Our software
Most calculations in the group are done with the aid of a number of
standard software packages.Furthermore, a number of programs have been
developed by, or in cooperation with, group members. The software packages
can be devided in two groups: packages based on quantumchemical methods (Hartree-Fock,
Self-Consistent Field, Density Functional Theory etc.) and classical
simulations based on statistical physics (molecular dynamics, Monte
Carlo). This page gives a short overview of the different packages used.
If available, links are given to pages where more information can be
found. Examples of applications can be found in the research pages of the
different group members.
Quantumchemical packages:
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VASP: the Vienna
Ab-initio Simulation Package, a package for performing periodic
ab-initio quantum-mechanical molecular dynamics using pseudopotentials
and a plane wave basis set. We use VASP with an improved NEB/Dimer module developed by the Jónnson Group.
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Gaussian: software package
for calculating electronic structures, energies and vibrational
frequencies using various quantumchemical methods.
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ADF/BAND: Amsterdam Density-Functional
program package for electronic structure calculations based on
density-functional theory.
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DGauss:
package for predicting molecular structures, properties and
energetics based on density functional theory.
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HighD: wavepacket dynamics program using the
Multi-Configuration
Time-Dependent Hartree (MCTDH) approximation. The code is written in
C++ and was developed by Tonek Jansen
, and was used by Robin Milot for
studying the scattering and dissociation of methane on transition
metal surfaces.
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AnharmND: a C++ program to compute anharmonic vibrational wave
functions, and transition dipoles between those wave functions, of
molecular systems. The program was developed by Eric Meijer.
Classical simulations:
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Camelion: a 3-dimensional Molecular-Dynamics and Dynamic
Monte Carlo-annealing program developed for use with Embedded Atom
Method (EAM) interactions. The program was initially written in
FORTRAN77 as a joint product of ComMaS and CRI->SIS, now part of the
Atomic Processes at Surfaces research group at the Technical
University in Delft.
In Eindhoven we use a version which employs the Modified
Embedded Atom Method (MEAM). Several MEAM-specific modifications were
introduced by
Paul van Beurden. Recently we have started using the parallellized
version of Camelion (FORTRAN90+MPI) as well. Contact person for Camelion
is Prof. Dr. B.J. Thijsse
(B.J.Thijsse@tnw.tudelft.nl). Camelion related software can be
found at http://www.tm.tudelft.nl/secties/fcm/matphy/software/software.htm.
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CARLOS: a
2-dimensional Dynamic Monte-Carlo program written in C by Johan
Lukkien.of the department of computer science, used for studying
catalytic surface reactions.
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PiZZaZZ: 2-D Dynamic Monte-Carlo program written in C++ by
Tonek
Jansen. This program is an implementation of the
first reaction method.
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Platipus: A Genetic Algorithm optimization engine written in C++ by
Tonek Jansen. This program has been
used at the moment mainly to optimize CARLOS
kinetic parameters.
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MD_ALKANE:a classical molecular dynamics program written in
FORTRAN77 to study the diffusion of linear and branched alkanes in
zeolites. This program was developed in the Computer Simulation in
Chemical Engineering group of Berend Smit at the University of Amsterdam.
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BIGMAC: a
Configurational Bias Monte Carlo (CBMC) program to study the
adsorptive properties of linear and branched alkanes and their
mixtures in zeolites. This program was developed by the group of
Berend Smit at the University of Amsterdam.
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RvS: classical
molecular dynamics program to study the rovibrational scattering of
methane on transition metal surfaces. This program was written in
FORTRAN77 by Robin Milot.
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BiPSimP: a hard-sphere dynamics program written in C++ to study the
diffusion and equilibrium properties of hard spheres in narrow
structured pores. This program was written by Danny Schuring.
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MD_pore: molecular dynamics program to study the diffusion of
Lennard-Jones particles in narrow pores. This program was written in
FORTRAN77 by Danny Schuring.
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MC_FreE: Monte Carlo program written in FORTRAN77 to calculate the
chemical potential, free entropy and and energy of alkanes in zeolites
using the Rosenbluth sampling technique. This program was written by
Danny Schuring.
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simanPEP: program to simulate and analyze PEP experiments of flow
and reaction in packed beds of porous particles by solving the mass
balances as a function of time and position. This FORTRAN77 program
uses the numerical method of lines (NUMOL) to solve the set of
partial differential equations. Experimental data can be analysed
by fitting the calculated concentration profiles. This program was
written by Danny Schuring.
Visualisation Software
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wxDragon: Created by Bernhard Eck of the Institut für Anorganische Chemie der RWTH-Aachen.
Visualization of VASP-, ADF- , Gaussian and other program-outputs
without converting it. It gives you the opportunity to multiply your
unit cell, visualize the forces on the atoms and to make movies of
configuration changes. You can also make DOS plots and rdf plots and
many other things....
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xMol: another visualisation program for all XWindows-desktops.
- MacMolecule2: visualisation program, fast and versatile, but unfortunately the company seems to have disappeared.
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MOrV: (Molecular Orbital Viewer) is a mixed Java/native program for 3D displaying of molecular orbitals and other surfaces from an ADF calculation. It is created by Alexei Yakovlev.
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