Introduction
Computer simulation, also known as computer modelling, is the use of computers to develop and explore numerical models that reproduce the properties of materials, structures, processes or phenomena. Atomic-level or atomistic computer simulation involves modelling the individual atoms and molecules (and sometimes electrons) that make up the material. The methods used range from rigorous (and computationally expensive) quantum-mechanical treatments based on Schrödinger's equation—referred to as ab initio (or first principles) quantum mechanical methods—to rapid (but less detailed) empirical techniques which use approximate or "effective" functions to describe the forces between particles (sometimes referred to as ‘molecular modelling’). The method chosen for any particular problem depends on the size of the system, the type of bonding in the material (ionic, covalent, van der Waals, etc), and the kind of information being sought.
Research Groups
Listed below are some research groups and individuals from around the globe using atomistic computer simulations to investigate ceramics:
Australia
- Centre for Computational Molecular Science at the University of Queensland
- Nanochemistry Research Institute (NRI) at Curtin University of Technology
- Computational and Theoretical Chemistry at the University of Sydney
Austria
- Computational Quantum Chemistry Group at the Vienna University of Technology
- Computational Materials Science Group at the University of Vienna
- Computational Materials Physics at the University of Vienna
Finland
Germany
- Department of Theory at the Fritz Haber Institute (Berlin) of the Max Planck Society
- Andersen Group at the Max Planck Institute for Solid State Research
- Computational Materials Design Group at the Max Planck Institute for Iron Research
- Institute of Theoretical Chemistry at Stuttgart University
- Institute for Theoretical and Applied Physics (ITAP) at Stuttgart University
Ireland
- Computational Physics Group at Trinity College Dublin
- Theoretical and Computational Chemistry at Trinity College Dublin
Italy
- Condensed Matter Group at the International School for Advanced Studies (SISSA)
- Theoretical Chemistry Group at the University of Torino
Japan
- Materials Simulation Laboratory at Kumamoto University
- Nano-System Computational Science Group at the National Institute for Materials Science
- Tanaka Laboratory at Kyoto University
- Kawamura Laboratory at Tokyo Institute of Technology
- Condensed Matter Physics Laboratory at Niigata University
- Dr K. Tsuruta in the Department of Electrical and Electronic Engineering at Okayama University
- Computational Materials Designing and Creation Laboratory at Osaka University
- Miyamoto Laboratory at Tohoku University
- Kawazoe Laboratory at Tohoku University
- Center for Computational Materials Science Working Group
The Netherlands
Sweden
- Materials and Surface Theory Group at Chalmers University
- Theoretical Inorganic Chemistry Group at the Uppsala University
Switzerland
- Computational Chemistry and Physics Group at IBM Zurich
- Prof. J. Weber's Group at the University of Geneva
United Kingdom
- Computational Solid State Chemistry Group at Bath University
- Computational Materials Chemistry Group at Bath University
- Theoretical Chemistry Group at Birmingham University
- Computational Solid State Chemistry Group at Bristol University
- Atomistic Simulation Group at Cambridge University
- Cambridge University Centre for Computational Chemistry (CUC3) at Cambridge University
- Mineral Sciences Group at Cambridge University
- Theory of Condensed Matter Group at Cambridge University
- Dr D. J. Willock at Cardiff University
- Computational Materials Science Group at STFC Daresbury Laboratory
- Computational Chemistry Group at STFC Daresbury Laboratory
- Molecular Modelling Group at Cranfield University
- Condensed Matter Group at Edinburgh University
- Atomistic Simulation Group at Imperial College
- Condensed Matter Theory Group at Imperial College
- Doctoral Training Centre for Theory and Simulation of Materials at Imperial College
- Dr R. A. Jackson at Keele University
- Computational Nanoscience Group at the University of Nottingham
- Materials Modelling Laboratory at Oxford University
- Atomistic Simulation Group at the Queen's University of Belfast
- Computational Chemistry at University College London
- Prof. C. R. A. Catlow at University College London
- Prof. N. de Leeuw at University College London
- Condensed Matter and Materials Physics Group at University College London
- Prof. G. D. Price at University College London
- Theory & Computational Chemistry Group at University of Warwick
- Thomas Young Centre for Theory and Simulation of Materials
USA
- Interfacial Materials Group at Argonne National Laboratory
- Materials and Process Simulation Center of the Beckman Institute at Caltech
