HPC/RPM

This is the catalog for HPC applications on Carbon. Applications are often referred to as modules because they are managed using the Environment Modules package.

Index

General Analysis

mathematica

gridMathematicaServer

comsol

Molecular Visualization

jmol
rasmol
vmd
xcrysden
GaussView

Quantum/DFT

dacapo

dacapo-python

g03
g09
gpaw

gpaw-setups

molpro
octopus
q-chem
quantum-espresso

wannier90

pwgui

siesta
vasp

vasp-vtst

vasp-vtstscripts

vasp5
wien2k

Classical MD

lammps
namd
asap
asap3

Nanophotonics and fabrication

lumerical
meep
layout-beamer

Toolkits

Numeric
ScientificPython
ase2
ase3
atk
campos
campos-ase3
vtk

Libraries

atlas
GotoBLAS
fftw3
harminv
h5utils
hdf5
libctl
libmatheval
netcdf
numpy
openmpi
charm

Development

icc
ifort
mkl
idb
impi
intel
intel-licenses

System

moab
gold
embody

Versions

Query date: 2011-05-19, 22:00.

Name	Summary	Versions
Carbon applications
asap	ASE calculator for Dacapo (python interface)	3.2.0-1
asap3	ASE calculator for Dacapo (python interface)	3.2.0-1
ase2	ASE is an Atomistic Simulation Environment in Python.	2.3.13-1 2.3.13-2 2.3.13-3
ase3	ASE is an Atomistic Simulation Environment in Python.	3.0.0-3 3.2.0-1 3.2.0-3 3.4.1-1
atk	Atomistix ToolKit (ATK) from QuantumWise	10.8.0-1 10.8.1-1 10.8.2-1 10.8.2-2 10.8.2-3 11.2.0-1 11.2.1-1
atlas	ATLAS - Automatically Tuned Linear Algebra Software (BLAS and a subset of LAPACK)	3.8.0-4
campos	Compound: The CAMPOS modelling suite	stable
campos-ase3	ASE is an Atomistic Simulation Environment in Python.	3.1.0-2
charm	Charm++ - message-passing parallel language and runtime system	6.0-mpi-linux-x86_64-ifort-mpicxx-1 6.0-mpi-linux-x86_64-ifort-smp-mpicxx-1 6.1b-2009-04-02-mpi-linux-x86_64-ifort-mpicxx-1
comsol	COMSOL Multiphysics simulation software	4.1-1
dacapo	Dacapo - a total energy program based on density functional theory	2.7.15-ifort-2 2.7.15-ifort-3 2.7.15-ifort-5 2.7.7
dacapo-python	ASE calculator for Dacapo (python interface)	0.9.4-1 0.9.4-2 0.9.4-3 0.9.4-4 0.9.4-5 0.9.4-5b 2.7.8-1
embody	EMBODY - Environment Modules Build system	0.9 0.9.17 0.9.18 0.9.19 0.9.20 0.9.21 0.9.22 0.9.23
fftw3	library for computing the discrete Fourier transform (DFT)	3.2.1-1 3.2.2-1
g03	Gaussian 03 - an electronic structure program	C.02.i386-2 C.02.i386-3
g09	Gaussian 09 - an electronic structure program	A.02.x86_64-1
GaussView	GaussView - graphical user interface for Gaussian09	5.0-1
gold	Open source accounting system for High Performance Computers	2.1.11.0-4 2.1.11.0-5 2.1.8.1-1
GotoBLAS	Goto BLAS - fast implementation of the Basic Linear Algebra Subroutines	1.26-gfortran-1 1.26-gfortran-smp-1 1.26-intel-1 1.26-intel-smp-1
gpaw	GPAW - a grid-based density-functional theory (DFT) Python code	0.4-gcc-4 0.4-gcc-5 0.4-gcc-6 0.4.1762-1 0.6-gcc-1 0.6-gcc-2 0.6-gcc-3
gpaw-setups	Pseudopotential data for GPAW (see module gpaw)	0.4.2039 0.5.3574 0.6.6300
gridMathematicaServer	Parallel computation extension for Mathematica.	7.0.1-1
h5utils	utilities for visualization and conversion of scientific data in HDF5 format	1.12.1-1 1.12.1-2 1.12.1-3
harminv	Harminv - program and library to solve harmonic inversion problems	1.3.1-mkl-4 1.3.1-netlib-4
hdf5	HDF5 - management of extremely large and complex data collections	1.8.3-parallel-4 1.8.3-serial-4
jmol	Molecule viewer for chemical structures in 3D	11.8.24-1 12.0.24-1 12.0.34-1 12.1.25-1 12.1.37-1 12.1.6-1
lammps	LAMMPS - Sandia's Large-scale Atomic/Molecular Massively Parallel Simulator	2010-09-09-parallel-1 2010-12-05-parallel-3
layout-beamer	LayoutBEAMER - layout preparation for e-beam lithography devices	3.2.0beta 3.3.0beta2_64 3.3.0beta_64 3.3.0beta_64-1
libctl	Guile-based library for control files for scientific simulations	3.0.3-4
libmatheval	library to parse and evaluate symbolic expressions	1.1.7-2 1.1.7-3
lumerical	Lumerical FDTD Solutions - microscale optics simulation	6.0.6-1 6.5.5-1
mathematica	Computing environment for modeling, simulation, visualization	7.0.1-1
meep	finite-difference time-domain (FDTD) simulation software from MIT	1.0-parallel-4 1.0-parallel-5 1.0-serial-4 1.0-serial-5 1.1.1-parallel-1 1.1.1-serial-1
moab	Moab Workload Manager - a policy-based job scheduler and event engine	5.2.4 5.3.3-1 5.3.4-1 5.3.5-1 5.3.6-1 5.3.6.s3-1 5.3.7.s15018-1 5.3.7.s15020-1 5.3.7.s15021-1 5.4.1-1 5.4.2.s16906-1 5.4.3-1 5.4.4-1 6.0.2-1 6.0.3-1
molpro	Quantum chemistry package	2009.1-1 2009.1-2
namd	NAMD - parallel, object-oriented molecular dynamics	2.6.2009-02-11-Linux-x86_64-MPI-icc-1 2.7b1-MPI-icc-1
netcdf	NetCDF - network Common Data Form libraries	3.6.3-gfortran-4 3.6.3-gfortran-5 3.6.3-intel10-4 3.6.3-intel10-5 3.6.3-intel11-4 3.6.3-intel11-5
Numeric	Numeric was the first arrayobject built for Python.	24.2-1 24.2-3
numpy	NumPy is a fundamental package needed for scientific computing with Python.	1.0.4-mkl-1
octopus	Octopus - time-dependent Density-Functional Theory (DFT)	3.0.1-intel10-mkl10.0.2.018-openmpi13-4 3.1.0-intel10-mkl10.1.1.019-1 3.1.0-intel10-mkl10.1.1.019-openmpi13-1
