Computing resources/Software/documentation

Computing resources

  • eXplor; site technique
  • Online Python2 or Python3 compiler at repl.it
  • state of PMMS (via VPN)

    Computing shells, environments

  • Atomic Simulation Environment

    SIESTA territory

  • SIESTA home; mailing list archives; my small personal tutorial; numbering of spherical harmonics ;
  • Basic papers:
    Soler et al. on the method - JPCM 14, 2745 (2002); cond-mat/0111138
    Junquera et al. on improved basis - PRB 64, 235111 (2001); cond-mat/0104170
    Anglada et al. on basis optimization - PRB 66, 205101 (2002); cond-mat/0207548
    Moreno and Soler on real/reciprocal meshes - PRB 45, 13891 (1992)
    Anglada and Soler on filtering - PRB 73, 115122 (2006); (different) arXiv:0807.5030
  • Alberto's Known issues for Siesta-2.0
  • tetr and lev00, post-processing utilities by Lev Kantorovich
  • Alex Voznyy's blog, notably on Bader analysis with Siesta
  • Normand Musseau's web page, with a link to Software, including ART nouveau method for Siesta
  • My lectures on magnetism and phonons at the SIESTA tutorial in Santander, June 2010
  • My lecture outlining my exercices at the SIESTA school by the European Centre of Excellence MaX, Barcelona, May 2017
  • My post-processing tools

    All-electron wisdom

  • WIEN2k home - on-line User's Guide - FAQ
  • G. Fecher's compilation notes
  • Workshops with lectures: 2004 (Penn State), 2006 (TU Wien)
  • The Elk FP-LAPW code

    Pseudopotential wisdom

  • NNIN Virtual Vault for Pseudopotentials maintained by Derek Stewart
  • Kerker on ab initio pseudopotential - J.Phys.C13, L189 (1980)
  • Notes on pseudopotential generation by Paolo Giannozzi
  • Louie et al. on core corrections - PRB 26, 1738 (1982)
  • Porezag et al. on core corrections - PRB 60, 14132 (1999)

    Phonons

  • PHON, A program to calculate phonons using the small displacement method by Dario Alfè
  • Phonopy, an open source package of phonon calculations based on the supercell approach

    UNIX stuff

  • O'Reilly's CD bookshelf in Ukraine
  • Karmic Koala, Simple comme Ubuntu
  • Linux HQ
  • The XFree86 Project, Inc.

    Fortran

  • Intel Premier Site - known bugs in Intel Fortran Compiler for Linux
  • PGF77 - Fortran77 Reference Manual (at the GSI site)
  • F90 FAN's by Michel Olagnon (many useful links)
  • High Performance Fortran Programming - Tutorial by Wilhelm Gehrke (Hannover)
  • Fortran 90 for the Fortran 77 Programmer - Tutorial by Bo Einarsson and Yurij Shokin (Hannover)
  • Software from Alan J. Miller
  • Georg Fecher's notes about compiling WIEN2k with Intel compiler and libraries

    Perl

  • Picking Up Perl by Bradley M. Kuhn
  • Perl 4 Tutorial by Nik Silver at the University of Leeds
  • Sample Chapter 4: Subroutines of O'Reilly's Learning Perl, Third Edition
  • Steve Litt's Perls of Wisdom

    Parallelization issues

  • Designing and Building Parallel Programs by Ian Foster
  • MPI Tutorial with many links
  • An introduction to MPI+Fortran (Uni of Kansas)
  • Examples in MPI/Fortran
  • SP Parallel Programming Workshop at Maui High Performance Computing Center
  • MPI documentation at the Uni Karlsruhe

    Electronic structure packages

  • FSatom - Free Software Project for Atomic-scale Simulations

    Tight-binding:

  • Python Tight Binding (PythTB) from D.Vanderbilt's group at Rutgers
  • The Stuttgart TB-LMTO
  • CRYSTAL (Gaussian bases)
  • NRLMOL (Gaussian bases)
  • OpenMX (pseudopots + numerical bases) by Taisuke Ozaki et al.
  • SIESTA (pseudopots + numerical bases)
  • FPLO

    FLAPW-like:

  • WIEN2k, FLEUR(Juelich), PAW (Clausthal)
  • FP-LMTO by S.Savrasov "NMT" full-potential LMTO;
  • MindLab (Savrasov et al.)

    Planewave:

  • Vanderbilt USPP site in Rutgers
  • VASP (Vienna Ab-initio Simulation Package)
  • CASTEP
  • Quantum Espresso
  • ABINIT (GNU license)
  • CPMD (Car-Parrinello Molecular Dynamics) Consortium
  • Fritz-Haber-Institut FHI98md package
  • PP generation programs maintained by J. L. Martins and Paolo Giannozzi;
    Interface     for calculating pseudos on-the-web as part of Octopus;
    Opium - pseudopotential generation project.

    Graphics, animation, vizualization tools

  • T. Kawano's very good Gnuplot page... and its copy resurrected by Nikos Karampatziakis
  • Grace: Typesetting - full User's Guide - Louic's Some xmgrace tips, notably Special symbols
  • Xd3d, a simple scientific visualization tool (in 2 and 3 dim.)
  • Overview of Plotmtv (for 3-dim. plots, contours etc.)
  • Avogadro, an advanced molecule editor and visualizer
  • GDIS, Graphical Display Interface for Structures
  • Geomview, an interactive 3D viewing program for Unix.
  • The MOLDEN - a pre- and post processing program of molecular and electronic structure
  • The Moviemol, an Easy-to-Use Molecular Display and Animation Program
  • XCrySDen - (X-Window) Crystalline Structures and Densities by Anton Kokalj
  • list of 3D Data Formats at the homepage by Paul Bourke, with many entries about math, geometry objects, computer graphics
  • Molekel - open-source multi-platform molecular visualization program
  • VESTA (a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies);
    Arai Masao's interface scripts to transform WIEN2 charge density for VESTA

    Numerics

  • Netlib Repository
  • Software and Tools, notably GotoBLAS, at TACC
  • Numerical Recipes Electronic Edition; obsolete (free) versions in Fortran 77, Fortran 90, and in C
  • ARPACK - Fortran77 subroutines designed to solve large scale eigenvalue problems
  • TRLan software package for the Thick-Restart Lanczos method by Kesheng Wu and Horst Simon
  • Routines for the diagonalization of complex matrices by Thomas Hann, described in physics/0607103