- The Smit Group in the Dept of Chemical and Biomolecular Engineering at the University of California, Berkeley
- Materials Process Design & Control Laboratory at Cornell University
- Electronic Structure Group at the University of Illinois Urbana-Champaign (UIUC)
- National Center for Supercomputing Applications (NCSA) at the University of Illinois Urbana-Champaign (UIUC)
- Condensed Matter Physics Program at Iowa State University
- Materials Theory Group at the Lawrence Livermore National Laboratory (LLNL)
- Dr J. M. Rickman at Lehigh University
- Theory and Computation in the Dept of Chemical Engineering & Materials Science at the University of Minnesota
- Scientific Computational Analysis and Research of Materials (SCRAM) group in the Department of Materials Science & Engineering at MIT
- Center for Computational Materials Science at the Naval Research Laboratory (NRL)
- Prof. M. H. Whangbo in the Department of Chemistry at North Carolina State University
- Computational Materials Science Group at North Carolina State University
- Professor V. Vitek at the University of Pennsylvania
- Dr E. A. Carter in the Dept of Mechanical & Aerospace Engineering at Princeton University
- Interfacial Molecular Science Laboratory at Rutgers University
- Theoretical Condensed Matter Theory Group at Rutgers University
- Materials and Modeling Simulation at Sandia National Laboratories
- Quantum Chemistry at Sandia National Laboratories
- Collaboratory for Advanced Computing and Simulations at the University of Southern California
Simulation Software
Free software for performing atomistic computer simulation can be found at these sites:
Classical
- DL_POLY, a molecular dynamics (MD) program for parallel computers by Bill Smith and Tim Forrester (STFC Daresbury Laboratory)
- DL Visualize, a graphics package for viewing atoms and molecules by the people at STFC Daresbury Laboratory
- DL_MONTE, a Monte Carlo program that supports DL_POLY-style inputs by STFC Daresbury Laboratory
- Gromacs, an MD program from the Biomolecular Sciences and Biotechnology Institute at the University of Groningen
- MOLDY, a general-purpose molecular dynamics program by Keith Refson (Rutherford Appleton Laboratory)
- GULP, a multi-purpose program for simulating crystals by Julian Gale (Curtin University)
- MCCCS Towhee, a Monte Carlo molecular simulation code by Marcus Martin (Useful Bias Inc)
- SHELL, a free energy minimization program by Mark Taylor (Bristol University) and Gus Barrera (University of Buenos Aires)
- The Molecular Modelling Toolkit (MMTK), a simulation suite written in Python by Konrad Hinsen at the Centre de Biophysique Moléculaire (CBM)
- Visual Molecular Dynamics (VMD), by the Theoretical Biophysics Group at the University of Illinois
- IMD, a massively parallel molecular dynamics program from the Institute for Theoretical and Applied Physics (Stuttgart University)
- LAMMPS, a massively parallel molecular dynamics program from Sandia National Laboratories
- Plumed, an open source plugin for free-energy calculations of molecular systems
Quantum mechanical
- CRYSTAL, a program for calculating the electronic structure of periodic systems by the Theoretical Chemistry Group at the University of Torino
- GAMESS-UK, a general purpose ab initio molecular electronic structure program.
- ABINIT, a DFT code from the Université Catholique de Louvain
- AIMPRO, an ab initio code based on local density functional theory
- CASTEP, a DFT code from the University of Cambridge
- NWChem, a computational chemistry package by the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory
- CPMD, a Carr-Parrinello MD code from the Max Planck Institute Stuttgart
- OpenMX, a DFT package for nano-scale materials simulation
- MOPAC, a semi-empirical quantum chemistry program
- Quantum ESPRESSO, an integrated suite of computer codes for electronic-structure calculations
- SeqQuest, a DFT code by Sandia National Laboratories
- Feram, a first-principles-based molecular dynamics code for simulating ferroelectric and relaxor materials
- Phonopy, an open-source phonon analyzer
- Phonon, a code for calculating phonon dispersion curves from ab initio data
- Elk, an all-electron full-potential linearised augmented-plane wave code
Visualization
- Aten, a visualization package hosted by TikiWiki
- GDIS, a graphics package for viewing atoms and molecules written by Sean Fleming at eResearch Australasia
- gOpenMol, a visualization program for atoms and molecules from the Finnish IT Center for Science
- VEGA, molecular visualization software by the Drug Design Laboratory at the University of Milan
- Molden, a molecular and electronic structure visualisation program by Gijs Schaftenaar at the Center for Molecular and Biomolecular Informatics
- VESTA, an electronic and nuclear density visualisation program.