openmpi	Open MPI - A High Performance Message Passing Library	1.2.7-gcc 1.3-gcc-4 1.3-gcc-4.orig 1.3-intel10-4 1.3-intel11-4 1.3.2-gcc-1 1.3.2-gcc-1.orig 1.3.2-intel10-1 1.3.2-intel10-2 1.3.2-intel11-1 1.4.1-gcc-2 1.4.1-intel10-2 1.4.1-intel11-1 1.4.1-intel11-2 1.4.1-intel11-3 1.4.1-intel11-4 1.4.1-intel11-5 1.4.2-intel10-1 1.4.2-intel11-1 1.4.2-intel12-1 1.4.3-gcc-1 1.4.3-intel10-1 1.4.3-intel11-1 1.4.3-intel12-1
pwgui	Quantum ESPRESSO GUI	4.2-1
q-chem	Q-Chem - ab initio quantum chemistry package	3.2.0.1-1 3.2.0.2-1
quantum-espresso	Quantum ESPRESSO suite, with plugins	4.2.1-2
rasmol	Fast molecular graphics program	2.6.4-foc-1 2.7.5-1
ScientificPython	ScientificPython is a Python library for scientific computing.	2.4.11-1 2.4.11-3 2.8-1 2.8-2
siesta	Spanish Initiative for Electronic Simulations with Thousands of Atoms	3.0-rc1-3
vasp	VASP - Vienna Ab-initio Simulation Package	4.6.35-mkl-10 4.6.35-mkl-11 4.6.35-mkl-12 4.6.35-mkl-7 4.6.35-mkl-8 4.6.35-mkl-nozheevx-8 vasp-4.6.35-3Apr08
vasp-vtst	VASP - Vienna Ab-initio Simulation Package	4.6.35-mkl-10 4.6.35-mkl-11 4.6.35-mkl-12 4.6.35-mkl-7 4.6.35-mkl-8
vasp-vtstscripts	Vasp TST Tools - scripts to help with VASP calculations	2.03d-1 2009-06-12-1
vasp5	VASP - Vienna Ab-initio Simulation Package	5.2-mkl-3 5.2-mkl-4 5.2-mkl-8 5.2.11-mkl-3 5.2.11-mkl-tbdyn-4 5.2.8-mkl-2 5.2.8-mkl-3
vmd	Mol-Vis for biomolecular systems, with 3-D graphics, built-in scripting	1.8.6 1.8.7-1
vtk	VTK - a system for 3D graphics, image processing, and visualization	5.0.4-icc-3
wannier90	Maximally-Localised Generalised Wannier Functions Code	1.2-1
wien2k	WIEN2k - electronic structure calculations of solids; all-electron DFT LAPW	09.2-1
xcrysden	Simple molecular viewer with isosurfaces and contours	1.5.21-1
Intel development tools
icc	The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025 11.0.074 11.0.081 11.0.083 11.1.056 11.1.059 11.1.064 11.1.072 11.1.073
icc/10	The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025
icc/11	The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture	11.0.074 11.0.081 11.0.083 11.1.056 11.1.059 11.1.064 11.1.072 11.1.073
icc/12	The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture	12.0.2 12.0.4
icc/ia32	The Intel C/C++ Compiler for the ia32 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025 11.0.074 11.0.081 11.0.083 11.1.056 11.1.059 11.1.064 11.1.072 11.1.073
idb	The Intel debugger for the x86_64/EM64T/Intel64 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025 11.0.074 11.0.081 11.0.083 11.1.059 11.1.064 11.1.072 11.1.073
idb/10	The Intel debugger for the x86_64/EM64T/Intel64 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025
idb/11	The Intel debugger for the x86_64/EM64T/Intel64 architecture	11.0.074 11.0.081 11.0.083 11.1.059 11.1.064 11.1.072 11.1.073
idb/12	The Intel debugger for the x86_64/EM64T/Intel64 architecture	12.0.2 12.0.4
idb/ia32	The Intel debugger for the ia32 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025 11.0.074 11.0.081 11.0.083 11.1.059 11.1.064 11.1.072 11.1.073
ifort	The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025 11.0.074 11.0.081 11.0.083 11.1.056 11.1.059 11.1.064 11.1.072 11.1.073
ifort/10	The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025
ifort/11	The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture	11.0.074 11.0.081 11.0.083 11.1.056 11.1.059 11.1.064 11.1.072 11.1.073
ifort/12	The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture	12.0.2
ifort/ia32	The Intel Fortran Compiler for the ia32 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025 11.0.074 11.0.081 11.0.083 11.1.056 11.1.059 11.1.064 11.1.072 11.1.073
impi	The Intel MPI implementation for the x86_64/EM64T/Intel64 architecture	3.0 3.1 3.2.0.011 3.2.2.006 4.0.0.025 4.0.0.028 4.0.1.007 4.0.2.003
impi/ia32	The Intel MPI implementation for the ia32 architecture	3.0 3.1 3.2.0.011 3.2.2.006
intel	Compound: Intel compilers and MKL version 11	10.1.015 10.1.022 11.0.074 11.0.081
intel-licenses	Enable non-version-specific licenses for the Intel compilers and libraries
intel/10	Compound: Intel compilers version 10	10.1.015 10.1.022 10.1.025
intel/11	Compound: Intel compilers and MKL version 11	11.0.074 11.0.081 11.0.083 11.1.056 11.1.064 11.1.073
mkl	The Intel Math Kernel Library for the x86_64/EM64T/Intel64 architecture	10.0.005 10.0.2.018 10.0.3.020 10.0.4.023 10.1.0.015 10.1.1.019 10.1.2.024 10.2.2.025 10.2.3.029 10.2.4.032 10.2.5.035 10.2.6.038 10.3.2 10.3.4 9.1.023
mkl/ia32	The Intel Math Kernel Library for the ia32 architecture	10.0.005 10.0.2.018 10.0.3.020 10.0.4.023 10.1.0.015 10.1.1.019 10.1.2.024 10.2.2.025 10.2.3.029 10.2.4.032 10.2.5.035 10.2.6.038 9.1.023
Default modules
dot	adds `.' to your PATH environment variable
module-cvs	get most recent module sources from CVS or ftp
module-info	returns all various module-info values
modules	loads the modules environment
null	does absolutely nothing
use.own	adds your own modulefiles directory to MODULEPATH
Name	Summary	Versions

Key to columns

• Name: Leads to the module descriptions below.
• Summary: A one-line description.
• Versions: The version shown in bold is the default.

