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.

Summaries

Query date: 2018-01-09, 14:56.

Name	Date	Summary	Versions
intel/11	2015-07-23	Intel compilers and MKL for the Intel64 architecture	11.1.073
abinit/7	2013-10-11	Electronic structure modeling package	openmpi-1.4/intel/7.4.2-1 openmpi-1.4/intel/7.4.2-10
amber/12	2015-07-28	Molecular mechanical force fields and simulation programs	openmpi-1.4/intel/12.0-5
ambertools/12	2014-01-29	Molecular mechanical force fields and simulation programs	openmpi-1.4/intel/12.0-5
ase/3.9	2017-04-12	ASE is an Atomistic Simulation Environment in Python.	3.9.1-1
atk/12	2015-07-23	Atomistix ToolKit (ATK) from QuantumWise	12.8.2-1
atk/2015	2016-05-23	Atomistix ToolKit (ATK) from QuantumWise	2015.1-1
atk/2016	2017-06-21	Atomistix ToolKit (ATK) from QuantumWise	2016.4-1
atlas/3	2009-01-30	ATLAS - Automatically Tuned Linear Algebra Software (BLAS and a subset of LAPACK)	intel/3.8.0-4
atomeye/kermode	2012-10-31	Atomistic configuration viewer	kermode-2010-1
beef/0	2016-02-03	DFT Bayesian error estimation ensemble XC functional (VASP addon)	0.1.2-1
boost/1	2011-08-09	Portable C++ source libraries	gcc/1.47.0-1
chargemol/2014	2015-06-30	DDEC charge partitioning scheme	intel/2014-09-14-2
chargemol/2015	2015-06-29	DDEC charge partitioning scheme	intel/2015-06-28-1
charm/6	2015-07-28	Charm++ - message-passing parallel language and runtime system	openmpi-1.4/intel/6.0-mpi-linux-x86_64-ifort-mpicxx-1 openmpi-1.4/intel/6.0-mpi-linux-x86_64-ifort-smp-mpicxx-1 openmpi-1.4/intel/6.1b-2009-04-02-mpi-linux-x86_64-ifort-mpicxx-1 openmpi-1.4/intel/6.4.0-mpi-linux-x86_64-ifort-mpicxx-1 openmpi-1.4/intel/6.4.0-mpi-linux-x86_64-ifort-smp-mpicxx-1
comsol/4	2015-07-28	COMSOL Multiphysics simulation software	4.1-1 4.2-1 4.2a-1 4.3-1 4.3a-1 4.3b-1 4.3b-2 4.4-1 4.4-2
comsol/5	2017-07-14	COMSOL Multiphysics simulation software	5.0-1 5.1-1 5.2-1 5.2a-1 5.3-1
cp2k/2	2012-05-15	Classical and DFT-based atomistic simulations	openmpi-1.4/intel/2.2-4
cuda/4	2012-09-25	Development environment for GPU-accelerated applications	4.2.9-1
cuda/5	2013-05-30	Development environment for GPU-accelerated applications	5.0-1
cuda/7	2015-08-25	Development environment for GPU-accelerated applications	7.0-1
dacapo/2	2015-07-28	Dacapo - a total energy program based on density functional theory	openmpi-1.4/intel/2.7.15-ifort-5
ddscat/7	2015-07-27	Scattering and absorption of light on irregular particles	intel/7.2.2-3
defaults/system	2017-01-17	Default set of modules for system use, not affected by 'module purge'.	2/1.0
defaults/user	2017-02-06	Load user default modules.	2/2.3
embody/1	2015-12-23	EMBODY - Environment Modules Build system	1.0.5 1.9.1 1.9.2 1.9.3 1.9.4 1.9.5 1.9.6 1.9.7 1.9.8 1.9.9
embody/2	2017-10-16	EMBODY - Environment Modules Build system	2.0.0 2.0.1 2.0.10 2.0.11 2.0.12 2.0.13 2.0.2 2.0.3 2.0.4 2.0.5 2.0.6 2.0.7 2.0.8 2.0.9
epics/3	2013-06-18	EPCIS	gcc/3.15.0.1-1
fftw3/3.3	1969-12-31		impi-5/intel-16/3.3.4-10 intel/3.3.2-1 openmpi-1.10 openmpi-1.10/intel-16/3.3.4-11 openmpi-1.4/intel/3.3.2-4
fox/4	2013-05-07	A Fortran library for XML	intel/4.1.2-1
garffield/1	2014-08-07	Genetic Algorithm based Reactive Force Field optimizer	openmpi-1.4/intel/1.0-1
gaussian/09	2015-12-02	Gaussian 09 - an electronic structure program	09.D.01.x86_64-3
gaussian/16	2017-10-16	Gaussian 16 - an electronic structure program	16-A.03-1 16-A.03-2
gaussview/5	2012-01-16	GaussView - graphical user interface for Gaussian09	5.0.9-1
gaussview/6	2017-10-20	GaussView - graphical user interface for Gaussian	6.0.16-1
gcc/4.4	2015-12-02		4.4.7
gcc/4.9	2015-11-20	GNU Compiler Collection	4.9.3-1
gnuplot/4.6	2017-06-27	Multi-platform command-line driven graphing utility	4.6.6-1
gnuplot/5.0	2017-06-27	Multi-platform command-line driven graphing utility	5.0.6-1
gnuplot/5.2	2017-06-27	Multi-platform command-line driven graphing utility	5.2.rc1-1
gold/2	2015-08-28	Open source accounting system for High Performance Computers	2.2.0.5-6-EL6
GotoBLAS/1	2009-02-09	Goto BLAS - fast implementation of the Basic Linear Algebra Subroutines	gcc/1.26-gfortran-1 gcc/1.26-gfortran-smp-1 intel/1.26-intel-1 intel/1.26-intel-smp-1
gpaw-setups/0	2011-09-21	Pseudopotential data for GPAW (see module gpaw)	0.8.7929
gpaw/0	2016-11-15	GPAW - a grid-based density-functional theory (DFT) Python code	openmpi-1.4/intel/0.9.0-gcc-3
gsl/1	2015-11-06	GNU Scientific Library -- a numerical library for C and C++ programmers	1.16-1
h5utils/1	2009-09-10	utilities for visualization and conversion of scientific data in HDF5 format	gcc/1.12.1-3
harminv/1	2015-07-27	Harminv - program and library to solve harmonic inversion problems	intel/1.3.1-mkl-4 intel/1.3.1-netlib-4
hdf5/1	1969-12-31		intel/1.8.13-intel11-serial intel/1.8.13-intel12-serial openmpi-1.4 openmpi-1.4/intel/1.8.13-intel11-parallel openmpi-1.4/intel/1.8.13-intel12-parallel
hoomd/0	2013-07-17	Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition	gcc/0.11.3
hydra/3	2014-07-29	Process management system for starting parallel jobs	gcc/3.1.2-2
idl/8	2013-06-05	Scientific programming language	8.2.2-1
impi/2017	2017-12-06	The Intel MPI implementation for the Intel64 architecture	2017.Build.20160721 2017.Update.2 2017.Update.3 2017.Update.4
impi/4	2015-07-23	The Intel MPI implementation for the Intel64 architecture	4.1.3
impi/5	2016-07-08	The Intel MPI implementation for the Intel64 architecture	5.0.3 5.1.1 5.1.1-3 5.1.2-2 5.1.3
intel/12	2015-07-23	Intel compilers and MKL for the Intel64 architecture	12.1.6
intel/13	2015-07-23	Intel compilers and MKL for the Intel64 architecture	13.1.3
intel/14	2015-07-23	Intel compilers and MKL for the Intel64 architecture	14.0.4
intel/15	2015-10-21	Intel compilers and MKL for the Intel64 architecture	15.0.2 15.0.3 15.0.4
intel/16	2016-07-08	Intel compilers and MKL for the Intel64 architecture	16.0.0-0 16.0.0-1 16.0.0-3 16.0.1-2 16.0.2 16.0.3
intel/17	2017-12-06	Intel compilers and MKL for the Intel64 architecture	17.0.0 17.0.3 17.0.4 17.0.5
java/1.7	2013-06-28	Java Platform Standard Edition Runtime Environment	1.7.0_25-fcs
jdftx/0	2015-12-08	Plane-wave density functional theory for solvated electronic systems	gcc-4.9/0.99-svn1205-1 gcc-4.9/0.99-svn1205-2
jmol/13	2013-11-18	Molecule viewer for chemical structures in 3D	13.2.8-1
lammps/2012	2012-09-27	LAMMPS - Sandia's Large-scale Atomic/Molecular Massively Parallel Simulator	openmpi-1.4/intel/2012-02-12-parallel-jr-11
lammps/2015	1969-12-31		openmpi-1.10 openmpi-1.10/intel-16/2015-05-15-4 openmpi-1.4/intel/2015-05-15-1 openmpi-1.4/intel/2015-05-15-2 openmpi-1.4/intel/2015-05-15-3
layout-beamer/3	2009-03-25	LayoutBEAMER - layout preparation for e-beam lithography devices	3.3.0beta2_64
libctl/3	2015-07-28	Guile-based library for control files for scientific simulations	intel/3.0.3-5
libctl/3.2	2017-10-25	Guile-based library for control files for scientific simulations	intel-17/3.2.2-2
libint/1	2012-05-14	library for two-body integrals over Gaussian functions	intel/1.1.4-1
libint2/2.0	2015-12-08	library for two-body integrals over Gaussian functions	intel/2.0.0-2 intel/2.0.5-1 intel/2.0.5-3
libmatheval/1	2009-09-10	library to parse and evaluate symbolic expressions	gcc/1.1.7-3
libxc/1	2011-11-11	Exchange-correlation functionals for density-functional theory	intel/1.1.0-1
libxc/2	2015-12-01	Exchange-correlation functionals for density-functional theory	gcc-4.9/2.2.2-2 gcc-4.9/2.2.2-3 intel-15/2.2.2-2 intel-15/2.2.2-3 intel-16/2.2.2-3
lumerical-DEVICE/6	2017-10-20	Lumerical DEVICE - Multiphysics modeling of charge and heat transport	6.0.1255-1
lumerical-FDTD/8	2017-10-20	Lumerical FDTD Solutions - microscale optics simulation	8.18.1365-1
lumerical-INTERCONNECT/7	2017-10-20	Lumerical INTERCONNECT - Photonic integrated circuit design and analysis environment	7.0.1365-1
lumerical-MODE/7	2017-10-20	Lumerical MODE - optical waveguide design environment	7.10.1365-1
lumerical/7	2012-03-05	Lumerical FDTD Solutions - microscale optics simulation	7.5.7-1
lumerical/8	2017-09-11	Lumerical FDTD Solutions - microscale optics simulation	8.11.422-1 8.15.736-1 8.16.931-1 8.16.931-1a
mathematica/10	2015-04-15	Computing environment for modeling, simulation, visualization	10.1.0-1
matlab/R2013a	2013-11-14	Language and interactive environment for numerical computation	R2013a-5 R2013a-8
