Available Science Applications

The following codes have been optimized to run on Tahoma and the consulting staff have written submission scripts (located in /home/scicons/tahoma/bin/) for most applications to facilitate setting up Tahoma jobs for these codes.

Running jobs are subject to the limits set within our Job Policy.

Biology and Bioinformatics

Diamond

Diamond can be used for high-throughput DNA or protein sequence alignment and database searches analogous to BLAST.

HMMer / MaxRebo

MaxRebo is tool developed at PNNL to perform high-throughput HMMer searches against hidden Markov model libraries of protein families. The available HMM libraries are: Pfam, TIGRFAM, dbCAN, FOAM, and PhyloFacts. The input sequence data can be protein or DNA sequences (DNA sequences will be translated).

Environmental and Hydrological

PFLOTRAN

PFLOTRAN is subsurface flow and reactive transport code, capable of solving a system of generally nonlinear partial differential equations describing multiphase, multicomponent and multiscale reactive flow and transport in porous materials.

Classical Molecular Dynamics

LAMMPS

LAMMPS can be used to model solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems.

submit_lammps

NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Quantum Chemistry

ADF

ADF is a quantum chemistry software package based on Density Functional Theory (DFT). It consists of the molecular DFT code ADF, the periodic DFT code BAND, and the post-ADF COSMO-RS program for liquid thermodynamics, as well as graphical interfaces for these engines and source code for ADF and BAND.

submit_adf

Important

Users need to provide their own license for ADF. Once we have proof of your ownership, we will make ADF available to you.

Molpro

Molpro is a complete system of ab initio programs for molecular electronic structure calculations. As distinct from other commonly used quantum chemistry packages, the emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods.

submit_molpro
submit_molpro_2012.1.8

NWChem

NWChem is a scalable computational Chemistry software actively developed and maintained by the EMSL staff.

submit_nwchem
submit_nwchem7.0.1
submit_nwchem7.0.2

VASP

VAMP/VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing.

submit_vasp
submit_vasp4
submit_vasp4_so
submit_vasp5
submit_vasp5_so
submit_vasp5_ts

Important

Users need to provide their own license for VASP. Once we have proof of your ownership, we will make VASP available to you.

WRF-Chem

WRF-Chem is the Weather Research and Forecasting (WRF) model coupled to Chemistry, which simulates the emission, transport, mixing, and chemcal transformation of trace gases and aerosols.