Computing Links

• Ohmms, molecular dynamics code
• Benchmarks, need to be rerun on newer platforms
• Platforms
• PAW, projected augmented plane wave for DFT
• OpenMP
• Object oriented programming
• Processors and compilers, tell me new links
• Packages for c++, biltz, petsc,
• Fortran packages
• MD help
• Special code help:LDA and TB: pseudopotentials, vasp (location/help), abinit, Kirchhoff MD/DFT, LMTO, Challocomber, goedecker linear scaling, Dongarra linalg, HPC, security, NRL TB paramters, HPC, white C++ classes, security, dictionaries, top 500.

1. OHMMS -- Molecular Dynamics, feature detection, free energy
   • Ohmms excutables:
     linuxgcc: /n/13/jnkim/Projects/Ohmms-v2.6/linuxgcc/bin/ohmmsapp
     has hdf5 and mcf; only pressure propagator needs work. 7 Oct 2005
   • OHMMS: general info   documentation   DTD
   • RTMRAS
   • Free energy method User guide   documentation
   • OhmmsVis, Michael Ray draft java visualizer, send comments.
   • Hierarchical Data Format (HDF)
       Documentation
       Tutorial
2. Benchmarking performance_*
3. Platforms
4. NCSA data link (technical info)
   • OSC
   • NERSC
   • SDSC, Hotpage, improving performance with most recent; Online
   • NT
   • Compaq DEC SV7 specification
   • Connecting the Platforms.
     • Access Grid
     • Globus
     • GriPhyN
     • Cactus
     • NPACI gridport (doesn't accept vt100 browsers)
5. PAW Page
6. Object Oriented Programming
   • Templates
   • CERN Lectures, see second section: OO Design and Implementation
7. Preprocessors and Compilers
   1. KAI/KAP, premier optimization software
   2. KAP for DEC OSF/1,
   3. C++
      • On alphas, use /usr/ucb/man to see C++ commands (since they are gzipped)
      • Use bnu to view; double click on entry:
          "Compaq Tru64 Unix online Documentation Library"
          under "Programming Tools and Languages"
          double click on "Compaq C++ for Tru64 UNIX"
        These and more are available at Mindview
      • books by Bruck Eckel:
        • Thinking in C++, 2nd Edition
          Volume 1 (try first chapter) Volume 2 (lots on templates) [gzipped pdf]
        • Thinking in Java, 3rd Edition:
          4th & final version: Frames All code on CD available. Non-Frames
          3rd version: Frames version   Non-Frames
   4. Forrtran 90
      • kf90 manual page (69K)
      • High Performance Fortran
      • Fortran 95 compilers and related info (local listing)
      • Latin 90 (humor, source unknown, posted by David Rabson)
   5. PGI, other software optimization company.
8. Packages for C++ Scientific Computing
   • Blitz, c++ class library for scientific computating
   • PETSc, portable, extensible toolkit for scientific computing
9. Packages for Fortran Scientific Computing
   • See PETSc above
   • First-principles electronic structure program (JEEP); FTP sites
10. Help for classical MD
    • CMS-ASU EAM potentials:Al, Cu, Ag, Ta, Au, Pt, Pd, Ni; Mg-Al, Al-Cu
11. Special code help: LDA and TB
    • Pseuopotential codes
      • Vanderbilt pseutopotentials
      • Real space pseudopotential
    • Crystal
      • How to Run Crystal
      • online manual converted from pdf file Needs to reformatted. [pdf]
      • Crystal "Tutorial"
      • EMSL Gaussian Basis Set order form
    • HSE, and older exchange-correlation potentials
      • 2005 JCP paper , compares HSE results for 40 semiconductors agains LSCA, PSE, and TFSS.
      • Data file for calcns in above [ps]
      • Intellectual comparison of EX correlation potential [N/A. bug wilkins who has started it]
    • VASP
      • VASP on-line help
      • VASP data viewere Visualization tools:Description [pdf]
      • installing VASP on osc
      • Installing VASP on IA64
      • Platfrom performance (page needs updatng by Richard Hennig
      • Feb 2001 revised VASP Usage Rules
12. ABINIT
    • ABINIT
    • HTH Pseudopotential files (Hartwigsen-Goedecker-Hutter)
13. CPMD DFT-MD including even B3YLP. Parallel version on bluegene.
14. Accessing LDA codes., LDA help page, from Douglas Allan
15. Density functional homepage
16. Florian Kirchhoff Tight-Binding codes:,
    local version of TB-MD user guide downloading instructions, Code location, need to get password from Florian.
17. LMTO review article [gzipped postscript]
18. Challacombe density-matrix minimization for linear scaling self-consistent field theory
19. Linear scaling electronic structure methods [pdf, RMP 71, 1085-1123 (1999), Linear scaling TB for metals, Goedecker [gzipped postscript]
20. GW implementation: object-oriented, efficiency, parallelization.
21. Documents on packages
    • REED-MD, Rare Event Enhanced Domain Following Molecular Dynamics REED, LANL.
    • Harwell Subroutine Library
    • Linear Solvers, Victor Eijkhout, July 1998.
    • NIST packages
22. Local, possibly useful, computing help
    • Physics Dept Computing Staff Pages
    • IMSL in the Physics Department
    • dxml - A library of linear algebra and signal processing routines; type man dxml; based on BLAS.
    • Numerical recipes and in C. Fortran 90. Fortran 77. See /usr/local/nrc and /usr/local/nrfor
    • OSU student computing competencies page
    • Definitions of pragam and gang scheduling
23. Other, possibly useful, computing help
    • Materials Computation Center software (MCC at NCSA)
    • Brief guide to Maple (at Indiana University)
    • Online source of random numbers to order. See also new sources: atmosphere or lava lamps
    • Top 500 computing sites, June 1999
    • HPC++ library [posted 2/24/99, comments?]
    • Spider coding standard for C++, Version 1.1 is 60 pages long.
    • The linear system analyzer (LSA) [posted 2/24/99, comments?]
    • Scalable parallel random number generators library for parallel MC computations (SPRNG) [posted 2/24/99, comments?]
    • Dongarra linear algebra software, free; in table listing serial/parallel, language, etc. See also ATLAS, analyze the machine and optimize the code package for linear algebra packages.
    • National HPCC Software Exchange
    • FFTW, new FFT package which automatically analyzes the machine and accordingly generates an optimal code.
    • DAGH, adaptive mesh refinement package + manuals, version.
    • Computing security
    • From Mike Mehl TB parameters, vt100 files
    • Rasmol info Postscript Manual
    • HPC Software and Tools Task Force
    • C++ classes of Steve White
       
      
    • Securiety Briefer, individualized for student, faculty and staff (James Madison University). After clicking level, then click "Go to the Password scenario."
24. Dictionaries of Computing
    • On-line Dictionaary, amazingly good for the examples I checked (frame and non-frame).
    • PC webopaedia good online encyclopedia and search engine dedicated to computing technology.
    • Free On-line Dictionary of Computing, extensive with search engine. It can be download for local access; update service available.
    • Dictionary of Computing, shorter. searchable dictionary of acronyms, jargon, programming languages, tools, architecture, operating systems
25. Top 500 Computers

Performance, n.:

A statement of the speed at which a computer system works. Or rather, might work under certain circumstances. Or was rumored to be working over in Jersey about a month ago.