Carbon applications

Found under: /opt/soft

asap

- 3.2.0-1

ASAP (As Soon As Possible) is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE). ASAP currently implements the Effective Medium Potential (EMT) for the elements Ni, Cu, Pd, Ag, Pt and Au (and their alloys). There is also experimental support for Mg and Mo. ASAP supports simulations on parallel clusters.

https://wiki.fysik.dtu.dk/asap/

asap3

- 3.2.0-1

ASAP (As Soon As Possible) is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE). ASAP currently implements the Effective Medium Potential (EMT) for the elements Ni, Cu, Pd, Ag, Pt and Au (and their alloys). There is also experimental support for Mg and Mo. ASAP supports simulations on parallel clusters.

https://wiki.fysik.dtu.dk/asap/

ase2

- 2.3.13-1, 2.3.13-2, 2.3.13-3

The Atomic Simulation Environment (ASE) is the common part of the simulation tools developed at CAMd. ASE provides Python modules for manipulating atoms, analyzing simulations, visualization etc.

The CAMPOS Atomic Simulation Environment is released under GPL2.

NOTE: ASE-2.x is no longer maintained but required for Dacapo.

https://wiki.fysik.dtu.dk/ase2/

ase3

- 3.0.0-3, 3.2.0-1, 3.2.0-3, 3.4.1-1

The Atomic Simulation Environment (ASE) is the common part of the simulation tools developed at CAMd. ASE provides Python modules for manipulating atoms, analyzing simulations, visualization etc.

The CAMPOS Atomic Simulation Environment is released under GPL2.

https://wiki.fysik.dtu.dk/ase/

atk

- 10.8.0-1, 10.8.1-1, 10.8.2-1, 10.8.2-2

Atomistix ToolKit - a quantum-mechanical modeling package

• atomic-scale electrical transport properties of nanodevices
• open architecture
• scripting language and graphical user interface
• accurate first-principles and fast semi-empirical methods.
• handles large-scale systems with upwards of 1,000 atoms
• advanced electrostatic model
• geometry optimization of molecules and periodic structures

http://www.quantumwise.com/

- 10.8.2-3, 11.2.0-1, 11.2.1-1

Atomistix ToolKit - a quantum-mechanical modeling package

• atomic-scale electrical transport properties of nanodevices
• open architecture
• scripting language and graphical user interface
• accurate first-principles and fast semi-empirical methods.
• handles large-scale systems with upwards of 1,000 atoms
• advanced electrostatic model
• geometry optimization of molecules and periodic structures

Note: This module should be loaded BEFORE vasp.

http://www.quantumwise.com/

atlas

- 3.8.0-4

The ATLAS (Automatically Tuned Linear Algebra Software) project is an ongoing research effort focusing on applying empirical techniques in order to provide portable performance. At present, it provides C and Fortran77 interfaces to a portably efficient BLAS implementation, as well as a few routines from LAPACK.

http://math-atlas.sourceforge.net/

campos

- stable

Compound: The CAMPOS modelling suite

vtk Numeric ScientificPython ase2 ase3 dacapo dacapo-python gpaw-setups gpaw

Details at the individual modules

campos-ase3

- 3.1.0-2

The Atomic Simulation Environment (ASE) is the common part of the simulation tools developed at CAMd. ASE provides Python modules for manipulating atoms, analyzing simulations, visualization etc.

The CAMPOS Atomic Simulation Environment is released under GPL2.

https://wiki.fysik.dtu.dk/ase/

charm

- 6.0-mpi-linux-x86_64-ifort-mpicxx-1, 6.1b-2009-04-02-mpi-linux-x86_64-ifort-mpicxx-1

Charm++ is a message-passing parallel language and runtime system. It is implemented as a set of libraries for C++, is efficient, and is portable to a wide variety of parallel machines. Source code is provided, and non-commercial use is free.

This version was compiled for mpi-linux-x86_64-ifort-mpicxx

Copyright (C) 1989-2000 Regents of the University of Illinois http://charm.cs.uiuc.edu/

- 6.0-mpi-linux-x86_64-ifort-smp-mpicxx-1

Charm++ is a message-passing parallel language and runtime system. It is implemented as a set of libraries for C++, is efficient, and is portable to a wide variety of parallel machines. Source code is provided, and non-commercial use is free.

This version was compiled for mpi-linux-x86_64-ifort-smp-mpicxx

Copyright (C) 1989-2000 Regents of the University of Illinois http://charm.cs.uiuc.edu/

comsol

- 4.1-1

Continuum-level simulation software including modeler and visualization.

• fluid flow (CFD)
• heat transfer
• structural mechanics
• electromagnetics

Material properties, source terms and boundary conditions can be arbitrary functions of the dependent variables.

http://www.comsol.com/products/multiphysics/

dacapo

- 2.7.15-ifort-2, 2.7.15-ifort-3, 2.7.15-ifort-5

Dacapo is a total energy program based on density functional theory. It uses a plane wave basis for the valence electronic states and describes the core-electron interactions with Vanderbilt ultrasoft pseudo-potentials.

The program performs self-consistent calculations for both Local Density Approximation (LDA) and various Generalized Gradient Approximation (GGA) exchange-correlations potentials, using state-of-art iterative algorithms. The code may perform molecular dynamics / structural relaxation simultaneous with solving the Schroedinger equations within density functional theory.

https://wiki.fysik.dtu.dk/dacapo/Dacapo

- 2.7.7

Dacapo is a total energy program based on density functional theory. It uses a plane wave basis for the valence electronic states and describes the core-electron interactions with Vanderbilt ultrasoft pseudo-potentials.

