BigDFT is a Density Functional Theory (DFT) parallel electronic structure code using a wavelet basis set. Wavelets form a real space basis set distributed on an adaptive mesh. Surfaces and isolated systems can be simulated with the proper boundary conditions and GTH or HGH pseudopotentials are used to remove the core electrons.

The taxonomy module is a very useful utility for Drupal sites, especially for those of any size. Primarily summarised from the Drupal Handbook on the subject, the following gives a basic summary of the subject.

Molden displays molecular density from the ab initio packages GAMESS and GAUSSIAN and others. Molden reads all the required information from the GAMESS / GAUSSIAN outputfile. Molden is capable of displaying molecular orbitals, electron density and molecular minus atomic density.

NCAR is the (US) National Centre for Atmospheric Research, NCARG is a graphics library, maps database and applications for the same, and NCAR Command Language (NCL) is interpreted language for the above. Installing the software from source is not recommended: "We highly recommend that you use a precompiled NCL binary rather than attempting a build from source code....

The GNU Compiler Collection (usually shortened to GCC) is a compiler system for C (gcc), C++ (g++), Java (gcj), Ada (GNAT), Objective-C (gobjc), Objective-C++ (gobjc++), and Fortran (gfortran). Circumstances will arise when you will want to use a particular version of GCC rather than the system version.

Set the environment variables manually for GMP, MPFR and MPC. Or use modules.


module load gmp/4.3.1
module load mpfr
module load mpc


When developing a website, and in particular an intranet, for an organisation there is often a debate on what should be on the frontpage.

Different departments and different individuals all seem to have "strong opinions" on the matter.

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is used to model atoms or as a parallel particle simulator at the atomic, meso, or continuum scale. It has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. You may remember a difficult install from the past.

MVAPICH and MVAPICH2 is an implementation of MPI for computing systems and servers using InfiniBand, 10GigE/iWARP and RoCE & etc networking technologies.

Installation consists of downloading the tarball into an appropriate directory, extracting it, loading the enviroment variable modules, using of some previously established configuration files, runnig make and make install, and establishing the symbolic links. Note that MVAPICH and MVAPICH2 are entirely different products.


cd /usr/local/src/MVAPICH2

Tuning and Analysis Utilities (TAU) is a program and performance analysis tool for high-performance parallel and distributed computing with a suite of tools for static and dynamic analysis of programs written in C, C++, FORTRAN 77/90, Python, High Performance FORTRAN, and Java.

You'll also need the Program Database Toolkit (PDT), also available from the same location. Let's install that first. You'll need to set your environment variables. You use modules, right?


module load gcc/4.4.4
modulel load openmpi-gcc/1.3.4