meep/1	1969-12-31		intel/1.1.1-serial-1 openmpi-1.4 openmpi-1.4/intel/1.1.1-parallel-1 openmpi-1.4/intel/1.3-parallel-1
mesa-gl/6	2017-10-20	Alternative OpenGL libraries	6.5.2-1
mesa-gl/7	2017-10-20	Alternative OpenGL libraries	7.2-1
moab/6	2017-10-18	Moab Workload Manager - a policy-based job scheduler and event engine	6.1.12-1
molpro/2009	2015-07-28	Quantum chemistry package	openmpi-1.4/intel/2009.1-1 openmpi-1.4/intel/2009.1-2
molpro/2012	2015-11-05	ab initio programs for molecular electronic structure calculations	2012.1.29-4 2012.1.29-6 2012.1.29-7 2012.1.29-8
mpb/1	2017-10-25	MIT Photonic Bands	1.5-4
mpich/3	2015-06-23	Implementation of the MPI-3.0 standard from the Argonne	gcc/3.1.2-2
namd/2	2012-11-05	NAMD - parallel, object-oriented molecular dynamics	openmpi-1.4/intel/2.9-MPI-icc-4 openmpi-1.4/intel/2.9plus-MPI-icc-3
netcdf/3	2015-07-28	NetCDF - network Common Data Form libraries	gcc/3.6.3-gfortran-5 intel/3.6.3-intel11-5
nlopt/2	2014-05-14	library for nonlinear optimization	gcc/2.4.1-1
numpy/1	2011-11-21	Numerical computing with Python	intel/1.6.1-5
nwchem/6	2015-04-06	Computational chemistry tool from PNNL	openmpi-1.4/intel/6.5-1
octave/4.0	2016-08-16	Octopus - time-dependent Density-Functional Theory (DFT)	4.0.3-1
octopus/4	2015-07-28	Octopus - time-dependent Density-Functional Theory (DFT)	openmpi-1.4/intel/4.0.1-8
openmpi/1.10	2016-12-02	Open MPI - A High Performance Message Passing Library	gcc-4.4/1.10.0-4 gcc-4.4/1.10.1-1 gcc-4.4/1.10.1-2 gcc-4.4/1.10.2-1 gcc-4.4/1.10.3-1 gcc-4.4/1.10.7-2 gcc-4.4/1.10.7-3 gcc-4.9/1.10.0-4 gcc-4.9/1.10.1-1 gcc-4.9/1.10.1-2 gcc-4.9/1.10.2-1 gcc-4.9/1.10.3-1 gcc-4.9/1.10.7-2 gcc-4.9/1.10.7-3 gcc/1.10.0-4 gcc/1.10.1-1 gcc/1.10.1-2 gcc/1.10.2-1 intel-15/1.10.0-4 intel-15/1.10.1-1 intel-15/1.10.1-2 intel-15/1.10.2-1 intel-15/1.10.3-1 intel-16/1.10.0-4 intel-16/1.10.1-1 intel-16/1.10.1-2 intel-16/1.10.2-1 intel-16/1.10.3-1 intel-17/1.10.7-2 intel-17/1.10.7-3 intel/1.10.0-4 intel/1.10.1-1 intel/1.10.1-2 intel/1.10.2-1
openmpi/1.4	2015-07-28	Open MPI - A High Performance Message Passing Library	gcc/1.4.5-gcc-2 intel/1.4.5-intel11-1 intel/1.4.5-intel11-2 intel/1.4.5-intel12-1 intel/1.4.5-intel12-2
openmpi/1.6	2015-07-29	Open MPI - A High Performance Message Passing Library	gcc/1.6.5-gcc-1 intel/1.6.5-intel11-1 intel/1.6.5-intel12-1
openmpi/1.8	2015-09-10	Open MPI - A High Performance Message Passing Library	gcc-4.4/1.8.8-7 gcc/1.8.8-7 intel-15/1.8.8-7 intel-16/1.8.8-7 intel/1.8.8-7
packmol/13	2014-02-12	Pack molecules in space as starting points for molecular dynamics	intel/13.243-1
periodic_NBO/2012	2015-07-28	Periodic NBO software	intel/2012-11-14-1
phonopy/1.10	2016-06-17	Phonon analyzer interfacing to various calculators	1.10.8-1
povray/3	2011-08-09	Persistence of Vision Ray-Tracer	gcc/3.7.0.RC3-1 gcc/3.7.0.RC3-2
profile/system	2017-01-17	Default set of modules for system use, not affected by 'module purge'.	2/1.0
profile/user	2017-02-06	Load user default modules.	2/2.3
pwgui/4	2011-02-24	Quantum ESPRESSO GUI	4.2-1
python-anaconda/2.7	2016-03-31	Open source analytics platform based on Python.	4/2.7.11-4.0.0-2
python-anaconda/3.5	2016-03-31	Open source analytics platform based on Python.	4/3.5.1-4.0.0-2
python-centos/2.6	2017-08-02		gcc-4.4/2.6.6
python-env-anaconda/2.7	2016-06-28	Python environment with custom tools for Carbon	4/2.7.11-09
python-env-anaconda/3.5	2016-06-28	Python environment with custom tools for Carbon	4/3.5.1-09
python-env-intel/2.7	2017-12-21	Python environment with custom tools for Carbon	2017/2.7-001 2017/2.7-004 2017/2.7-01 2018/2.7-01
python-env-intel/3.5	2017-12-21	Python environment with custom tools for Carbon	2017/3.5-001 2017/3.5-004 2017/3.5-01
python-env-intel/3.6	2017-12-21	Python environment with custom tools for Carbon	2018/3.6-01
python-intel/2.7	2017-12-20	Intel Distribution for Python with MKL support	2015/2.7.20150803_184913 2017/2.7.12 2017/2.7.13-2017.3.053-1 2018/2.7.14-2018.1.023-1
python-intel/3.5	2017-12-20	Intel Distribution for Python with MKL support	2015/3.5.20150803_185146 2017/3.5.2 2017/3.5.3-2017.3.052-1
python-intel/3.6	2017-12-20	Intel Distribution for Python with MKL support	2018/3.6.3-2018.1.023-1
python/2.7	2018-01-07	An interpreted, interactive, object-oriented programming language.	gcc-4.1/2.7.3-1 gcc-4.4/2.7.11-1
python/3.5	2017-08-01	An interpreted, interactive, object-oriented programming language.	gcc-4.4/3.5.1-1
q-chem/4.1	2015-05-05	Q-Chem - ab initio quantum chemistry package	4.1.0.1-1
quantum-espresso/4	2013-01-18	Quantum ESPRESSO suite, with plugins	openmpi-1.4/intel/4.3.2-2
quantum-espresso/5.4	2016-07-21	Quantum ESPRESSO suite, with plugins	openmpi-1.10/intel-16/5.4.0-1
rasmol/2.6	2010-05-19	Fast molecular graphics program	2.6.4-foc-1
rasmol/2.7	2010-05-19	Fast molecular graphics program	2.7.5-1
readline/6	2013-06-25	Library for editing typed command lines	6.2-1
rings/1	2013-03-26	Rigorous Investigation of Networks Generated using Simulations	openmpi-1.4/intel/1.2.3-1
ScientificPython/2	2016-02-19	ScientificPython is a Python library for common tasks in scientific computing.	intel/2.8-1
scipy/0	2011-11-22	Scientific computing with Python	openmpi-1.4/gcc/0.9.0-1 openmpi-1.4/intel/0.10.0-1
siesta/3	2015-07-28	Spanish Initiative for Electronic Simulations with Thousands of Atoms	openmpi-1.4/intel/3.2-1
siesta/4.0	2017-02-08	Spanish Initiative for Electronic Simulations with Thousands of Atoms	impi-5/intel-16/4.0-1
siesta/4.1	2017-05-22	Spanish Initiative for Electronic Simulations with Thousands of Atoms	impi-5/intel-16/4.1-b2-1 impi-5/intel-16/4.1-b2-2
siesta/4.1-b2	2017-05-22	Spanish Initiative for Electronic Simulations with Thousands of Atoms	impi-5/intel-16/4.1-b2-1 impi-5/intel-16/4.1-b2-2
spglib/1	2014-10-16	library for finding and handling crystal symmetries	gcc/1.6.4
stress-ng/0	2017-10-25	stress test a computer system in selectable ways	0.08.18-1
stress/1	2014-07-31	simple workload generator for POSIX systems	1.0.4-1
vasp-vtst/4	2015-07-28	VASP - Vienna Ab-initio Simulation Package	openmpi-1.4/intel/4.6.35-mkl-12
vasp-vtstscripts/2012	2012-12-10	Vasp TST Tools - scripts to help with VASP calculations	2012-11-11-1
vasp-vtstscripts/926	2016-08-18	Vasp TST Tools - scripts to help with VASP calculations	926-1
vasp/4.6	2015-07-28	VASP - Vienna Ab-initio Simulation Package	openmpi-1.4/intel/4.6.35-mkl-13 openmpi-1.4/intel/4.6.35-mkl-nozheevx-8 openmpi-1.4/intel/4.6.36-mkl-4
vasp5/5.3	2015-07-28	VASP - Vienna Ab-initio Simulation Package	impi-5/intel-16/5.3.5-2 openmpi-1.10 openmpi-1.10/intel-16/5.3.5-1 openmpi-1.4/intel/5.3.2-mkl-beef-1 openmpi-1.4/intel/5.3.3p3-mkl-3 openmpi-1.4/intel/5.3.3p3-mkl-cellz-1
vasp5/5.3-scan	2016-12-15	VASP - Vienna Ab-initio Simulation Package	impi-5/intel-16/5.3.5-scan-1 openmpi-1.10/intel-16/5.3.5-scan-1
vasp5/5.4	2017-02-13	VASP - Vienna Ab-initio Simulation Package	impi-5/intel-16/5.4.1.3-10 impi-5/intel-16/5.4.1.3-11 impi-5/intel-16/5.4.1.3-6 impi-5/intel-16/5.4.1.3-8 impi-5/intel-16/5.4.1.3-9 impi-5/intel-16/5.4.4.0-1 openmpi-1.10/intel-16/5.4.1.3-10 openmpi-1.10/intel-16/5.4.1.3-11 openmpi-1.10/intel-16/5.4.1.3-6 openmpi-1.10/intel-16/5.4.1.3-8 openmpi-1.10/intel-16/5.4.1.3-9
vasp5/5.4-z2pack	2016-11-04	VASP - Vienna Ab-initio Simulation Package	impi-5/intel-16/5.4.1.3-z2pack-1 impi-5/intel-16/5.4.1.3-z2pack-2 openmpi-1.10/intel-16/5.4.1.3-z2pack-1
vesta/3	2014-12-12	3D visualization program for structural models	3.2.1-1
vmd/1	2014-03-17	Mol-Vis for biomolecular systems, with 3-D graphics, built-in scripting	1.9.1-2
voro++/0	2013-08-15	Library for three-dimensional Voronoi tessellations	intel/0.4.5-1
vtk/5	2015-07-28	VTK - a system for 3D graphics, image processing, and visualization	intel/5.0.4-icc-3
wannier90/1	2016-02-04	Maximally-Localised Generalised Wannier Functions Code	1.2-1 1.2-2
wannier90/1-z2pack	2016-11-04	Maximally-Localised Generalised Wannier Functions Code	1.2-z2pack-1
wannier90/2	2016-01-26	Maximally-Localised Generalised Wannier Functions Code	impi-5/intel-16/2.0.1-3 openmpi-1.10/intel-16/2.0.1-3
wien2k/09	2010-01-17	WIEN2k - electronic structure calculations of solids; all-electron DFT LAPW	intel/09.2-1
wien2k/14.2	2016-03-11	WIEN2k - electronic structure calculations of solids; all-electron DFT LAPW	impi-5/intel-16/14.2-7
xcrysden/1	2011-02-24	Simple molecular viewer with isosurfaces and contours	1.5.21-1