The program performs self-consistent calculations for both Local Density Approximation (LDA) and various Generalized Gradient Approximation (GGA) exchange-correlations potentials, using state-of-art iterative algorithms. The code may perform molecular dynamics / structural relaxation simultaneous with solving the Schroedinger equations within density functional theory.

This is a fairly old build from Jan. 2008.

https://wiki.fysik.dtu.dk/dacapo/Dacapo

dacapo-python

- 0.9.4-1, 0.9.4-2, 0.9.4-3, 0.9.4-4, 0.9.4-5, 0.9.4-5b, 2.7.8-1

This is the ASE calculator interface for Dacapo.

https://wiki.fysik.dtu.dk/dacapo/Installation#dacapo-python-interface

embody

- 0.9

EMBODY (Environment Modules Build) is a simple build tool with support for the Environment-Modules package.

The tool eases and automates the task of building and installing software packages from source, as well as the management of associated modulefiles.

Michael Sternberg, 2009-01

- 0.9.17, 0.9.18

EMBODY (Environment Modules Build) is a build tool with support for the environment-modules package at http://modules.sourceforge.net/.

The tool eases and automates the task of building and installing software from source or binary packages, and integrated the management of associated modulefiles.

(C) 2009, Michael Sternberg; https://trac.anl.gov/embody/

- 0.9.19, 0.9.20, 0.9.21, 0.9.22, 0.9.23

EMBODY (Environment Modules Build) is a build tool with support for the environment-modules package at http://modules.sourceforge.net/.

The tool eases and automates the task of building and installing software from source or binary packages, and integrated the management of associated modulefiles.

Copyright (C) 2009, UChicago Argonne, LLC; All Rights Reserved.

fftw3

- 3.2.1-1, 3.2.2-1

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). FFTW is free software and is highly recommended as FFT library of choice for most applications.

http://www.fftw.org/

g03

- C.02.i386-2, C.02.i386-3

Gaussian 03 is the latest in the Gaussian series of electronic structure programs. Gaussian 03 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest.

Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures. This article introduces several of its new and enhanced features.

Available to Argonne users only.

http://gaussian.com/

g09

- A.02.x86_64-1

Gaussian 09 is the latest in the Gaussian series of electronic structure programs. Gaussian 09 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest.

Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures. This article introduces several of its new and enhanced features.

Available only to Argonne employees and students under confidentiality.

http://gaussian.com/ Help on running with Linda: http://gaussian.com/g_tech/g_ur/m_linda.htm

GaussView

- 5.0-1

GaussView is a graphical user interface designed to help you prepare input for submission to Gaussian and to examine graphically the output that Gaussian produces. GaussView is not integrated with the computational module of Gaussian, but rather is a front-end/back-end processor to aid in the use of Gaussian.

http://gaussian.com/g_tech/gv5ref/gv5ref_toc.htm

gold

- 2.1.11.0-4, 2.1.11.0-5, 2.1.8.1-1

Gold is an open source accounting system developed by Pacific Northwest National Laboratory (PNNL) as part of the Department of Energy (DOE) Scalable Systems Software Project (SSS). It tracks resource usage on High Performance Computers and acts much like a bank, establishing accounts in order to pre-allocate user and project resource usage over specific nodes and timeframe. Gold provides balance and usage feedback to users, managers, and system administrators.

http://www.clusterresources.com/pages/products/gold-allocation-manager.php

GotoBLAS

- 1.26-intel-1

The GotoBLAS codes are fast implementations of the Basic Linear Algebra Subroutines, written by Kazushige Goto /goat-toe/.

The performance depends in part on the code from which you call the GotoBLAS subroutine(s) and on the combination of architecture and operating system under which you are running. Your own tuning here can make a big difference.

This version was compiled using: COMPILER_OPTION='BINARY64=1 F_COMPILER=INTEL'

http://www.tacc.utexas.edu/resources/software/software.php

- 1.26-gfortran-1

The GotoBLAS codes are fast implementations of the Basic Linear Algebra Subroutines, written by Kazushige Goto /goat-toe/.

The performance depends in part on the code from which you call the GotoBLAS subroutine(s) and on the combination of architecture and operating system under which you are running. Your own tuning here can make a big difference.

This version was compiled using: COMPILER_OPTION='BINARY64=1 F_COMPILER=GFORTRAN'

http://www.tacc.utexas.edu/resources/software/software.php

- 1.26-gfortran-smp-1

The GotoBLAS codes are fast implementations of the Basic Linear Algebra Subroutines, written by Kazushige Goto /goat-toe/.

The performance depends in part on the code from which you call the GotoBLAS subroutine(s) and on the combination of architecture and operating system under which you are running. Your own tuning here can make a big difference.

This version was compiled using: COMPILER_OPTION='BINARY64=1 F_COMPILER=GFORTRAN SMP=1'

http://www.tacc.utexas.edu/resources/software/software.php

- 1.26-intel-smp-1

The GotoBLAS codes are fast implementations of the Basic Linear Algebra Subroutines, written by Kazushige Goto /goat-toe/.

The performance depends in part on the code from which you call the GotoBLAS subroutine(s) and on the combination of architecture and operating system under which you are running. Your own tuning here can make a big difference.

This version was compiled using: COMPILER_OPTION='BINARY64=1 F_COMPILER=INTEL SMP=1'

http://www.tacc.utexas.edu/resources/software/software.php

gpaw

- 0.4-gcc-4, 0.4-gcc-5, 0.4-gcc-6, 0.6-gcc-1, 0.6-gcc-2, 0.6-gcc-3

GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method. It uses real-space uniform grids and multigrid methods or atom-centered basis-functions. It features flexible boundary conditions, k-points and gradient corrected exchange-correlation functionals.

https://wiki.fysik.dtu.dk/gpaw/

- 0.4.1762-1

GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method. It uses real-space uniform grids and multigrid methods or atom-centered basis-functions.

https://wiki.fysik.dtu.dk/gpaw/

gpaw-setups

- 0.4.2039, 0.5.3574, 0.6.6300

Pseudopotential data for GPAW (see module gpaw).

https://wiki.fysik.dtu.dk/gpaw/

gridMathematicaServer

- 7.0.1-1

gridMathematica enables parallel computations in Mathematica.

http://www.wolfram.com/

h5utils

- 1.12.1-1, 1.12.1-2, 1.12.1-3

h5utils is a set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format. Besides providing a simple tool for batch visualization as PNG images, h5utils also includes programs to convert HDF5 datasets into the formats required by other free visualization software (e.g. plain text, Vis5d, and VTK).

http://ab-initio.mit.edu/wiki/index.php/H5utils

harminv

- 1.3.1-mkl-4, 1.3.1-netlib-4

Harminv is a program and accompanying library to solve the problem of harmonic inversion -- given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.

http://ab-initio.mit.edu/wiki/index.php/Harminv

hdf5

- 1.8.3-parallel-4, 1.8.3-serial-4

The HDF5 suite includes:

• A data model that can represent complex data objects and metadata.
• A portable file format with no limit on the number or size of data objects.
• A portable library with high-level APIs for C, C++, Fortran 90, and Java.
• Tools and applications.

