OSC is refreshing the software stack on Oakley on September 15, 2015 (during the scheduled downtime); something we have not done since Oakley entered service in 2012. During the software refresh, some default versions are updated to be more up-to-date and some older versions are removed. Information about the old and new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.
Chemical Engineering & Chemistry
Q-Chem is a general purpose ab initio electronic structure program. Its latest version emphasizes Self-Consistent Field, especially Density Functional Theory, post Hartree-Fock, and innovative algorithms for fast performance and reduced scaling calculations. Geometry optimizations, vibrational frequencies, thermodynamic properties, and solution modeling are available.
SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. More information can be found from here.
The February 2014 SUG HPC Tech Talk focused on using the NVIDIA GPUs for computational chemistry. Slides are attached.
The Cambridge Structural Database (CSD) contains complete structure information on hundreds of thousands of small molecule crystals. The Cambridge Crystallographic Data Centre (CCDC) is a suite of programs for CSD search and analysis. The Cambridge Crystallographic Data Centre Home Page has additional information.
Several versions of the software package are available at OSC. Search for csd in this list:
module avail csd
TURBOMOLE is an ab initio computational chemistry program that implements various quantum chemistry algorithms. It is developed at the group of Prof. Reinhart Ahlrichs at the University of Karlsruhe.
Quantum ESPRESSO is a program package for ab-initio molecular dynamics (MD) simulations and electronic structure calculations. It is based on density-functional theory, plane waves, and pseudopotentials.
LS-DYNA is a general purpose finite element code for simulating complex structural problems, specializing in nonlinear, transient dynamic problems using explicit integration. LS-DYNA is one of the codes developed at Livermore Software Technology Corporation (LSTC).
The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a classical molecular dynamics code designed for high-performance simulation of large atomistic systems. LAMMPS generally scales well on OSC platforms, provides a variety of modeling techniques, and offers GPU accelerated computation.