Key to columns

Name: Leads to the package descriptions below.
Date: Modification date of the the default version's modulefile (not necessarily of the package itself).
Summary: A one-line description.
Versions: The version shown in bold is the default.

Descriptions

Deprecated

intel/11

11.1.073

Intel compilers and MKL for the Intel64 architecture

Uncategorized

ABINIT is an electronic structure modeling package to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

ABINIT can optimize geometries and perform molecular dynamics, generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory (for molecules). Different utility programs are provided.

ABINIT is distributed under the GNU General Public Licence.

This module version supports netcdf+etsf_io+fox and libxc+wannier90 .

http://www.abinit.org/

openmpi-1.4/intel/7.4.2-10

ABINIT is an electronic structure modeling package to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

ABINIT can optimize geometries and perform molecular dynamics, generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory (for molecules). Different utility programs are provided.

ABINIT is distributed under the GNU General Public Licence.

This module version supports and libxc+wannier90 .

http://www.abinit.org/

amber/12

openmpi-1.4/intel/12.0-5

AMBER refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

This module contains both AmberTools and AMBER, version 12.0, with binary flavors for serial, parallel, and single-GPU. Amber GPU binaries require:

module load cuda/5.0-1

Amber is distributed by UCSF subject to a licensing agreement. Request access to amber by email to [email protected].

If you only need AmberTools, load the 'ambertools' module, which is available to any user.

http://ambermd.org/

ambertools/12

openmpi-1.4/intel/12.0-5

AMBER refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

This module contains AmberTools only, version 12.0, distributed under the GPL.

http://ambermd.org/

ase/3.9

3.9.1-1

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/12

12.8.2-1

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/

atk/2015

2015.1-1

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/

atk/2016

2016.4-1

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

intel/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/

atomeye/kermode

kermode-2010-1

AtomEye is a molecular visualization tool with these key features:

XYZ, PDB, and native CFG formats
periodic boundary conditions
high-resolution bitmap PNG/JPEG/EPS screenshots (bitmap only)
handles gzip- or bzip2-compressed input
order-N in execution time and memory; supports more than 1 million atoms
coordination number color-encoding with customizable cutoff radii and invisibility controls
local atomic von Mises shear strain invariant color-encoding
up to 16 arbitrary cutting planes with advancing / rotation / flipping controls
animation script for making movies
interactive command line

AtomEye (c) Ju Li. http://mt.seas.upenn.edu/Archive/Graphics/A

Modifications to read XYZ and NetCDF files and Python interface (c) James Kermode 2008-2010 <[email protected]>

http://www.jrkermode.co.uk/AtomEye

beef/0

0.1.2-1

Library for DFT Bayesian error estimation ensemble XC functional with van der Waals correlation (BEEF–vdW), a semilocal approximation with an additional nonlocal correlation term.

http://prb.aps.org/abstract/PRB/v85/i23/e235149

https://confluence.slac.stanford.edu/display/SUNCAT/VASP

boost/1

gcc/1.47.0-1

Boost provides free peer-reviewed portable C++ source libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.

Boost libraries are intended to be suitable for eventual standardization. Ten Boost libraries are already included in the C++ Standards Committee's Library Technical Report (TR1) and will be in the new C++0x Standard now being finalized. C++0x will also include several more Boost libraries in addition to those from TR1. More Boost libraries are proposed for TR2.

To use Boost, supply in your Makefile:

CPPFLAGS += -I$BOOST_HOME LDFLAGS += -L$BOOST_HOME/lib -lboost_<component>

http://www.boost.org/

chargemol/2014

intel/2014-09-14-2

Implements the Density Derived Electrostatic and Chemical (DDEC) charge partitioning scheme - performs atomic population analysis to determine net atomic charges, atomic spin moments, and effective bond orders.

The program analyzes electron and spin density distributions generated by a quantum chemistry (e.g., DFT, coupled-cluster, etc.) calculation performed with a software such as VASP, Gaussian 09, CP2K, GPAW, SIESTA, etc.

DDEC net atomic charges are optimized to simultaneously reproduce atomic chemical states and the electrostatic potential surrounding a material, and thus are well-suited for constructing force-fields used in atomistic simulations (e.g., classical molecular dynamics or Monte Carlo simulations) and for quantifying electron transfer between atoms in complex materials and during chemical reactions.

NOTE: This Carbon version has been modified so that the job control tag <atomic densities directory complete path> is *optional*, with the default being $CHARGEMOL_HOME/lib/atomic_densities/.

License: open-source; citation required.

http://sourceforge.net/projects/ddec/files/

chargemol/2015

intel/2015-06-28-1

Implements the Density Derived Electrostatic and Chemical (DDEC) charge partitioning scheme - performs atomic population analysis to determine net atomic charges, atomic spin moments, and effective bond orders.

Because the DDEC net atomic charges are simultaneously optimized to reproduce atomic chemical states and the electrostatic potential surrounding a material, they are well-suited for constructing force-fields used in atomistic simulations (e.g., classical molecular dynamics or monte carlo simulations) and for quantifying electron transfer between atoms in complex materials and during chemical reactions.

The program analyzes electron and spin density distributions generated by a quantum chemistry (e.g., DFT, coupled-cluster, etc.) calculation performed with a software such as VASP, Gaussian 09, CP2K, GPAW, SIESTA, etc.

http://sourceforge.net/projects/ddec/files/

charm/6

openmpi-1.4/intel/6.4.0-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

http://charm.cs.uiuc.edu/

openmpi-1.4/intel/6.0-mpi-linux-x86_64-ifort-mpicxx-1, openmpi-1.4/intel/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

http://charm.cs.uiuc.edu/

openmpi-1.4/intel/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

http://charm.cs.uiuc.edu/

openmpi-1.4/intel/6.4.0-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

http://charm.cs.uiuc.edu/

comsol/4

4.1-1, 4.2-1, 4.2a-1, 4.3-1, 4.3a-1, 4.3b-1, 4.3b-2, 4.4-1, 4.4-2

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/

comsol/5

5.0-1, 5.1-1, 5.2-1, 5.2a-1, 5.3-1

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/

cp2k/2

openmpi-1.4/intel/2.2-4

CP2K performs atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. It provides a general framework for different methods such as e.g., density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) and classical pair and many-body potentials.

Warning: There is little documentation, no warranty, no official release. Using the code for production quality simulations is possible but requires detailed knowledge about the active development.

Freely available under the GPL.

http://www.cp2k.org/

cuda/4

4.2.9-1

The NVIDIA CUDA Toolkit provides a comprehensive development environment for C and C++ developers building GPU-accelerated applications. The CUDA Toolkit includes a compiler for NVIDIA GPUs, math libraries, and tools for debugging and optimizing the performance of your applications. You’ll also find programming guides, user manuals, API reference, and other documentation to help you get started quickly accelerating your application with GPUs.

http://developer.nvidia.com/cuda/cuda-toolkit

cuda/5

5.0-1

The NVIDIA CUDA Toolkit provides a comprehensive development environment for C and C++ developers building GPU-accelerated applications. The CUDA Toolkit includes a compiler for NVIDIA GPUs, math libraries, and tools for debugging and optimizing the performance of your applications. You’ll also find programming guides, user manuals, API reference, and other documentation to help you get started quickly accelerating your application with GPUs.

http://developer.nvidia.com/cuda/cuda-toolkit

cuda/7

7.0-1

The NVIDIA CUDA Toolkit provides a comprehensive development environment for C and C++ developers building GPU-accelerated applications. The CUDA Toolkit includes a compiler for NVIDIA GPUs, math libraries, and tools for debugging and optimizing the performance of your applications. You will also find programming guides, user manuals, API reference, and other documentation to help you get started quickly accelerating your application with GPUs.

http://developer.nvidia.com/cuda/cuda-toolkit

dacapo/2

openmpi-1.4/intel/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

ddscat/7

intel/7.2.2-3

Discrete Dipole Scattering (DDSCAT) calculates scattering and absorption of light by irregular particles and periodic arrangement of irregular particles.

scattering and absorption by isolated particles (e.g., dust grains, ice crystals).
scattering and absorption by periodic structures
very fast near field calculation
display scattering targets, their composition with support for 3D graphics
conversion code between DDSCAT shape file format and VTK format.
single and double precision options.

The binaries were compiled with Intel's MKL and OpenMP, but not MPI. Performance gains under OpenMP are modest.

License: GNU GPL v3

http://code.google.com/p/ddscat/

defaults/system

2/1.0

The default set of modules for use by the system, not affected by 'module purge'.

https://wiki.anl.gov/cnm/HPC/Module_Setup

defaults/user

2/2.3

Regular default set of modules for use by users.

https://wiki.anl.gov/cnm/HPC/Module_Setup

embody/1

1.0.5

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.

1.9.1, 1.9.2, 1.9.3, 1.9.4, 1.9.5, 1.9.6, 1.9.7, 1.9.8, 1.9.9

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.

embody/2

2.0.0

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.