The HDF5 data model, file format, API, library, and tools are open and distributed without charge.

http://www.hdfgroup.org/HDF5/

jmol

- 11.8.24-1, 12.0.24-1, 12.0.34-1, 12.1.25-1, 12.1.37-1, 12.1.6-1

Jmol is a molecule viewer platform for researchers in chemistry and biochemistry, implemented in Java for multi-platform use. This is the standalone application. It offers high-performance 3D rendering with no hardware requirements and supports many popular file formats.

http://jmol.sourceforge.net/ http://wiki.jmol.org/

lammps

- 2010-09-09-parallel-1

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator)

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

This version has been compiled with support for the following modules: kspace manybody meam molecule poems reax atc

LAMMPS is open source, distributed by Sandia National Laboratories.

http://lammps.sandia.gov/

- 2010-12-05-parallel-3

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator)

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

This version has been compiled with support for the following modules: class2 colloid kspace manybody meam molecule poems reax atc

LAMMPS is open source, distributed by Sandia National Laboratories.

http://lammps.sandia.gov/

layout-beamer

- 3.2.0beta, 3.3.0beta2_64, 3.3.0beta_64, 3.3.0beta_64-1

LayoutBEAMER is a tool for the preparation of layout data for e-beam lithography devices.

http://www.genisys-gmbh.com/

libctl

- 3.0.3-4

libctl is a Guile-based library implementing flexible control files for scientific simulations. It was written to support the MIT Photonic Bands and Meep software, but has proven useful in other programs too.

http://ab-initio.mit.edu/wiki/index.php/Libctl

libmatheval

- 1.1.7-2, 1.1.7-3

GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. It supports expressions in any number of variables of arbitrary names, decimal and symbolic constants, basic unary and binary operators, and elementary mathematical functions. In addition to parsing and evaluation, libmatheval can also compute symbolic derivatives and output expressions to strings.

http://www.gnu.org/software/libmatheval/

lumerical

- 6.0.6-1, 6.5.5-1

Lumerical FDTD Solutions is a high performance microscale optics simulation software. Employing a finite-difference time-domain (FDTD) algorithm, FDTD Solutions allows study of light propagation on the nanoscale.

http://www.lumerical.com/fdtd.php

mathematica

- 7.0.1-1

Mathematica is an extensive computer algebra system. Features include:

• Elementary mathematical function library
• Special mathematical function library
• Matrix and data manipulation tools including support for sparse arrays
• Support for complex number, arbitrary precision, interval arithmetic and symbolic computation
• 2D and 3D data and function visualization and animation tools
• Solvers for systems of equations, diophantine equations, ODEs, PDEs, DAEs, DDEs and recurrence relations
• Numeric and symbolic tools for discrete and continuous calculus
• Multivariate statistics libraries
• Constrained and unconstrained local and global optimization
• Programming language supporting procedural, functional and object oriented constructs
• Toolkit for adding user interfaces to calculations and applications
• Tools for image processing and morphological image processing
• Tools for visualizing and analysing graphs
• Tools for combinatoric problems
• Data mining tools such as cluster analysis, sequence alignment and pattern matching
• Number theory function library
• Continuous and discrete integral transforms
• Import and export filters for data, images, video, sound, CAD, GIS, document and biomedical formats
• Database collection for mathematical, scientific, and socio-economic information
• Notebook interface for review and re-use of previous inputs and outputs including graphics and text annotations
• Technical word processing including formula editing and automated report generating
• Tools for connecting to SQL, Java, .NET, C++, FORTRAN and http based systems
• Tools for parallel programing

http://www.wolfram.com/

meep

- 1.0-parallel-4, 1.0-parallel-5, 1.0-serial-4, 1.0-serial-5, 1.1.1-parallel-1, 1.1.1-serial-1

MEEP (MIT Electromagnetic Equation Propagation) is a finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems, along with the MPB eigenmode package.

http://ab-initio.mit.edu/meep/meep-1.0.tar.gz

moab

- 5.2.4, 5.3.3-1, 5.3.4-1, 5.3.5-1, 5.3.6-1, 5.3.6.s3-1, 5.3.7.s15018-1, 5.3.7.s15020-1, 5.3.7.s15021-1, 5.4.1-1, 5.4.2.s16906-1, 5.4.3-1, 5.4.4-1, 6.0.2-1, 6.0.3-1

Moab Workload Manager is a policy-based job scheduler and event engine that enables utility-based computing for clusters. It simplifies management across one or multiple hardware, operating system, storage, network, license and resource manager environments to increase the ROI of clustered resources, improve system utilization to run between 90-99 percent, and allow for expansion.

Moab Workload Manager combines intelligent scheduling of resources with advanced reservations to process jobs on the right resources at the right time. It also provides flexible policy and event engines that process workloads faster and in line with set business requirements and priorities.

http://www.clusterresources.com/pages/products/moab-cluster-suite/

molpro

- 2009.1-1, 2009.1-2

Molpro is a system of ab initio programs for molecular electronic structure calculations. 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. Integral-direct local electron correlation methods reduce computational scaling.

Available for Argonne users.

http://www.molpro.net/

namd

- 2.6.2009-02-11-Linux-x86_64-MPI-icc-1, 2.7b1-MPI-icc-1

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code.

Subject to Univ. of Illinois Non-Exclusive, Non-Commercial Use License.

