, PASJ, xxx, yyy) overviews the current state of NEMO and introduces a proposal to use FITS as a vehicle to interchange and archive NBODY data (see also the QUESTIONNAIRE ). A gzip compressed postscript version of this paper is also available. The Sci.Data.Formats FAQ discussion may be relevant. The example program mentioned in PASJ94 writes an NBODY BINTABLE .
• ADASS (1994) paper , adass.org version. I also keep a postscript version around.
• GRAPE User Workshop
• other miscellaneous papers

Teuben, P.J. The Stellar Dynamics Toolbox NEMO, in: 
Astronomical Data Analysis Software and Systems IV, 
ed. R. Shaw, H.E. Payne and J.J.E. Hayes. (1995),
PASP Conf Series 77, p398.

Installation

• The now recommended CVS based installation. You can browse some example scripts in the install scripts directory, this is the basic 3 lines:

          wget  ftp://ftp.astro.umd.edu/pub/nemo/nemo_cvs.tar.gz 
          tar zxf nemo_cvs.tar.gz 
  	  # or combine these two with this one-liner (wget also has a similar mode):
  	curl ftp://ftp.astro.umd.edu/pub/nemo/nemo_cvs.tar.gz | tar zxf -
  
  		# wget could need --active-ftp, since --passive-ftp is default
  		# curl has a similar option, --ftp-pasv
  
          cd nemo_cvs
          cvs login ; cvs update -d          # just to be sure to be up to date
          source AAA_SOURCE_ME
  

  and you should have a working NEMO with PGPLOT as the plotting engine.
• There are a number of optional libraries you will need to install all of the programs:
  • pgplot or plplot (with this X11 of course)
  • hdf4
  • cfitsio
  • pvm
  • png
  • gsl
  • miriad
  • fftw
  • rdl (readline)
• automatic build logfile of NEMO are now produced as soon as new code has been checked into CVS.
• nemo_3.3.2.tar.gz (March 14, 2014; Pi Day and Pi Month!) , a (normally gzip compressed) tar file, that contains the latest official release. Note this contains a full src tree, and small sections of the so-called usr tree. If you plan to use a stable NEMO and probably won't upgrade for a while, this would be the recommended path of installing.
• Some older MacOSX related installation notes, although the regular installation method should work fine as long as you have compilers and various external libraries (notably X11) installed.
• You can also download the latest nemo_cvs.tar.gz , which is an anonymous- CVS enabled directory tree. Just install it as usual (i.e. read the blurbs in the file INSTALL). If you want bleeding edge (read: fast and reliable) updates, this command will do it:

  	    cd $NEMO ; make cvslogin              # one time setup
  	    cvs -n -q update                      # check what's new, locally
  	    cvs update -d -P                      # update the tree locally
  	

  We currently don't use any CVS branching, just a single mainline CVS. After this you can update your libraries/programs, e.g.

  	    cd $NEMO ; make libs                  # redo libraries, if needed
  	    mknemo tsf mkplummer ....             # relink selected binaries
  	

  If you plan to use NEMO in any development way, this would be the recommended path of installing. If you prefer to stay more "stable", you can always use our tagnames to update only to the most recent update, e.g.

              cd $NEMO
              cvs update -r nemo_3_0_16
  	

  i.e. replace the dot with an underscore in your VERSION. Notice that this operation will create sticky tags, if you change a file for your own purporse, CVS will flag you a conflict.
• A binary release of NEMO is also available within astromake, either download astromake and update via the astromake procedure, or download the binary from ftp://ftp.astro.umd.edu/pub/astro/.
• Aarseth's nbody0. Although the source code is taken directly from NEMO, the Makefile contains targets to create standalone versions, both in FORTRAN-77 (the exact copy from Binney & Tremaine, 1st Ed), and a C version. A very popular item to download, hence also available "standalone". See also Sverre's anonymous ftp for the more advanced versions. NEMO also contains nbody1 and nbody2 with NEMO interfaces.
• NEMO nbody fits proposal (This is now an outdated version, please refer to the 1994 PASJ paper
• tkrun, automatic GUI builder and frontend to run shell scripts or programs.
• optional software that can be installed to enrich NEMO (this is where you find links to PGPLOT, HDF, CFITSIO etc.)
• The Linux for Astronomy CD-ROM contains a release of NEMO. Also check latest LFA comments.

If you download NEMO, we ask that you register the software, you can also optionally be notified of new releases, but please: Send us an email!