2.0.1, 2.0.10, 2.0.11, 2.0.12, 2.0.13, 2.0.2, 2.0.3, 2.0.4, 2.0.5, 2.0.6, 2.0.7, 2.0.8, 2.0.9

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.

epics/3

gcc/3.15.0.1-1

The Experimental Physics and Industrial Control Systems (EPICS) is an extensible set of software components and tools with which application developers can create a control system. This control system can be used to control accelerators, detectors, telescopes, or other scientific experimental equipment. EPICS base is the set of core software, i.e. the components of EPICS without which EPICS would not function. EPICS base allows an arbitrary number of target systems, IOCs (input/output controllers), and host systems, OPIs (operator interfaces) of various types.

Distributed under ...

http://www.aps.anl.gov/epics/

fftw3/3.3

openmpi-1.10

impi-5/intel-16/3.3.4-10

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.

This version was built with MPI support, using impi/5

http://www.fftw.org/

intel/3.3.2-1, openmpi-1.4/intel/3.3.2-4

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/

openmpi-1.10/intel-16/3.3.4-11

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.

This version was built with MPI support, using openmpi/1.10/intel-16

http://www.fftw.org/

fox/4

intel/4.1.2-1

FoX is an XML library written in Fortran 95. It allows software developers to read, write and modify XML documents from Fortran applications without the complications of dealing with multi-language development.

FoX can be freely redistributed as part of open source and commercial software packages.

http://www1.gly.bris.ac.uk/~walker/FoX/

garffield/1

openmpi-1.4/intel/1.0-1

GARFfield is a multi-platform, multi-objective parallel hybrid genetic algorithm (GA) / conjugate-gradient (CG) based force field optimization framework. It enables first-principles based force fields prepared from large quantum mechanical data sets, which are now the norm in predictive molecular dynamics simulations for complex chemical processes, as well as from phenomenological data. The former allow improved accuracy and transferability over a wider range of molecular compositions, interactions and environmental conditions unexplored by experiments.

GARFfield currently supports a range of force field engines, via the LAMMPS Parallel Molecular Dynamics Simulator, including the adiabatic ReaxFF and COMB potentials for modeling reaction processes, the non-adiabatic eFF electron force field with effective core potentials, and Morse potentials (atomistic and coarse-grain).

http://www.wag.caltech.edu/home/ajaramil/GARFfield.html

gaussian/09

09.D.01.x86_64-3

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.

Documentation: http://www.gaussian.com/g_tech/g_ur/g09help.htm

http://gaussian.com/

gaussian/16

16-A.03-1, 16-A.03-2

Gaussian 16 is the latest in the Gaussian series of electronic structure programs. Gaussian 16 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.

Available only to Argonne employees and students, under confidentiality.

Documentation: http://gaussian.com/man/

gaussview/5

5.0.9-1

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.

To start: gview (NOT: gv)

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

gaussview/6

6.0.16-1

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.

To start: gview (NOT: gv)

http://gaussian.com/gaussview6/

http://gaussian.com/remote/

http://gaussian.com/wp-content/uploads/dl/gv6.pdf

gcc/4.4

4.4.7

WARNING: Unable to find ModulesHelp in /opt/apps/M/el6/gcc/4.4/4.4.7.

gcc/4.9

4.9.3-1

The GNU Compiler Collection.

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

gnuplot/4.6

4.6.6-1

Gnuplot is a multi-platform command-line driven graphing utility. It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986.

Gnuplot supports many different types of 2D and 3D plots and many types of output:

interactive screen display: cross-platform (Qt, wxWidgets, x11) or system-specific (MS Windows, OS/2)
direct output to file: postscript (including eps), pdf, png, gif, jpeg, LaTeX, metafont, emf, svg, ...
mouseable web display formats: HTML5, svg

http://gnuplot.info/

gnuplot/5.0

5.0.6-1

Gnuplot is a multi-platform command-line driven graphing utility. It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986.

Gnuplot supports many different types of 2D and 3D plots and many types of output:

interactive screen display: cross-platform (Qt, wxWidgets, x11) or system-specific (MS Windows, OS/2)
direct output to file: postscript (including eps), pdf, png, gif, jpeg, LaTeX, metafont, emf, svg, ...
mouseable web display formats: HTML5, svg

http://gnuplot.info/

gnuplot/5.2

5.2.rc1-1

Gnuplot is a multi-platform command-line driven graphing utility. It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986.

Gnuplot supports many different types of 2D and 3D plots and many types of output:

interactive screen display: cross-platform (Qt, wxWidgets, x11) or system-specific (MS Windows, OS/2)
direct output to file: postscript (including eps), pdf, png, gif, jpeg, LaTeX, metafont, emf, svg, ...
mouseable web display formats: HTML5, svg

http://gnuplot.info/

gold/2

2.2.0.5-6-EL6

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

intel/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

gcc/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

gcc/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

intel/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-setups/0

0.8.7929

Pseudopotential data for GPAW (see module gpaw).

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

gpaw/0

openmpi-1.4/intel/0.9.0-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/

gsl/1

1.16-1

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.

The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.

Unlike the licenses of proprietary numerical libraries the license of GSL does not restrict scientific cooperation. It allows you to share your programs freely with others.

Free software under the GNU General Public License.

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

h5utils/1

gcc/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

intel/1.3.1-mkl-4, intel/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

openmpi-1.4

intel/1.8.13-intel11-serial, openmpi-1.4/intel/1.8.13-intel11-parallel

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.

This version was build for Intel version 11 compilers.

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

intel/1.8.13-intel12-serial, openmpi-1.4/intel/1.8.13-intel12-parallel

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.

This version was build for Intel version 12 compilers.

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

hoomd/0

gcc/0.11.3

HOOMD performs general purpose particle dynamics simulations on a single workstation with NVIDIA GPUs. Various types of potentials, integration methods and file formats are supported. Simulations are configured and run using python scripts, allowing complete control over the force field choice, integrator, all parameters, how many time steps are run, etc. The scripting system is designed to be as simple as possible to the non-programmer.

The code is open source, with a literature citation required in any work that uses HOOMD-blue.

http://codeblue.umich.edu/hoomd-blue/

hydra/3

gcc/3.1.2-2

Hydra is a process management system for starting parallel jobs. Hydra is designed to natively work with existing launcher daemons (such as ssh, rsh, fork), as well as natively integrate with resource management systems (such as slurm, pbs, sge).

More information about using Hydra can be found here:

http://wiki.mpich.org/mpich/index.php/Using_the_Hydra_Process_Manager

idl/8

8.2.2-1

IDL is a cross-platform scientific programming language to extract visualizations from complex numerical data. IDL interprets data and the IDL Development Environment may be used to build applications.

http://www.exelisvis.com/ProductsServices/IDL.aspx

impi/2017

2017.Build.20160721, 2017.Update.2, 2017.Update.3, 2017.Update.4

The Intel MPI implementation for the Intel64 architecture

https://software.intel.com/en-us/intel-mpi-library-support/documentation

https://software.intel.com/en-us/articles/intel-mpi-library-51-release-notes

https://software.intel.com/en-us/get-started-with-mpi-for-linux

impi/4

4.1.3

The Intel MPI implementation for the Intel64 architecture

impi/5

5.0.3, 5.1.1

The Intel MPI implementation for the Intel64 architecture

5.1.1-3, 5.1.2-2, 5.1.3

The Intel MPI implementation for the Intel64 architecture

https://software.intel.com/en-us/intel-mpi-library-support/documentation

https://software.intel.com/en-us/articles/intel-mpi-library-51-release-notes

https://software.intel.com/en-us/get-started-with-mpi-for-linux

intel/12

12.1.6

Intel compilers and MKL for the Intel64 architecture

intel/13

13.1.3

Intel compilers and MKL for the Intel64 architecture

intel/14

14.0.4

Intel compilers and MKL for the Intel64 architecture

intel/15

15.0.2, 15.0.3, 15.0.4

Intel compilers and MKL for the Intel64 architecture

intel/16

16.0.0-0, 16.0.0-1

Intel compilers and MKL for the Intel64 architecture

16.0.0-3, 16.0.1-2, 16.0.2, 16.0.3

Intel compilers and MKL for the Intel64 architecture

https://software.intel.com/en-us/intel-parallel-studio-xe-support/documentation

https://software.intel.com/en-us/articles/intel-parallel-studio-xe-2016-update-1-readme

intel/17

17.0.0, 17.0.3, 17.0.4, 17.0.5

Intel compilers and MKL for the Intel64 architecture

https://software.intel.com/en-us/intel-parallel-studio-xe-support/documentation

https://software.intel.com/en-us/articles/intel-parallel-studio-xe-2017

java/1.7

1.7.0_25-fcs

The Java Platform Standard Edition Runtime Environment (JRE) contains everything necessary to run applets and applications designed for the Java platform. This includes the Java virtual machine, plus the Java platform classes and supporting files.

The JRE is freely redistributable, per the terms of the included license.

http://www.java.com/en/download/manual.jsp

jdftx/0

gcc-4.9/0.99-svn1205-1

JDFTx is a plane-wave density functional code designed for Joint Density Functional Theory (JDFT), a framework for ab initio calculations of electronic systems in contact with liquid environments. It evolved from an earlier in-house research code in the Arias research group at Cornell called DFT++,

Unlike most other electronic structure codes, JDFTx performs total energy minimization using analytically continued energy functionals implemented within an algebraic formulation, rather than density-mixing SCF schemes. JDFTx also incorporates advanced algorithms for converging metallic systems with finite temperature Fermi function fillings, critical for the study of electrochemical systems.

Distributed under the GPL license (version 3 or higher); publications must include several literature citations. For any given calculation, JDFTx prints out a list of relevant citations for optional features of the code used in that run.

http://sourceforge.net/p/jdftx/wiki/Home/

gcc-4.9/0.99-svn1205-2

JDFTx is a plane-wave density functional code designed for Joint Density Functional Theory (JDFT), a framework for ab initio calculations of electronic systems in contact with liquid environments. It evolved from an earlier in-house research code in the Arias research group at Cornell called DFT++.

JDFTx performs total energy minimization using analytically continued energy functionals implemented within an algebraic formulation rather than density-mixing SCF schemes, and incorporates advanced algorithms for converging metallic systems with finite temperature Fermi occupation at a fixed chemical potential, critical for the study of electrochemical systems.

JDFTx supports norm-conserving and ultrasoft pseudopotentials with LDA/GGA/hybrid functionals, DFT+U, spin-orbit coupling, and non-collinear magnetism. Modules for phonon calculation, wannier functions, and ab initio molecular dynamics are included.