The NAMD project is funded by the National Institutes of Health (grant number PHS 5 P41 RR05969).

http://www.ks.uiuc.edu/Research/NAMD/

netcdf

- 3.6.3-intel11-4

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

This version uses the intel/11.0.081 compilers.

http://www.unidata.ucar.edu/software/netcdf/

- 3.6.3-gfortran-4, 3.6.3-gfortran-5

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

This version uses the GNU compilers.

http://www.unidata.ucar.edu/software/netcdf/

- 3.6.3-intel10-4

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

This version uses the intel/10.1.022 compilers.

http://www.unidata.ucar.edu/software/netcdf/

- 3.6.3-intel10-5

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

This version uses the icc/10.1.025 ifort/10.1.025 compilers.

http://www.unidata.ucar.edu/software/netcdf/

- 3.6.3-intel11-5

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

This version uses the icc/11.1.064 ifort/11.1.064 compilers.

http://www.unidata.ucar.edu/software/netcdf/

Numeric

- 24.2-1

Numeric was the first arrayobject built for Python. It has been quite successful and is used in a wide variety of settings and applications. Maintenance has ceased for Numeric, and users should transisition to NumPy as quickly as possible.

This package is needed for Dacapo.

http://numpy.scipy.org/#older_array

- 24.2-3

Numeric is a Python module for high-performance, numeric computing. It provides much of the functionality and performance of commercial numeric software such as Matlab; in some cases, it provides more functionality than commercial software.

numpy

- 1.0.4-mkl-1

NumPy is a fundamental package needed for scientific computing with Python. It contains:

• a powerful N-dimensional array object
• sophisticated broadcasting functions
• basic linear algebra functions
• basic Fourier transforms
• sophisticated random number capabilities
• tools for integrating Fortran code.
• tools for integrating C/C++ code.

This version uses the Intel MKL libraries. There is also an OS version which uses the OS versions of blas and lapack.

WARNING: This package is currently unstable and may lead to MPI errors and segfaults.

http://numpy.scipy.org/

octopus

- 3.0.1-intel10-mkl10.0.2.018-openmpi13-4

Octopus is an ab initio virtual experimentation program for a range of systems. Electrons are described quantum-mechanically within the Density-Functional Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the Pseudopotential approximation.

This version was built with:

• intel/10.1.02210.1.022 mkl/10.0.2.018
• openmpi/1.3-intel10-4
• netcdf/3.6.3-intel10-4

Octopus is free software, released under the GPL license, so you are free to use it and modify it.

http://www.tddft.org/programs/octopus/

- 3.1.0-intel10-mkl10.1.1.019-1

Octopus is an ab initio virtual experimentation program for a range of systems. Electrons are described quantum-mechanically within the Density-Functional Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the Pseudopotential approximation.

This version was built with:

• intel/10/10.1.02210/10.1.022 mkl/10.1.1.019
• without MPI
• netcdf/3.6.3-intel10-4

Octopus is free software, released under the GPL license, so you are free to use it and modify it.

http://www.tddft.org/programs/octopus/

- 3.1.0-intel10-mkl10.1.1.019-openmpi13-1

Octopus is an ab initio virtual experimentation program for a range of systems. Electrons are described quantum-mechanically within the Density-Functional Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the Pseudopotential approximation.

This version was built with:

• intel/10/10.1.02210/10.1.022 mkl/10.1.1.019
• openmpi/1.3.2-intel10-1
• netcdf/3.6.3-intel10-4

Octopus is free software, released under the GPL license, so you are free to use it and modify it.

http://www.tddft.org/programs/octopus/

openmpi

- 1.4.3-intel11-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/11 ifort/11 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.2.7-gcc

The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

This version uses the Intel compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.3-gcc-4, 1.3-gcc-4.orig, 1.3.2-gcc-1, 1.3.2-gcc-1.orig, 1.4.1-gcc-2, 1.4.3-gcc-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the GNU compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.3-intel10-4

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the intel/10.1.022 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.3-intel11-4

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the intel/11.0.081 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.3.2-intel10-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the intel/10/10.1.022 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.3.2-intel10-2

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the intel/10/10.1.025 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.3.2-intel11-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the intel/11/11.0.083 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.4.1-intel10-2

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/10.1.025 ifort/10.1.025 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.4.1-intel11-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the intel/11/11.1.056 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.4.1-intel11-2

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/11.1.064 ifort/11.1.064 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.4.1-intel11-3, 1.4.1-intel11-4, 1.4.1-intel11-5

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/11/11.1.072 ifort/11/11.1.072 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.4.2-intel10-1, 1.4.3-intel10-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/10 ifort/10 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.4.2-intel11-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/11/11.1.073 ifort/11/11.1.073 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

- 1.4.2-intel12-1, 1.4.3-intel12-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/12 ifort/12 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

pwgui

- 4.2-1

PWgui - a GUI for the PWscf subset of the Quantum ESPRESSO suite, supporting creation and editing of input files, and support for interactive runs of the PWscf programs.

The GUI can also use the XCRYSDEN program (http://www.xcrysden.org/) for the visualization of atomic structures from the pw.x input/output files, or for the visualization of properties calculated via the sequence: pw.x-->pp.x (when the property was saved into an XSF file).

The following PWscf programs are supported:

• pw.x
• ph.x
• pp.x
• projwfc.x
• d3.x
• ld1.x (atomic)

See also: module help quantum-espresso

Installed in $QUANTUM_ESPRESSO_GUI_HOME .

http://www.quantum-espresso.org/

q-chem

- 3.2.0.1-1, 3.2.0.2-1

Q-Chem is a comprehensive ab initio quantum chemistry package. Its capabilities range from the highest performance DFT/HF calculations to high level post-HF correlation methods. Q-Chem tackles a wide range of problems including:

• Molecular Structures
• Chemical Reactions
• Molecular Vibrations
• Electronic Spectra
• NMR Spectra
• Solvation Effects

Q-Chem offers Fast DFT calculations with accurate linear scaling algorithms A wide range of post-HF correlation methods that are efficient and unique Quantum calculations extended with QM/MM and molecular dynamics Detailed description in Q-Chem paper

http://www.q-chem.com/

quantum-espresso

- 4.2.1-2

Quantum ESPRESSO (opEn Source Package for Research in Electronic Structure, Simulation, and Optimization) is a suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).