Other Software

• STARLAB ; created by Piet Hut, Steve McMillan and Jun Makino, was loosely modeled after NEMO.
• ZENO is NEMO's close relative; created by Josh Barnes (he also maintains an anonymous ftp directory with updated versions of the treecode in C as well as fortran, see also his Software Distribution).
• The Art of Computational Science, A series of e-books on how to build a computational lab (Hut & Makino) - alos has lots of code and examples available.
• TIPSY , an interactive X-windows based display package maintained by Neal Katz and Tom Quinn. Their HPCC project also maintains a software archive. You should also read about their new N-Chilada visualization and analysis software SALSA
• partiview, a 4D (space and time) OpenGL-based visualization tool that also understand starlab data.
• IFRIT (Gnedin's general purpose visualization utility)
• AMUSE: a software framework for large-scale simulations of dense stellar systems, in which existing codes for dynamics, stellar evolution, hydrodynamics and radiative transfer can be easily coupled.
• initialconditions.org, a blog on Astrophysical Initial conditions (for the N-body problem).
• pynbody, a framework for N-body and SPH astrophysical simulations, written in python.
• Cosmo.Lab: (AstroMD) A Multi Dimensional visualization and analysis toolkit for astrophysics.
• Gravit, gravity simulator with viewing of orbit histories. Uses OpenGL/SDL.
• Gravetat: gravity and electromagnetism simulator
• nMod: modelling planatary systems, including replicating the orbits of moons around planets while those planets orbit a central sun.
• Moody, a cross platform concurrent n-body modelling framework written in C++.
• John Salmon's home page, which pointers and references to parallel treecodes.
• John Fregeau's fewbody and glstarview
• DPMTA: Bill Rankin's implementation of the Fast Multipole Algorithm. (see also NAMD)
• ENZO (Terascale application for cosmological hydrodynamics)
• TPM (Paul Bode's Tree-Particle-Mesh code)
• GADGET, Volker Springer's and Naoki Yoshida's tree-code for (cosmological) N- body/SPH simulations .
• StarCrash, an parallel SPH code.
• MLAPM: Alexander Knebe's recursively refined Cartesian grid code. A new version under the name AMIGA is now available.
• Rainer Spurzem's version of NBODY6++ can be downloaded from this Silk Road Project site. There's a wiki page on it as well, though will migrate to its new location later in 2012. Also some interesting N-body lectures
• glnemo is an interactive visualization 3D program, using Qt, that comes with NEMO. This has now been superseded by glnemo2.
• Xnbody: an online visualization tool for nbody6++
• Walter Dehnen's new and Very Fast and Momentum-Conserving Tree Code. It was first introduced in NEMO as YancNemo, but later renamed to gyrfalcON
• NagBody (Numerical Algorithms for General Body Dynamics) , an N-body code plus toolset by Mario Alberto Rodriguez-Meza
• PMFAST particle-mesh N-body code (f90) with MPI/OpenMP.
• HNBody Symplectic Integration Package (Rauch & Hamilton)
• SWIFT: A solar system integration software package (Levison/Duncan).
• Anatoly Klypin's PM code. See also their ann.ftp. files.
• Hugh Couchman's home page. His adaptive P3M code ( A3PM) is also available with a NEMO frontend in (pstart, prun). See also HYDRA below. Manual also available from astro-ph.
• The XStar N-body Solver
• The Hydra Consortium, Purveyors of fine N-body algorithms and simulation data, (or their UK mirror), provide public domain software and data for N-body hydrodynamical simulations.
  New pages (Spring 2000) are now at: Hydra.
• VIRGO, a consortium of a number of N-Body related key projects, including a page with Software, and now Data.
• Sverre Aarseth's collection of nbody codes. Douglas Heggie's homepage contains the material for A collaborative experiment on star cluster evolution
• Sverre's new interactive movie website
• Derek Richardson's web-page contains the Box Tree Code as well as xa, an X11 animation tool.
• Galactic Collider, interactive Toomre-type galaxy collisions.
• plotting and manipulating 3D particle distributions with PGPLOT (Andrey Kravtsov)
• The N-Body Site, Ben Moore's compilation (formerly www.nbody.net) with lots of pictures and movies.
• Galaxy Dynamics N-Body Simulations (Jakub Schwarzmeier's self-teaching project)
• The Leiden Dynamics Group is also maintaining a software page.
• Hugo Martel has organized The Texas P3M Database, a database of COBE-Normalized CDM Simulations. Send email to database@galileo.as.utexas.edu if you want any of their 68 models. Their abbreviated paper is available on ASTRO-PH, and there are routines within NEMO to read the data.
• GRAVSIM, Mark Bellon's N-body solver.
• Mark Ridler's grav-sim simulator
• FLASH (also incoorporates poisson solvers). See also COSMOS, a Fortran 90 code for parallel computers that solves the evolution equations for gravitationally coupled gas and collisionless matter in one, two, or three dimensions.