Distributed under the GPL license (version 3 or higher); publications must include several literature citations. The output of each run will include a list of citations corresponding to optional features used.

http://sourceforge.net/p/jdftx/wiki/Home/

jmol/13

13.2.8-1

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/2012

openmpi-1.4/intel/2012-02-12-parallel-jr-11

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 mc meam molecule poems reax replica user-atc user-misc user-reaxc user-omp

LAMMPS is open source, distributed by Sandia National Laboratories.

http://lammps.sandia.gov/

http://lammps.sandia.gov/doc/Manual.html

lammps/2015

openmpi-1.10

openmpi-1.10/intel-16/2015-05-15-4, openmpi-1.4/intel/2015-05-15-3

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 the following packages: body, class2, colloid, dipole, kspace, manybody, mc, meam, misc, molecule, poems, qeq, reax, replica, rigid, user-atc, user-misc, user-omp, user-phonon, user-reaxc, voronoi.

LAMMPS is open source, distributed by Sandia National Laboratories.

http://lammps.sandia.gov/

http://lammps.sandia.gov/doc/Manual.html

openmpi-1.4/intel/2015-05-15-1, openmpi-1.4/intel/2015-05-15-2

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 the following packages: body, class2, colloid, kspace, manybody, mc, meam, misc, molecule, poems, qeq, reax, replica, user-atc, user-misc, user-omp, user-phonon, user-reaxc, voronoi.

LAMMPS is open source, distributed by Sandia National Laboratories.

http://lammps.sandia.gov/

http://lammps.sandia.gov/doc/Manual.html

layout-beamer/3

3.3.0beta2_64

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

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

libctl/3

intel/3.0.3-5

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

libctl/3.2

intel-17/3.2.2-2

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

libint/1

intel/1.1.4-1

A library of C/C++ functions for efficient evaluation of several kinds of two-body molecular integrals over Gaussian functions.

http://libint.valeyev.net/

libint2/2.0

intel/2.0.5-3

A library of C/C++ functions for efficient evaluation of several kinds of two-body molecular integrals over Gaussian functions.

The libint compiler for this build was configured with options:

--enable-eri=0 --with-max-am=7 --enable-contracted-ints

https://github.com/evaleev/libint/wiki

intel/2.0.0-2

A library of C/C++ functions for efficient evaluation of several kinds of two-body molecular integrals over Gaussian functions.

http://libint.valeyev.net/

intel/2.0.5-1

A library of C/C++ functions for efficient evaluation of several kinds of two-body molecular integrals over Gaussian functions.

This library was generated with options:

--enable-eri=0 --with-max-am=7

http://libint.valeyev.net/

libmatheval/1

gcc/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/

libxc/1

intel/1.1.0-1

Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals that can be used by all the ETSF codes and also other codes. In libxc you can find different types of functionals: LDA, GGA, hybrids, mGGA (experimental) and LCA (not working). This functionals depend on local information, in the sense that the value of the potential at a given point depends only on the values of the density - and the gradient of the density and the kinetic energy density, for the GGA and mGGA cases, or the vorticity for LCA - at a given point.

It can calculate the functional itself and its derivative, for some functionals higher order derivatives are available. Libxc is written in C and has Fortran bindings. It is released under the LGPL license (v. 3.0). Contributions are welcome.

http://www.tddft.org/programs/octopus/wiki/index.php/Libxc

libxc/2

gcc-4.9/2.2.2-2, gcc-4.9/2.2.2-3, intel-15/2.2.2-2, intel-15/2.2.2-3, intel-16/2.2.2-3

Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals that can be used by all the ETSF codes and also other codes. In libxc you can find different types of functionals: LDA, GGA, hybrids, mGGA (experimental) and LCA (not working). This functionals depend on local information, in the sense that the value of the potential at a given point depends only on the values of the density - and the gradient of the density and the kinetic energy density, for the GGA and mGGA cases, or the vorticity for LCA - at a given point.

It can calculate the functional itself and its derivative, for some functionals higher order derivatives are available. Libxc is written in C and has Fortran bindings. It is released under the LGPL license (v. 3.0). Contributions are welcome.

http://www.tddft.org/programs/octopus/wiki/index.php/Libxc

lumerical-DEVICE/6

6.0.1255-1

Lumerical DEVICE is an advanced, finite element multiphysics simulation environment for:

Semiconductor devices
Electro-optic modulators
Photovoltaic devices
Active metamaterials
Thermal tuning/switching
Plasmonic heating

Solvers Available:

DEVICE CT: Integrated design environment, charge transport solver
DEVICE HT: Integrated design environment, heat transfer solver

https://www.lumerical.com/tcad-products/device/

https://kb.lumerical.com/en/index.html?getting_started.html

lumerical-FDTD/8

8.18.1365-1

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

https://kb.lumerical.com/en/index.html?getting_started.html

lumerical-INTERCONNECT/7

7.0.1365-1

Lumerical INTERCONNECT is a photonic integrated circuit design and analysis environment in time or frequency domains. It supports:

Optical Transceiver
Advanced Modulation Analysis
WDM Circuits
Fiber modelling
EDFA modelling
Switch design
Laser modelling
Electronic/Photonic design automation
Compact model libraries for PDKs
Yield Analysis

https://www.lumerical.com/tcad-products/interconnect/

https://kb.lumerical.com/en/index.html?getting_started.html

lumerical-MODE/7

7.10.1365-1

Lumerical MODE is a comprehensive optical waveguide design environment for applications in:

Integrated Optics
Tapers
Couplers and Resonators
Bragg Gratings
Thermal tuning / switching
Electro-optic modulators
Surface plasmon waveguides
Graphene waveguides
Fibers
Transmission Lines

https://www.lumerical.com/tcad-products/mode/

https://kb.lumerical.com/en/index.html?getting_started.html

lumerical/7

7.5.7-1

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

lumerical/8

8.11.422-1, 8.15.736-1, 8.16.931-1, 8.16.931-1a

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/10

10.1.0-1

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

Start the kernel (text UI): math Start the GUI frontend: mathematica

http://www.wolfram.com/

matlab/R2013a

R2013a-8

MATLAB is a high-level language and interactive environment for numerical computation, visualization, and programming. You can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java.

To run the GUI remotely, VNC is recommended instead of X11.

This is a network-concurrent license, and includes the Compiler (for login5 only), for use by Argonne employees only.

http://www.mathworks.com/

R2013a-5

MATLAB is a high-level language and interactive environment for numerical computation, visualization, and programming. You can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java.

To run the GUI remotely, VNC is recommended instead of X11.

Licensed to run on login5, by Argonne employees only.

http://www.mathworks.com/

meep/1

openmpi-1.4

intel/1.1.1-serial-1, openmpi-1.4/intel/1.1.1-parallel-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

openmpi-1.4/intel/1.3-parallel-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/wiki/index.php/Meep

mesa-gl/6

6.5.2-1

Provide alternative versions of libGL.so and libGLU.so, needed in certain sitations for running graphical applications remotely over X11 or VNC, e.g. Lumerical FDTD, DEVICE, and MODE.

https://kb.lumerical.com/en/installation_and_setup_update-mesa-graphics-driver.html

mesa-gl/7

7.2-1

Provide alternative versions of libGL.so and libGLU.so, needed in certain sitations for running graphical applications remotely over X11 or VNC.

moab/6

6.1.12-1

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.adaptivecomputing.com/products/moab-hpc-suite-basic.php

molpro/2009

openmpi-1.4/intel/2009.1-1, openmpi-1.4/intel/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/

molpro/2012

2012.1.29-4, 2012.1.29-6, 2012.1.29-7, 2012.1.29-8

Molpro is a system of ab initio programs for molecular electronic structure calculations, designed and maintained by H.-J. Werner and P. J. Knowles, and containing contributions from a number of other authors. 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. The recently developed explicitly correlated coupled-cluster methods yield CCSD(T) results with near basis set limit accuracy already with double-zeta or triple-zeta basis sets, thus reducing the computational effort for calculations of this quality by two orders of magnitude. Using local electron correlation methods, which significantly reduce the increase of the computational cost with molecular size, accurate ab initio calculations can be performed for much larger molecules than with most other programs.

http://www.molpro.net/

mpb/1

1.5-4

MPB is a free software package for computing the band structures, or dispersion relations, and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers. MPB is an acronym for MIT Photonic Bands. MPB computes definite-frequency eigenstates, or harmonic modes, of Maxwell's equations in periodic dielectric structures for arbitrary wavevectors, using fully-vectorial and three-dimensional methods. It is applicable to many problems in optics, such as waveguides and resonator systems, and photonic crystals. For example, it can solve for the modes of waveguides with arbitrary cross-sections.

See also our complementary Meep package for time-domain simulations, reflection/transmission spectra, etc.

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

http://ab-initio.mit.edu/mpb/

mpich/3

gcc/3.1.2-2

MPICH is a high-performance and widely portable implementation of the MPI-3.0 standard from the Argonne National Laboratory. This release has all MPI 3.0 functions and features required by the standard with the exception of support for the 'external32' portable I/O format and user-defined data representations for I/O.

The MPICH web site http://www.mpich.org/ contains information on bug fixes and new releases.

namd/2

openmpi-1.4/intel/2.9-MPI-icc-4, openmpi-1.4/intel/2.9plus-MPI-icc-3

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

intel/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/

gcc/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/

nlopt/2

gcc/2.4.1-1

NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. Its features include:

Callable from C, C++, Fortran, Matlab or GNU Octave, Python, GNU Guile, Julia, GNU R, Lua, and OCaml.
A common interface for many different algorithms—try a different algorithm just by changing one parameter.
Support for large-scale optimization (some algorithms scalable to millions of parameters and thousands of constraints).
Both global and local optimization algorithms.
Algorithms using function values only (derivative-free) and also algorithms exploiting user-supplied gradients.
Algorithms for unconstrained optimization, bound-constrained optimization, and general nonlinear inequality/equality constraints.

Free/open-source software under the GNU LGPL (and looser licenses for some portions of NLopt).

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

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

numpy/1

intel/1.6.1-5

NumPy is a fundamental package for scientific computing in Python. It is a Python library that provides a multidimensional array object, various derived objects (such as masked arrays and matrices), and an assortment of routines for fast operations on arrays, including mathematical, logical, shape manipulation, sorting, selecting, I/O, discrete Fourier transforms, basic linear algebra, basic statistical operations, random simulation and much more.

NumPy also contains tools for integrating C/C++ and Fortran code.

Besides numeric applications, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to interface with databases.

Numpy is licensed under the BSD license, enabling reuse with few restrictions.

http://numpy.org/

nwchem/6

openmpi-1.4/intel/6.5-1

NWChem provides computational chemistry tools scalable to large problems and parallel computing. It can handle:

Biomolecules, nanostructures, and solid-state
From quantum to classical, and all combinations
Gaussian basis functions or plane-waves
Scaling from one to thousands of processors
Properties and relativity

NWChem is developed and maintained by EMSL at Pacific Northwest National Laboratory (PNNL).

