Main Page

Welcome to the SNIC knowledge base and documentations site.

NOTE: This site is under constant development and is still in the early days of it's existence!

The aim of this site is that you should be able to get information, help, tips-and-tricks, etc. regarding the most widely used computational tools.

Application Experts

• Rossen Apostolov, PDC
• Lilit Axner, PDC
• Chandan Basu, NSC
• Mattias Chevalier, PDC
• Michael Djurfeldt, PDC
• Torgny Faxén, NSC
• Anders Hast, Uppmax
• Joel Hedlund, NSC, Bioinformatics
• Joachim Hein, Lunarc
• Jonas Lindemann, Lunarc
• Johan Raber, NSC
• Torben Rasmussen, NSC, Computational Chemistry
• Åke Sandgren, HPC2N
• Mattias Slabanja, C3SE
• Ola Spjuth, Uppmax
• Daniel Spångberg, Uppmax
• Olav Vahtras, PDC
• Jonathan Vincent, PDC

Scientific Topics

Computational Chemistry

Prominent Software

• Quantum Chemistry
  1. Gaussian
  2. NWChem

• Molecular Dynamics
  1. GROMACS
  2. Namd
  3. Amber

• Monte Carlo Thermodynamics
• QSAR

Computational Physics

Prominent Software

Condensed Matter

• VASP

Fluid simulations

• Edge - Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency.
• Fluent
• OpenFOAM
• Sinsom - Simson is a software package that implements an efficient spectral integration technique to solve the Navier-Stokes equations for incompressible channel and boundary layer flows.

Bioinformatics

Bioinformatics is the science of handling information in biology. See also the Bioinformatics category page.

Prominent software

• Sequence analysis
  • BLAST, FASTA - sequence similarity search and pairwise local alignment.
  • HMMER - pattern recognition for protein families or domains.
  • Multiple sequence alignment - simultaneous alignment of multiple biological sequences.
• Computational evolutionary biology
  • PHYLIP - Phylogeny.
  • MrBayes - MCMC prediction of phylogenetic trees.
• Molecular Modeling
  • GROMACS - molecular dynamics, Newtonian simulation of motion.
  • Dalton - Dalton is a powerful molecular electronic structure program, with an extensive functional for the calculation of molecular properties at the HF, DFT, MCSCF, and CC levels of theory.
• Neurobiology
  • MUSIC - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.

Meteorology and Climatology

• ECEARTH
• RCA
• RCO
• NEMO

Visualization and post-processing

• Grace
• Gnuplot

Software Development

• Compilers and Libraries
  1. Intel, PGI, GNU Compilers
  2. MPI
  3. BLAS
  4. MKL
• Profiling and Debugging
  1. TotalView
  2. Vampir
  3. Valgrind
  4. Intel trace analyzer

Using This Wiki

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