• NBodyLab Stellar Dynamics Simulation Testbed
• VINE, a particle based astrophysical simulation code using a tree structure and SPH for gas dynamical effects.
• ORSA (Orbit Reconstruction, Simulation and Analysis).
• Java Applet for Gravitational Orbit Simulation (includes source code)
• TRIP : a general computer algebra system dedicated to celestial mechanics. (Laskar and Gastineau)
• IASG : Kavan Ratnatunga's Galactic Structure Analysis package. It contains a modified version of the Bahcall-Soneira Galaxy model .
• GalactICS Software, developed by John Dubinski and Konrad Kuijken, for generating N-body realizations of axisymmetric galaxy models consisting of disk, bulge and halo. We keep a local copy within in NEMO in standard Fortran, so it also compiles under Linux.
• Chris Mihos' Models of Merging Galaxies.
• The Laboratory for Computational Astrophysics (LCA) maintains an archive of their codes and documentation .
• The Grand Challenge Cosmology Consortium (GC3) figures out the origin of large scale structure in the universe. They have a software archive , a data archive , and lot's of other interesting pages and links.
• The GalMer database contains many galaxy merger simulations.
• The COSMICS and Grafic (Cosmological Initial Conditions Codes) (Bertschinger)
• GRACOS, a parallel cosmological N-body code (Shirokov/Bertschinger)
• Sirko's Cosmological Initial conditions
• Multi-body Gravity Simulator(MGS), A java-3d based package to perform realtime simulations, three dimensional visualizations, design simulations in XML and with a GUI.
• Tomasz Plewa's (Warsaw University Observatory) Smooth Particle Hydrodynamics list, part of the CFD codes list document, which is regularly posted to the sci.physics.computational.fluid-dynamics newsgroup . The current list is now maintained by Wayne Christopher. It also included Greg Lindahl's SPH list.
• astrophysical simulation codes
• Geant4, a toolkit for the simulation of the passage of particles through matter.
• The IDL Astronomy User's Library has some routines to aid in plotting N-body systems. (see also Marc Davies' IDL resources)
• Particula Numerica, a real-time Gravitational N-Body Simulator. (mac/windows)
• galaxy, a free linux program which simulates the motion of stars under the influence of gravity.
• Meta-information
  • N-Body Methods Resources by Mario Antonioletti.
  • Parallel N-Body Simulations
  • Amara Graps's N-body/Particle simulation methods home page. (This also includes a nice summary from a sci.math.num-analysis newsgroup discussion on N-body/Particle simulation numerical schemes.
  • Astrophysics Source Code Library contains references to ``referreed'' codes in the major astronomical journals. The new discussion forum is here.
  • Student Projects of John Hibbard, with lots of useful links to simulation software.
• PC-Based programs
  • GalaSimu is a PC-based simulation of interacting galaxies written by Christian Sturm.
  • Galaxy software (also has a cool interactive web based tool)
  • Astronomy Software from Zephyr. They have several programs with which N-body systems can be created and evolved, but expect to pay some money.
• Animations (you probably need to have mpeg_play or mtv ) and other pretty pictures:
  • A sample movie by Chris Mihos and Lars Hernquist show an encounter between two equal mass galaxy disks.
  • The 1996 Saas-Fee lectures by Josh Barnes contain a number of pictures and animations.
  • The Indiana University Astronomy Department also has some animations containing N-body simulations.
  • The Cosmic Explorer has (well, had) various animations on cosmological simulations from the UIUC group.
  • The LCA Cosmology simulations. Check out the recent record breaker
  • A sample of GC3 Cosmology simulations. Some overlap with the previous item. -- BAD --
  • SPH Simulations from the Cardiff Star Formation group
  • Jun Makino's homepage has some interesting animations.
  • HPCC-UW Multimedia Show.
  • Max Planck Institute fuer Astrophysik Galaxy Formation Group movies
  • Matthias Steinmetz Galaxy Formation movies.
  • Some of Dubinsky's animations: M31/MW merger,
  • Language shootout: (n-body problem) gentoo Intel P4, debian AMD Sempron, P4 (alpha), AMD (alpha).
• Some Related Fields
  • Fast, Free and Flexible MD and their wiki
  • VMD: Molecular Dynamics Vizualisation. (see also NAMD)
  • MDBNCH , A molecular dynamics benchmark.
  • AMBER, a molecular dynamics
  • LASSPTools is a collection of Unix utilities for numerical analysis and graphics, built very much in the philosophy of NEMO, and may be useful in NEMO shell scripts.
  • XGobi vizualization and selecting data from general multi-variate data. (see also: ggobi, mirage)
• Some software information banks that may be relevant:
  • ASDS (Astronomical Software & Documentation Service)
  • AstroWeb

N-Body Data Interchange Format

Local Information