Distributed as open-source under the terms of the Educational Community License version 2.0 (ECL 2.0).

Please cite the following reference when publishing results obtained with NWChem:

M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha, E. Apra, T.L. Windus, W.A. de Jong, 'NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations' Comput. Phys. Commun. 181, 1477 (2010)

http://www.nwchem-sw.org/

octave/4.0

4.0.3-1

GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable.

Octave is distributed under the terms of the GNU General Public License.

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

octopus/4

openmpi-1.4/intel/4.0.1-8

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 contains both the serial and parallel executables.

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/1.10

gcc-4.4/1.10.0-4, gcc-4.4/1.10.1-1, gcc-4.4/1.10.1-2, gcc/1.10.0-4, gcc/1.10.1-1, gcc/1.10.1-2

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 gcc-4.4 compilers for mpicc, mpif90, etc.

This version supports the TORQUE TM API and CUDA (on GPU machines).

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

https://www.open-mpi.org/faq/?category=runcuda

gcc-4.4/1.10.2-1, gcc-4.4/1.10.3-1, gcc-4.4/1.10.7-2, gcc-4.4/1.10.7-3, gcc-4.9/1.10.2-1, gcc-4.9/1.10.3-1, gcc-4.9/1.10.7-2, gcc-4.9/1.10.7-3, gcc/1.10.2-1, intel-15/1.10.2-1, intel-15/1.10.3-1, intel-16/1.10.2-1, intel-16/1.10.3-1, intel-17/1.10.7-2, intel-17/1.10.7-3, intel/1.10.2-1

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 compilers for mpicc, mpif90, etc.

This version supports the TORQUE TM API and CUDA (on GPU machines).

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

https://www.open-mpi.org/faq/?category=runcuda

gcc-4.9/1.10.0-4, gcc-4.9/1.10.1-1, gcc-4.9/1.10.1-2

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 gcc-4.9 compilers for mpicc, mpif90, etc.

This version supports the TORQUE TM API and CUDA (on GPU machines).

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

https://www.open-mpi.org/faq/?category=runcuda

intel-15/1.10.0-4, intel-15/1.10.1-1, intel-15/1.10.1-2, intel/1.10.0-4, intel/1.10.1-1, intel/1.10.1-2

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-15 compilers for mpicc, mpif90, etc.

This version supports the TORQUE TM API and CUDA (on GPU machines).

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

https://www.open-mpi.org/faq/?category=runcuda

intel-16/1.10.0-4, intel-16/1.10.1-1, intel-16/1.10.1-2

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-16 compilers for mpicc, mpif90, etc.

This version supports the TORQUE TM API and CUDA (on GPU machines).

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

https://www.open-mpi.org/faq/?category=runcuda

openmpi/1.4

intel/1.4.5-intel12-2

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/12 ifort/12 compilers for mpicc, mpif90, etc.

This version supports the TORQUE TM API.

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

gcc/1.4.5-gcc-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 GNU compilers for mpicc, mpif90, etc.

This version supports the TORQUE TM API.

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

intel/1.4.5-intel11-1, intel/1.4.5-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 ifort/11 compilers for mpicc, mpif90, etc.

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

intel/1.4.5-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/

openmpi/1.6

intel/1.6.5-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.

This version supports the TORQUE TM API.

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

gcc/1.6.5-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.

This version supports the TORQUE TM API.

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

intel/1.6.5-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.

This version supports the TORQUE TM API.

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

openmpi/1.8

gcc-4.4/1.8.8-7, gcc/1.8.8-7

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 gcc compilers for mpicc, mpif90, etc.

This version supports the TORQUE TM API and CUDA (on GPU machines).

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

https://www.open-mpi.org/faq/?category=runcuda

intel-15/1.8.8-7, intel/1.8.8-7

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/15 compilers for mpicc, mpif90, etc.

This version supports the TORQUE TM API and CUDA (on GPU machines).

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

https://www.open-mpi.org/faq/?category=runcuda

intel-16/1.8.8-7

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-16 compilers for mpicc, mpif90, etc.

This version supports the TORQUE TM API and CUDA (on GPU machines).

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

https://www.open-mpi.org/faq/?category=runcuda

packmol/13

intel/13.243-1

Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.

The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.

The user must provide only the coordinates of one molecule of each type, the number of molecules of each type and the spatial constraints that each type of molecule must satisfy.

The package is compatible with input files of PDB, TINKER, XYZ and MOLDY formats.

http://www.ime.unicamp.br/~martinez/packmol/

periodic_NBO/2012

intel/2012-11-14-1

This is a Natural Bond Orbital algorithm, generalized to handle periodic systems. While the code only requires information that can be obtained from the output of any periodic electronic structure calculation, it requires specifically formatted input files. An interface for VASP-4 is available, with binaries named *nbo.

The code is freely available, its use requires citation of the paper: Dunnington, B. D.; Schmidt, J. R. J. Chem. Theory Comput., 2012, 8, 1902–1911.

http://schmidt.chem.wisc.edu/nbosoftware

phonopy/1.10

1.10.8-1

Phonopy is a phonon analyzer based on the supercell approach and using:

force constants from forces on atoms with finite displacements (Parlinski-Li-Kawazoe method)
non-analytical-term correction (LO-TO splitting)

Selected features:

Phonon dispersion relation (band structure)
Phonon DOS and partial-DOS
Phonon thermal properties, free energy, heat capacity, and entropy
Thermal expansion and heat capacity at constant pressure within quasi-harmonic approximation (phonopy-qha)

Provides built-in interfaces for: VASP, VASP DFPT, Wien2k, FHI-aims; extensible for the other calculators via formatted files or a Python module.

License: LGPL after ver. 0.9.3 and GPL before 0.9.2.

http://phonopy.sourceforge.net/

povray/3

gcc/3.7.0.RC3-1, gcc/3.7.0.RC3-2

POVRay - The Persistence of Vision Ray-Tracer creates three-dimensional, photo-realistic images using a rendering technique called ray-tracing. It reads in a text file containing information describing the objects and lighting in a scene and generates an image of that scene from the view point of a camera also described in the text file. Ray-tracing is not a fast process by any means, but it produces very high quality images with realistic reflections, shading, perspective and other effects.

Renderings of the scene samples and the include portfolio are located in $POVRAY_HOME/share/rendered/.

Requires: module load boost

http://www.povray.org/

profile/system

2/1.0

The default set of modules for use by the system, not affected by 'module purge'.

https://wiki.anl.gov/cnm/HPC/Module_Setup

profile/user

2/2.3

Regular default set of modules for use by users.

https://wiki.anl.gov/cnm/HPC/Module_Setup

pwgui/4

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/

python-anaconda/2.7

4/2.7.11-4.0.0-2

Anaconda is a Python-based open data science analytics platform. The platform can be used for ad hoc and production deployments, for batch and interactive to real-time use. Anaconda is tuned for modern computing environments.

https://www.continuum.io/why-anaconda

python-anaconda/3.5

4/3.5.1-4.0.0-2

Anaconda is a Python-based open data science analytics platform. The platform can be used for ad hoc and production deployments, for batch and interactive to real-time use. Anaconda is tuned for modern computing environments.

https://www.continuum.io/why-anaconda

python-centos/2.6

gcc-4.4/2.6.6

WARNING: Unable to find ModulesHelp in /opt/apps/M/el6/python-centos/2.6/gcc-4.4/2.6.6.

python-env-anaconda/2.7

4/2.7.11-09

Python environment within the Anaconda suite, with selected native and external packages added:

numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 ase netCDF4 deap inspyred

python-env-anaconda/3.5

4/3.5.1-09

Python environment within the Anaconda suite, with selected native and external packages added:

numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 ase netCDF4 deap inspyred

python-env-intel/2.7

2017/2.7-001

Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.

The following selected native and external packages were added:

numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 ase netCDF4 deap inspyred

See 'conda list' for all packages installed.

https://software.intel.com/en-us/python-distribution

2017/2.7-004

Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.

The following selected native and external packages were added:

numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 intelpython ase netCDF4 deap inspyred

See 'conda list' for all packages installed.

https://software.intel.com/en-us/python-distribution

https://software.intel.com/en-us/articles/intel-distribution-for-python-support-and-documentation

https://software.intel.com/en-us/forums/intel-distribution-for-python

2017/2.7-01, 2018/2.7-01

Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.

The following selected native and external packages were added:

numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 intelpython ase netCDF4 deap inspyred pytest See 'conda list' for all packages installed.

https://software.intel.com/en-us/python-distribution

https://software.intel.com/en-us/articles/intel-distribution-for-python-support-and-documentation

https://software.intel.com/en-us/forums/intel-distribution-for-python

python-env-intel/3.5

2017/3.5-01

Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.

The following selected native and external packages were added:

numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 intelpython ase netCDF4 deap inspyred pytest See 'conda list' for all packages installed.

https://software.intel.com/en-us/python-distribution

https://software.intel.com/en-us/articles/intel-distribution-for-python-support-and-documentation

https://software.intel.com/en-us/forums/intel-distribution-for-python

2017/3.5-001

Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.

The following selected native and external packages were added:

numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 ase netCDF4 deap inspyred

See 'conda list' for all packages installed.

https://software.intel.com/en-us/python-distribution

2017/3.5-004

Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.

The following selected native and external packages were added:

numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 intelpython ase netCDF4 deap inspyred

See 'conda list' for all packages installed.

https://software.intel.com/en-us/python-distribution

https://software.intel.com/en-us/articles/intel-distribution-for-python-support-and-documentation

https://software.intel.com/en-us/forums/intel-distribution-for-python

python-env-intel/3.6

2018/3.6-01

Customized Python conda environment for Carbon of the Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.

The following selected native and external packages were added:

numpy numexpr scipy matplotlib ipython mkl mkl-service cython pandas mpi4py hdf5 intelpython ase netCDF4 deap inspyred pytest See 'conda list' for all packages installed.

https://software.intel.com/en-us/python-distribution

https://software.intel.com/en-us/articles/intel-distribution-for-python-support-and-documentation

https://software.intel.com/en-us/forums/intel-distribution-for-python

python-intel/2.7

2015/2.7.20150803_184913, 2017/2.7.12

Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.

The following popular packages are included:

cpython cython dateutil ipython jinja2 jsonschema markupsafe matplotlib mistune mock mpmath nose numexpr numpy pandas pip pygments-main pytz pyzmq scipy setuptools six sympy tempita tornado

https://software.intel.com/en-us/python-distribution

2017/2.7.13-2017.3.053-1, 2018/2.7.14-2018.1.023-1

The Intel Distribution for Python ships with many specialized packages that offer accelerated workflows and advanced functionality.