Quantum ESPRESSO builds onto newly-restructured electronic-structure codes (PWscf, PHONON, CP90, FPMD, Wannier) that have been developed and tested by some of the original authors of novel electronic-structure algorithms - from Car-Parrinello molecular dynamics to density-functional perturbation theory - and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency is still our main focus.

This build contains the 'historical' QE core set, plus the WanT (Wannier transport) plugin. GPL-licensed.

See also: module help wannier90 module help pwgui module help xcrysden

Installed in $QUANTUM_ESPRESSO_HOME .

http://www.quantum-espresso.org/ http://www.wannier-transport.org/

rasmol

- 2.6.4-foc-1, 2.7.5-1

RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems. The UNIX and VMS systems require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The program reads in a molecule co-ordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.

http://www.openrasmol.org/

ScientificPython

- 2.4.11-1

ScientificPython is a collection of Python modules that are useful for scientific computing. In this collection you will find modules that cover basic geometry (vectors, tensors, transformations, vector and tensor fields), quaternions, automatic derivatives, (linear) interpolation, polynomials, elementary statistics, nonlinear least-squares fits, unit calculations, Fortran-compatible text formatting, 3D visualization via VRML, and two Tk widgets for simple line plots and 3D wireframe models. There are also interfaces to the netCDF library (portable structured binary files), to MPI (Message Passing Interface, message-based parallel programming), and to BSPlib (Bulk Synchronous Parallel programming).

http://dirac.cnrs-orleans.fr/plone/software/scientificpython/

- 2.4.11-3, 2.8-1, 2.8-2

ScientificPython is a collection of Python modules useful for scientific computing. Modules cover basic geometry (vectors, tensors, transformations, vector and tensor fields), quaternions, automatic derivatives, (linear) interpolation, polynomials, elementary statistics, nonlinear least-squares fits, unit calculations, Fortran-compatible text formatting, 3D visualization via VRML, and two Tk widgets for simple line plots and 3D wireframe models. There are also interfaces to the netCDF library (portable structured binary files), to MPI (Message Passing Interface, message-based parallel programming), and to BSPlib (Bulk Synchronous Parallel programming).

http://dirac.cnrs-orleans.fr/plone/software/scientificpython/

siesta

- 3.0-rc1-3

SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Its main characteristics are:

• Kohn-Sham self-consistent density functional method in the local density (LDA-LSD) or generalized gradient (GGA) approximations.
• norm-conserving pseudopotentials in their fully nonlocal (Kleinman-Bylander) form.
• numeric finite-range atomic orbital basis, unlimited multiple-zeta and angular momenta, polarization and off-site orbitals.
• Projects the electron wavefunctions and density onto a real-space grid in order to calculate the Hartree and exchange-correlation potentials and their matrix elements.
• localized linear combinations of the occupied orbitals (valence-bond or Wannier-like functions), for O(N) time and memory scaling.
• dynamic memory allocation
• serial or parallel execution

Available for users with confirmed licenses.

http://www.icmab.es/siesta/

vasp

- 4.6.35-mkl-10, 4.6.35-mkl-11, 4.6.35-mkl-12, 4.6.35-mkl-7, 4.6.35-mkl-8, 4.6.35-mkl-nozheevx-8

VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.

Available to licensed users only.

http://cms.mpi.univie.ac.at/vasp/

- vasp-4.6.35-3Apr08

VASP (Vienna Ab-initio Simulation Package) is a package for performing quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in 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. These techniques avoid all problems occurring in the original Car-Parrinello method which is based on the simultaneous integration of electronic and ionic equations of motion. The interaction between ions and electrons is described using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Both techniques allow a considerable reduction of the necessary number of plane-waves per atom for transition metals and first row elements. Forces and stress can be easily calculated with VASP and used to relax atoms into their instantaneous groundstate.

This is version vasp-4.6.35-3Apr08

Available to licensed users only.

http://cms.mpi.univie.ac.at/vasp/

vasp-vtst

- 4.6.35-mkl-10, 4.6.35-mkl-11, 4.6.35-mkl-12, 4.6.35-mkl-7, 4.6.35-mkl-8

VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.

This version contains the VTST patch by Graeme Henkelman, http://theory.cm.utexas.edu/vtsttools/downloads/

Available to licensed users only.

http://cms.mpi.univie.ac.at/vasp/

vasp-vtstscripts

- 2.03d-1, 2009-06-12-1

Vasp TST Tools - a set of scripts to perform common tasks to help with VASP calculations, and particularly with transition state finding. The included Vasp.pm perl module contains several simple routines that are used by many of the scripts.

http://theory.cm.utexas.edu/vtsttools/scripts/

vasp5

- 5.2-mkl-3, 5.2-mkl-4, 5.2-mkl-8, 5.2.11-mkl-3, 5.2.11-mkl-tbdyn-4, 5.2.8-mkl-2, 5.2.8-mkl-3

VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.

Available to licensed users only.

http://cms.mpi.univie.ac.at/vasp/

vmd

- 1.8.7-1

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

http://www.ks.uiuc.edu/Research/vmd/

- 1.8.6

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Copyright © 1995-2006 Board of Trustees of the nUiv. of Illinois and others

http://www.ks.uiuc.edu/Research/vmd/

vtk

- 5.0.4-icc-3

The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. VTK consists of a C++ class library, and several interpreted interface layers including Tcl/Tk, Java, and Python. Professional support and products for VTK are provided by Kitware, Inc. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as implicit modelling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. In addition, dozens of imaging algorithms have been directly integrated to allow the user to mix 2D imaging / 3D graphics algorithms and data. The design and implementation of the library has been strongly influenced by object-oriented principles.

http://www.vtk.org/

wannier90

- 1.2-1

The wannier90 code obtains maximally-localised generalised Wannier functions, using them to calculate bandstructures, Fermi surfaces, dielectric properties, sparse Hamiltonians and many things besides.

The method is those of Marzari and Vanderbilt, except for entangled energy bands, where the method of Souza, Marzari and Vanderbilt is used.

See also: module help quantum-espresso

Installed in $WANNIER90_HOME .

http://www.wannier.org/

wien2k

- 09.2-1

WIEN2k allows to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. WIEN2k is an all-electron scheme including relativistic effects and has many features.

Available to registered users only.

http://www.wien2k.at/

xcrysden

- 1.5.21-1

XCrySDen (Crystalline Structures and Densities and X) is a crystalline and molecular visualisation program with support for superimposed isosurfaces and contours.

