Chemistry Computational Cluster (CCC)

TTU Home Chemistry CCC


CCC Computational Application Packages

NAME Software URL URL – Tutorial
ABINIT http://www.abinit.org/ http://www.abinit.org/documentation/helpfiles/for-v6.8/tutorial/welcome.html
AMBER http://ambermd.org/ http://ambermd.org/tutorials/
CARLOS http://www.win.tue.nl/~johanl/projects/Carlos/ http://www.win.tue.nl/~johanl/projects/Carlos/
COLUMBUS http://www.univie.ac.at/columbus/ http://www.univie.ac.at/columbus/docs_COL70/documentation_main.html
CPMD http://www.cpmd.org/ http://www.cpmd.org/cpmd_on_line_manual.html
CP2K http://cp2k.berlios.de/ http://cp2k.berlios.de/quickstep.html
GAMES http://www.msg.ameslab.gov/GAMESS/ http://www.msg.ameslab.gov/GAMESS/documentation.html
GROMACS http://www.gromacs.org/ http://www.gromacs.org/Support/Online_Manual
LAMMPS http://lammps.sandia.gov/ http://lammps.sandia.gov/doc/Manual.html
MOLPRO http://www.molpro.net/ http://www.molpro.net/info/users?portal=user
NAMD http://www.ks.uiuc.edu/Research/namd/ http://www.ks.uiuc.edu/Research/namd/2.6/ug/
NWCHEM http://www.nwchem-sw.org/index.php/Main_Page http://www.nwchem-sw.org/index.php/Main_Page
Quantum ESPRESSO http://www.quantum-espresso.org/ http://www.quantum-espresso.org/learn.php
TURBOMOLE http://www.turbomole.com/ http://www.turbomole-gmbh.com/turbomole-manuals.html
VMD http://www.ks.uiuc.edu/Research/vmd/ http://www.ks.uiuc.edu/Research/vmd/allversions/what_is_vmd.html

NWCHEM-VENUS –Texas Tech University Packages. It is Large-scale Molecular Reaction Dynamics, Atomic/Molecular Massively Parallel Simulator. NWCHEM-NENUS has potentials for solar materials (biomolecules, polymers) and solid-state materials and coarse-grained or mesoscopic systems. The packages are designed by Dr Hase in chemistry of Texas Tech University. It is a mainly application package in his group and world groups.

PACE is a large-scale quantum dynamics code that implements various electron nuclear dynamics (END) methods and coherent-states (CS) models. PACE features advanced parallel programming and a Python environment for rapid method development inter alia. The END methods and CS models in PACE can be applied to the simulation of a large variety of chemical reactions, such as ion-molecule, SN2, Diels-Alder, and proton cancer therapy reactions inter alia. PACE is developed by Dr. Morales of the chemistry department at Texas Tech University. PACE’s main application is for Dr. Morales group and other university research groups in The United States of America.

ScalIT stands a large-scale quantum molecular reaction dynamics package with Massively Parallel Computing which is designed by Dr. Poirier of Chemistry at Texas Tech University. The application from ScalIT includes molecular spectroscopy and molecular reaction dynamics properties with the system less than 10 atoms.

The CCC Compiler

NAME Compiler URL URL – Tutorial
The Intel compilers (icc,icpc,and ifort) http://www.intel.com/ClusterStudio  
GNU Compilers (gcc, g++, gfortran) http://gcc.gnu.org/ http://gcc.gnu.org/onlinedocs/
Python http://www.python.org/ http://www.python.org/doc
Intel MPI 4.0 (mpiicc, mpicxx, mpiifort) http://www.intel.com/ClusterStudio http://www.intel.com/ClusterStudio
OpenMPI (mpicc, mpicxx, mpif90, mpif77) http://www.open-mpi.org http://www.open-mpi.org/doc
MVAPICH http://mvapich.cse.ohio-state.edu http://mvapich.cse.ohio-state.edu/support/mvapich_user_guide-1.1.html
MVAPICH2 http://mvapich.cse.ohio-state.edu/overview/mvapich2 http://mvapich.cse.ohio-state.edu/support/user_guide_mvapich2-1.6.html;

The CCC Library

NAME Library URL URL – Tutorial
FFTW http://www.fftw.org http://www.fftw.org/#documentation
TCL http://www.tcl.tk/ http://www.tcl.tk/doc/
MKL http://www.qft.iqfr.csic.es/docs/intel/mkl/ http://www.qft.iqfr.csic.es/docs/intel/mkl/mkl_documentation.htm
BLAS http://www.qft.iqfr.csic.es/docs/intel/mkl/ http://www.qft.iqfr.csic.es/docs/intel/mkl/mkl_documentation.htm
LAPACK http://www.qft.iqfr.csic.es/docs/intel/mkl/ http://www.qft.iqfr.csic.es/docs/intel/mkl/mkl_documentation.htm
ScaLAPACK http://www.qft.iqfr.csic.es/docs/intel/mkl/ http://www.qft.iqfr.csic.es/docs/intel/mkl/mkl_documentation.htm

MKL: The Intel(R) Math Kernel Library (Intel(R) MKL) enables improving performance of scientific, engineering, and financial software that solves large computational problems. Intel MKL provides a set of linear algebra routines, fast Fourier transforms, as well as vectorized math and random number generation functions, all optimized for the latest Intel(R) processors.

BLAS and LAPACK: Linear algebra, implemented in LAPACK (solvers and eigensolvers) plus level 1, 2, and 3 BLAS, offering the vector, vector-matrix, and matrix-matrix operations needed for complex mathematical software. If you prefer the FORTRAN 90/95 programming language, you can call LAPACK driver and computational subroutines through specially designed interfaces with reduced numbers of arguments.

ScaLAPACK (SCAlable LAPACK) with its support functionality including the Basic Linear Algebra Communications Subprograms (BLACS) and the Parallel Basic Linear Algebra Subprograms (PBLAS).

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). And SPRNG is the Scalable Parallel Random Number Generators library.