Numerical and Scientific

NumPy - The most popular numerical library for Python, accelerated with the Intel MKL
SciPy - The de-facto standard for a scientific toolset in the Python language, accelerated with the Intel MKL
numba - A Just-In-Time Compiler for decorated Python code that allows latest SIMD features and multi-core execution in order to fully utilize modern CPUs
numexpr - A Python interface to symbolic and algebraic acceleration, via the Intel MKL

Data Analytics

Scikit-learn – A popular machine learning Python package, now accelerated with Intel's highest performance libraries.
* Pre-built and accelerated with Intel MKL, Intel DAAL, and Intel Thread Building Blocks through direct source code changes to the package
pyDAAL - A package for Python bindings to the Intel Data Analytics Acceleration Library
* Delivers a Python-interfaced solution for many of the steps in a data analytics pipeline, such as pre-processing, data transformations, dimensionality reduction, data modeling, prediction, and several drivers for reading and writing in most of the common data formats.
* Supports many computation modes, including Batch, Distributed, and Online modes for many of the support algorithms
daal4py (Tech Preview) – A high-level API to the Intel DAAL Library
* A package providing a higher-level abstraction to the Intel DAAL Library, made to cater to the needs of Data Scientists and the rapid pace of production seen in the analytics space

https://software.intel.com/en-us/distribution-for-python

https://software.intel.com/en-us/distribution-for-python/get-started

https://software.intel.com/en-us/distribution-for-python/get-help

python-intel/3.5

2017/3.5.3-2017.3.052-1

The Intel Distribution for Python ships with many specialized packages that offer accelerated workflows and advanced functionality.

Numerical and Scientific

NumPy - The most popular numerical library for Python, accelerated with the Intel MKL
SciPy - The de-facto standard for a scientific toolset in the Python language, accelerated with the Intel MKL
numba - A Just-In-Time Compiler for decorated Python code that allows latest SIMD features and multi-core execution in order to fully utilize modern CPUs
numexpr - A Python interface to symbolic and algebraic acceleration, via the Intel MKL

Data Analytics

Scikit-learn – A popular machine learning Python package, now accelerated with Intel's highest performance libraries.
* Pre-built and accelerated with Intel MKL, Intel DAAL, and Intel Thread Building Blocks through direct source code changes to the package
pyDAAL - A package for Python bindings to the Intel Data Analytics Acceleration Library
* Delivers a Python-interfaced solution for many of the steps in a data analytics pipeline, such as pre-processing, data transformations, dimensionality reduction, data modeling, prediction, and several drivers for reading and writing in most of the common data formats.
* Supports many computation modes, including Batch, Distributed, and Online modes for many of the support algorithms
daal4py (Tech Preview) – A high-level API to the Intel DAAL Library
* A package providing a higher-level abstraction to the Intel DAAL Library, made to cater to the needs of Data Scientists and the rapid pace of production seen in the analytics space

https://software.intel.com/en-us/distribution-for-python

https://software.intel.com/en-us/distribution-for-python/get-started

https://software.intel.com/en-us/distribution-for-python/get-help

2015/3.5.20150803_185146, 2017/3.5.2

Intel Python distribution, including NumPy & SciPy packages used in numerical and scientific computing and data analysis. The distribution leverages Intel MKL for improved performance.

The following popular packages are included:

cpython cython dateutil ipython jinja2 jsonschema markupsafe matplotlib mistune mock mpmath nose numexpr numpy pandas pip pygments-main pytz pyzmq scipy setuptools six sympy tempita tornado

https://software.intel.com/en-us/python-distribution

python-intel/3.6

2018/3.6.3-2018.1.023-1

The Intel Distribution for Python ships with many specialized packages that offer accelerated workflows and advanced functionality.

Numerical and Scientific

NumPy - The most popular numerical library for Python, accelerated with the Intel MKL
SciPy - The de-facto standard for a scientific toolset in the Python language, accelerated with the Intel MKL
numba - A Just-In-Time Compiler for decorated Python code that allows latest SIMD features and multi-core execution in order to fully utilize modern CPUs
numexpr - A Python interface to symbolic and algebraic acceleration, via the Intel MKL

Data Analytics

Scikit-learn – A popular machine learning Python package, now accelerated with Intel's highest performance libraries.
* Pre-built and accelerated with Intel MKL, Intel DAAL, and Intel Thread Building Blocks through direct source code changes to the package
pyDAAL - A package for Python bindings to the Intel Data Analytics Acceleration Library
* Delivers a Python-interfaced solution for many of the steps in a data analytics pipeline, such as pre-processing, data transformations, dimensionality reduction, data modeling, prediction, and several drivers for reading and writing in most of the common data formats.
* Supports many computation modes, including Batch, Distributed, and Online modes for many of the support algorithms
daal4py (Tech Preview) – A high-level API to the Intel DAAL Library
* A package providing a higher-level abstraction to the Intel DAAL Library, made to cater to the needs of Data Scientists and the rapid pace of production seen in the analytics space

https://software.intel.com/en-us/distribution-for-python

https://software.intel.com/en-us/distribution-for-python/get-started

https://software.intel.com/en-us/distribution-for-python/get-help

python/2.7

gcc-4.1/2.7.3-1, gcc-4.4/2.7.11-1

Python is an interpreted, interactive, object-oriented programming language often compared to Tcl, Perl, Scheme or Java. Python includes modules, classes, exceptions, very high level dynamic data types and dynamic typing. Python supports interfaces to many system calls and libraries, as well as to various windowing systems (X11, Motif, Tk, Mac and MFC).

Programmers can write new built-in modules for Python in C or C++. Python can be used as an extension language for applications that need a programmable interface. This package contains most of the standard Python modules, as well as modules for interfacing to the Tix widget set for Tk and RPM.

http://www.python.org/

python/3.5

gcc-4.4/3.5.1-1

Python is an interpreted, interactive, object-oriented programming language often compared to Tcl, Perl, Scheme or Java. Python includes modules, classes, exceptions, very high level dynamic data types and dynamic typing. Python supports interfaces to many system calls and libraries, as well as to various windowing systems (X11, Motif, Tk, Mac and MFC).

Programmers can write new built-in modules for Python in C or C++. Python can be used as an extension language for applications that need a programmable interface. This package contains most of the standard Python modules, as well as modules for interfacing to the Tix widget set for Tk and RPM.

http://www.python.org/

q-chem/4.1

4.1.0.1-1

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, and quantum calculations extended with QM/MM and molecular dynamics.

Documentation: http://www.q-chem.com/qchem-website/technical-info4.html

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

quantum-espresso/4

openmpi-1.4/intel/4.3.2-2

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/

quantum-espresso/5.4

openmpi-1.10/intel-16/5.4.0-1

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.

rasmol/2.6

2.6.4-foc-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/

rasmol/2.7

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/

readline/6

6.2-1

The Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.

The history facilites are also placed into a separate library, the History library, as part of the build process. The History library may be used without Readline in applications which desire its capabilities.

Distributed under the terms of the (GNU) General Public License, v3.

http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html

rings/1

openmpi-1.4/intel/1.2.3-1

The R.I.N.G.S. code (Rigorous Investigation of Networks Generated using Simulations) analyzes the results of molecular dynamics simulations. Its main feature connectivity analysis using ring statistics.

Installed in $RINGS_HOME .

http://rings-code.sourceforge.net/

ScientificPython/2

intel/2.8-1

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/

scipy/0

openmpi-1.4/gcc/0.9.0-1, openmpi-1.4/intel/0.10.0-1

SciPy (pronounced 'Sigh Pie') is a library for mathematics, science, and engineering, named after a popular conference on scientific programming with Python

SciPy depends on NumPy, which provides convenient and fast N-dimensional array manipulation. SciPy works with NumPy arrays, and provides user-friendly and efficient numerical routines e.g. for integration and optimization.

Open-Source, free of charge.

http://www.scipy.org/

siesta/3

openmpi-1.4/intel/3.2-1

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.

This version has been compiled without NetCDF support.

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

siesta/4.0

impi-5/intel-16/4.0-1

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.

This version has been compiled without NetCDF support.

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

siesta/4.1

impi-5/intel-16/4.1-b2-1, impi-5/intel-16/4.1-b2-2

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.

This version has been compiled without NetCDF support.

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

siesta/4.1-b2

impi-5/intel-16/4.1-b2-1, impi-5/intel-16/4.1-b2-2

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.

This version has been compiled without NetCDF support.

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

spglib/1

gcc/1.6.4

Spglib is a C library for finding and handling crystal symmetries with these features:

Find symmetry operations
Identify space-group type
Wyckoff position assignment
Refine crystal structure
Search irreducible k-points
Find a primitive cell

http://spglib.sourceforge.net

stress-ng/0

0.08.18-1

stress-ng will stress test a computer system in various selectable ways. It was designed to exercise various physical subsystems of a computer as well as the various operating system kernel interfaces. Stress-ng features:

Over 180 stress tests
70 CPU specific stress tests that exercise floating point, integer, bit manipulation and control flow
Over 20 virtual memory stress tests

stress-ng was originally intended to make a machine work hard and trip hardware issues such as thermal overruns as well as operating system bugs that only occur when a system is being thrashed hard. Use stress-ng with caution as some of the tests can make a system run hot on poorly designed hardware and also can cause excessive system thrashing which may be difficult to stop.

stress-ng can also measure test throughput rates; this can be useful to observe performance changes across different operating system releases or types of hardware. However, it has never been intended to be used as a precise benchmark test suite, so do NOT use it in this manner.

http://kernel.ubuntu.com/~cking/stress-ng/

stress/1

1.0.4-1

stress is a deliberately simple workload generator for POSIX systems. It imposes a configurable amount of CPU, memory, I/O, and disk stress on the system.

stress is a tool designed to put given subsytems under a specified load. Instances in which this is useful include those in which a system administrator wishes to perform tuning activities, a kernel or libc programmer wishes to evaluate denial of service possibilities, etc.

It is free software licensed under the GPLv2.

vasp-vtst/4

openmpi-1.4/intel/4.6.35-mkl-12

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/2012

2012-11-11-1

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/

vasp-vtstscripts/926

926-1

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/

vasp/4.6

openmpi-1.4/intel/4.6.35-mkl-13

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 provides a full set of binaries resulting from various compile-time configuration options, plus the VTST patch by Graeme Henkelman, http://theory.cm.utexas.edu/vtsttools/downloads/ .

Likewise, there are binaries to calculate the DOS projected in Bader Volumes, http://theory.cm.utexas.edu/bader/ .