See also: module help quantum-espresso

Installed in $XCRYSDEN_HOME .

http://www.xcrysden.org/

Intel development tools

Found under: /opt/intel

icc

- 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025, 11.0.074, 11.0.081, 11.0.083, 11.1.056, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture

icc/10

- 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025

The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture

icc/11

- 11.0.074, 11.0.081, 11.0.083, 11.1.056, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture

icc/12

- 12.0.2, 12.0.4

The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture

icc/ia32

- 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025, 11.0.074, 11.0.081, 11.0.083, 11.1.056, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel C/C++ Compiler for the ia32 architecture

idb

- 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025, 11.0.074, 11.0.081, 11.0.083, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel debugger for the x86_64/EM64T/Intel64 architecture

idb/10

- 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025

The Intel debugger for the x86_64/EM64T/Intel64 architecture

idb/11

- 11.0.074, 11.0.081, 11.0.083, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel debugger for the x86_64/EM64T/Intel64 architecture

idb/12

- 12.0.2, 12.0.4

The Intel debugger for the x86_64/EM64T/Intel64 architecture

idb/ia32

- 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025, 11.0.074, 11.0.081, 11.0.083, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel debugger for the ia32 architecture

ifort

- 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025, 11.0.074, 11.0.081, 11.0.083, 11.1.056, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture

ifort/10

- 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025

The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture

ifort/11

- 11.0.074, 11.0.081, 11.0.083, 11.1.056, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture

ifort/12

- 12.0.2

The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture

ifort/ia32

- 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025, 11.0.074, 11.0.081, 11.0.083, 11.1.056, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel Fortran Compiler for the ia32 architecture

impi

- 3.0, 3.1, 3.2.0.011, 3.2.2.006, 4.0.0.025, 4.0.0.028, 4.0.1.007, 4.0.2.003

The Intel MPI implementation for the x86_64/EM64T/Intel64 architecture

impi/ia32

- 3.0, 3.1, 3.2.0.011, 3.2.2.006

The Intel MPI implementation for the ia32 architecture

intel

- 11.0.081

Compound: Intel compilers and MKL version 11

icc/11.0.081 ifort/11.0.081 mkl/10.1.1.019 idb/11.0.081

Details at the individual modules

- 10.1.015

Compound: Intel compilers version 10

icc/10.1.015 ifort/10.1.015 idb/10.0.023

Details at the individual modules

- 10.1.022

Compound: Intel compilers version 10

icc/10.1.022 ifort/10.1.022 idb/10.1.022

Details at the individual modules

- 11.0.074

Compound: Intel compilers version 11 and the MKL 10.1

icc/11.0.074 ifort/11.0.074 mkl/10.1.1.019 idb/11.0.074

Details at the individual modules

intel-licenses

(No Module Specific Help for intel-licenses)

intel/10

- 10.1.025

Compound: Intel compilers version 10

icc/10.1.025 ifort/10.1.025 idb/10.1.025

Details at the individual modules

- 10.1.015

Compound: Intel compilers version 10

icc/10.1.015 ifort/10.1.015 idb/10.0.023

Details at the individual modules

- 10.1.022

Compound: Intel compilers version 10

icc/10.1.022 ifort/10.1.022 idb/10.1.022

Details at the individual modules

intel/11

- 11.1.073

Compound: Intel compilers and MKL version 11

icc/11.1.073 ifort/11.1.073

Details at the individual modules

- 11.0.074

Compound: Intel compilers version 11 and the MKL 10.1

icc/11.0.074 ifort/11.0.074 mkl/10.1.1.019 idb/11.0.074

Details at the individual modules

- 11.0.081

Compound: Intel compilers and MKL version 11

icc/11.0.081 ifort/11.0.081 mkl/10.1.1.019 idb/11.0.081

Details at the individual modules

- 11.0.083

Compound: Intel compilers and MKL version 11

icc/11.0.083 ifort/11.0.083 mkl/10.1.2.024 idb/11.0.083

Details at the individual modules

- 11.1.056

Compound: Intel compilers and MKL version 11

icc/11.1.056 ifort/11.1.056

Details at the individual modules

- 11.1.064

Compound: Intel compilers and MKL version 11

icc/11.1.064 ifort/11.1.064

Details at the individual modules

mkl

- 10.0.005, 10.0.2.018, 10.0.3.020, 10.0.4.023, 10.1.0.015, 10.1.1.019, 10.1.2.024, 10.2.2.025, 10.2.3.029, 10.2.4.032, 10.2.5.035, 10.2.6.038, 10.3.2, 10.3.4, 9.1.023

The Intel Math Kernel Library for the x86_64/EM64T/Intel64 architecture

mkl/ia32

- 10.0.005, 10.0.2.018, 10.0.3.020, 10.0.4.023, 10.1.0.015, 10.1.1.019, 10.1.2.024, 10.2.2.025, 10.2.3.029, 10.2.4.032, 10.2.5.035, 10.2.6.038, 9.1.023

The Intel Math Kernel Library for the ia32 architecture

Default modules

Found under: /usr/share/Modules

dot

Adds `.' to your PATH environment variable

This makes it easy to add the current working directory to your PATH environment variable. This allows you to run executables in your current working directory without prepending ./ to the excutable name

Version 3.2.6

module-cvs

This module will set up aliases and environment variables for easy check-out of the most recent version of the environment modules package.

For CVS access - do the 'login' first then the 'get' when prompted for a password - just hit return

• modules-login - login into the modules CVS repository anonymously
• modules-get - retrieve modules sources

For anonymous ftp access cd to /pub/modules once logged in when prompted for a username/password - give it anonymous and your email address

• modules-ftp - ftp into the modules tar ball directory anonymously. Go to /pub/sourceforge/m/mo/modules

Version 3.2.6

module-info

This module returns all the various module-info values in whatever mode you use (except in `whatis' mode)

Version 3.2.6

modules

modules - loads the modules software & application environment

This adds /usr/share/Modules/* to several of the environment variables.

Version 3.2.6

null

This module does absolutely nothing. It's meant simply as a place holder in your dot file initialization.

Version 3.2.6

use.own

This module file will add $HOME/privatemodules to the list of directories that the module command will search for modules. Place your own module files here. This module, when loaded, will create this directory if necessary.

Version 3.2.6