Available to licensed users only.

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

openmpi-1.4/intel/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/

openmpi-1.4/intel/4.6.36-mkl-4

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 provides binaries for various compile-time options of:

The original sources.
Schmidt's patch for a periodic Natural Bond Orbital algorithm; see 'module help periodic_NBO'.

Available to licensed users only.

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

vasp5/5.3

openmpi-1.4/intel/5.3.3p3-mkl-cellz-1

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 provides binaries modified to constrain cell relaxations along the z-axis (N. Charles).

Available to licensed users only.

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

, openmpi-1.10

impi-5/intel-16/5.3.5-2

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 provides binaries modified to constrain cell relaxations along the z-axis (user request).

All binaries support the LWANNIER90 option.

Available to licensed users only.

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

https://wiki.anl.gov/cnm/HPC/Applications/vasp

openmpi-1.10/intel-16/5.3.5-1

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 provides binaries modified to constrain cell relaxations along the z-axis (N. Charles).

All binaries support the LWANNIER90 option.

Available to licensed users only.

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

openmpi-1.4/intel/5.3.2-mkl-beef-1

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 provides binaries for various compile-time options of:

BEEF-vdW ensemble XC energies (see 'module help beef').

Available to licensed users only.

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

openmpi-1.4/intel/5.3.3p3-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.

This version provides a full set of binaries resulting from various compile-time configuration options, plus the VTST patch by Graeme Henkelman, http://theory.cm.utexas.edu/vtsttools/downloads/ .

Likewise, there are binaries to calculate the DOS projected in Bader Volumes, http://theory.cm.utexas.edu/bader/ .

All binaries support the LWANNIER90 option.

Available to licensed users only.

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

vasp5/5.3-scan

openmpi-1.10/intel-16/5.3.5-scan-1

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 supports the 2015 Perdew Strongly Constrained and Appropriately Normed Semilocal Density Functional (SCAN), see https://doi.org/10.1103/PhysRevLett.115.036402 .

This version provides binaries modified to constrain cell relaxations along the z-axis (N. Charles).

All binaries support the LWANNIER90 option.

Available to licensed users only.

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

impi-5/intel-16/5.3.5-scan-1

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 supports the 2015 Perdew Strongly Constrained and Appropriately Normed Semilocal Density Functional (SCAN), see https://doi.org/10.1103/PhysRevLett.115.036402 .

This version provides binaries modified to constrain cell relaxations along the z-axis (user request).

All binaries support the LWANNIER90 option.

Available to licensed users only.

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

https://wiki.anl.gov/cnm/HPC/Applications/vasp

vasp5/5.4

impi-5/intel-16/5.4.1.3-10, impi-5/intel-16/5.4.1.3-11, impi-5/intel-16/5.4.1.3-9, openmpi-1.10/intel-16/5.4.1.3-10, openmpi-1.10/intel-16/5.4.1.3-11, openmpi-1.10/intel-16/5.4.1.3-9

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 provides the standard set of binaries for the 5.4 build system:

vasp_std - Multiple k-point version
vasp_gam - GAMMA-point only version
vasp_ncl - Non-collinear version

Patches applied: patch.5.4.1.14032016.gz

All binaries support the following features (some previously required third-party add-ons):

advanced MD algorithms, http://cms.mpi.univie.ac.at/vasp/vasp/MDALGO.html
Cell relaxations constrained along cartesian axes (input file CELL_RELAX)
VASPsol solvation model (U. Florida)
auto-locating of the vdW kernel file (Carbon-specific modification).
LWANNIER90 option, http://cms.mpi.univie.ac.at/wiki/index.php/LWANNIER90
BEEF support (Bayesian error estimation functional)

Alternate sets of binaries provide:

Transition state tools by Graeme Henkelman, as binaries vasp_vtst_{std,gam,ncl}, http://theory.cm.utexas.edu/vtsttools/

VASP is available to licensed users only.

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

https://wiki.anl.gov/cnm/HPC/Applications/vasp

impi-5/intel-16/5.4.1.3-6, openmpi-1.10/intel-16/5.4.1.3-6

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 provides the standard set of binaries for the 5.4 build system:

vasp_std - Multiple k-point version
vasp_gam - GAMMA-point only version
vasp_ncl - Non-collinear version

Further sets of binaries are included to provide:

Transition state tools by Graeme Henkelman, as binaries vasp_vtst_{std,gam,ncl}, http://theory.cm.utexas.edu/vtsttools/
Cell relaxations constrained along the z-axis, with binaries vasp_cellz_{std,gam,ncl}

All binaries support the following features (some previously required third-party add-ons):

advanced MD algorithms, http://cms.mpi.univie.ac.at/vasp/vasp/MDALGO.html
auto-locating of the vdW kernel file (Carbon-specific modification).
LWANNIER90 option, http://cms.mpi.univie.ac.at/wiki/index.php/LWANNIER90
BEEF support (Bayesian error estimation functional)

VASP is available to licensed users only.

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

https://wiki.anl.gov/cnm/HPC/Applications/vasp

impi-5/intel-16/5.4.1.3-8, openmpi-1.10/intel-16/5.4.1.3-8

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 provides the standard set of binaries for the 5.4 build system:

vasp_std - Multiple k-point version
vasp_gam - GAMMA-point only version
vasp_ncl - Non-collinear version

The following patches are built-in to all binaries:

Alternate sets of binaries provide:

Transition state tools by Graeme Henkelman, as binaries vasp_vtst_{std,gam,ncl}, http://theory.cm.utexas.edu/vtsttools/

All binaries support the following features (some previously required third-party add-ons):

advanced MD algorithms, http://cms.mpi.univie.ac.at/vasp/vasp/MDALGO.html
Cell relaxations constrained along cartesian axes (input file CELL_RELAX)
VASPsol solvation model (U. Florida)
auto-locating of the vdW kernel file (Carbon-specific modification).
LWANNIER90 option, http://cms.mpi.univie.ac.at/wiki/index.php/LWANNIER90
BEEF support (Bayesian error estimation functional)

VASP is available to licensed users only.

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

https://wiki.anl.gov/cnm/HPC/Applications/vasp

impi-5/intel-16/5.4.4.0-1

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 provides the standard set of binaries for the 5.4 build system:

vasp_std - Multiple k-point version
vasp_gam - GAMMA-point only version
vasp_ncl - Non-collinear version

Patches applied:

All binaries support the following features (some previously required third-party add-ons):

advanced MD algorithms, http://cms.mpi.univie.ac.at/vasp/vasp/MDALGO.html
Cell relaxations constrained along cartesian axes (input file CELL_RELAX)
VASPsol solvation model (U. Florida)
auto-locating of the vdW kernel file (Carbon-specific modification).
LWANNIER90 option, http://cms.mpi.univie.ac.at/wiki/index.php/LWANNIER90
BEEF support (Bayesian error estimation functional)

Alternate sets of binaries provide:

Transition state tools by Graeme Henkelman, as binaries vasp_vtst_{std,gam,ncl}, http://theory.cm.utexas.edu/vtsttools/

VASP is available to licensed users only.

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

https://wiki.anl.gov/cnm/HPC/Applications/vasp

vasp5/5.4-z2pack

impi-5/intel-16/5.4.1.3-z2pack-1, impi-5/intel-16/5.4.1.3-z2pack-2, openmpi-1.10/intel-16/5.4.1.3-z2pack-1

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 provides the standard set of binaries for the 5.4 build system:

vasp_std - Multiple k-point version
vasp_gam - GAMMA-point only version
vasp_ncl - Non-collinear version

Patches applied: patch.5.4.1.14032016.gz

All binaries support the following features (some previously required third-party add-ons):

advanced MD algorithms, http://cms.mpi.univie.ac.at/vasp/vasp/MDALGO.html
Cell relaxations constrained along cartesian axes (input file CELL_RELAX)
VASPsol solvation model (U. Florida)
auto-locating of the vdW kernel file (Carbon-specific modification).
LWANNIER90 option, http://cms.mpi.univie.ac.at/wiki/index.php/LWANNIER90
BEEF support (Bayesian error estimation functional)

Alternate sets of binaries provide:

Transition state tools by Graeme Henkelman, as binaries vasp_vtst_{std,gam,ncl}, http://theory.cm.utexas.edu/vtsttools/

VASP is available to licensed users only.

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

https://wiki.anl.gov/cnm/HPC/Applications/vasp

vesta/3

3.2.1-1

VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. Some of the novel features of VESTA are listed below.

Deal with multiple structural models, volumetric data, and crystal morphologies in the same window.
Support multiple tabs corresponding to files.
Support multiple windows with more than two tabs in the same process.
Deal with virtually unlimited number of objects such as atoms, bonds polyhedra, and polygons on isosurfaces (theoretical limit on 32bit operating system is 1,073,741,823)
Support lattice transformation from conventional to non-conventional lattice by using matrix. The transformation matrix is also used to create superlattice and sublattice.
Visualize interatomic distances and bond angles that are restrained in Rietveld analysis with RIETAN-FP.
Transparent isosurfaces can be overlap with structural models.
Isosurface can be colored on the basis of another physical quantity.
Arithmetic operations among multiple volumetric data files.
High quality smooth rendering of isosurfaces and sections.
Export high-resolution graphic images exceeding Video card limitation.
VESTA is a successor to two 3D visualization programs, VICS and VEND, in the VENUS (Visualization of Electron/NUclear and Structures) software package.

This installation includes the PowderPlot utility.

Contributed free of charge for non-commercial users.

http://jp-minerals.org/vesta/en/

vmd/1

1.9.1-2

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.

This build includes the VMD Density Profile Tool (1.1).

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

http://multiscalelab.org/utilities/DensityProfileTool

voro++/0

intel/0.4.5-1

Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles.

Voro++ comprises of several C++ classes that can be built as a static library. A command-line utility is also provided that can use most features of the code. The direct cell-by-cell construction makes the library particularly well-suited to handling special boundary conditions and walls. It employs algorithms that are tolerant for numerical precision errors, it exhibits high performance, and it has been successfully employed on very large particle systems.

The directory $VOROXX_HOME/share/ contains examples and scripts.

http://math.lbl.gov/voro++/doc/

http://math.lbl.gov/voro++/

vtk/5

intel/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/

https://visualization.hpc.mil/wiki/VTK

https://visualization.hpc.mil/wiki/Getting_Started_with_VTK

wannier90/1

1.2-1, 1.2-2

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/

wannier90/1-z2pack

1.2-z2pack-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/

wannier90/2

impi-5/intel-16/2.0.1-3, openmpi-1.10/intel-16/2.0.1-3

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

intel/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/

wien2k/14.2

impi-5/intel-16/14.2-7

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

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/