- Vimes, the "Visual Interface to Materials Simulation".
- XCrySDen, a crystalline and molecular structure visualisation program which can display isosurfaces and contours.
Other
- THOR, a hybrid MD, stochastic MC and Density Functional Theory program by Kleber Mundim (University of Brazilia)
- FEFF, a program for calculating X-ray spectra from clusters of atoms by the Department of Physics at the University of Washington
- Sginfo, C routines for the handling of space group symmetry by Ralf W. Grosse-Kunstleve
- Computational Crystallography Toolbox (cctbx), an open-source project developing C++ libraries and scripting language interfaces for crystallography.
Free software specifically for academic users is also available from the CCP5 Program Library.
Other academic software requiring a licence fee include
- BALSAC, a program for constructing crystal lattices and surfaces by Klaus Hermann at the Fritz Haber Institute
- VASP, an ab-initio molecular dynamics package from the University of Vienna
- WIEN2k, a DFT package by the Computational Quantum Chemistry Group at Vienna University of Technology
A comprehensive list of scientific software can be found at the National HPCC Software Exchange.
A library of software for modelling materials is also maintained by the Materials Algorithms Project (MAP).
Commercial software used in computational materials science can be found at these sites:
- Accelrys Inc (formerly MSI)
- Advanced Visual Systems Inc (AVS)
- Crystal Impact
- CrystalMaker
- Gaussian Inc
- Materials Design
- Oxford Materials Ltd (OxMat)
- Q-Chem
- Quantum Materials Design, Inc.
- ITT Visualization Information Solutions
- Shape Software
- CrystalKitX
- Scienomics
Resources
Online tutorials
Web sites featuring tutorials on the fundamentals of atomistic simulation, and molecular modelling (for systems other than ceramics) in general:
- Democritus - an MD tutorial from STFC Daresbury Laboratory
- Franz Vezely's tutorial on statistical physics and simulation at the University of Vienna
- An Introduction to Atomistic Simulation Methods by Martin T. Dove of the University of Cambridge.
Textbooks
Electronic Structure: Basic Theory and Practical Methods
Academic Press, Inc. Orlando, FL, USA 1997
ISBN-10: 012164135X | ISBN-13: 978-0121641351
Computer Modeling in Inorganic Crystallography
Academic Press, Cambridge, UK, 2004
ISBN-13: 9780521782852 | ISBN-10: 0521782856
DOI: 10.2277/0521782856
Electronic Structure Calculations for Solids and Molecules: Theory and Computational Methods
Cambridge University Press, Cambridge, UK 2006
ISBN-10: 0521815916 | ISBN-13: 978-0521815918
DOI: 10.2277/0521815916
Understanding Molecular Simulation, 2nd Edition: From Algorithms to Applications (Computational Science Series, Vol 1)
Academic Press, Inc. Orlando, FL, USA 2002
ISBN-10: 0122673514 | ISBN-13: 978-0122673511
Computer Simulation Methods in Theoretical Physics
Springer-Verlag, 2nd edition, Heidelberg, Germany 1990
ISBN-10: 0387522107 | ISBN-13: 978-0387522104
The Art of Molecular Dynamics Simulation
Cambridge University Press, 2nd edition, Cambridge, UK 2005
ISBN-10: 0521599423 | ISBN-13: 978-0521599429
Molecular Modelling: Principles and Applications (2nd Edition)
Prentice Hall, 2nd edition, 2001
ISBN-10: 0582382106 | ISBN-13: 978-0582382107
Computer Modelling of Microporous Materials
Elsevier Academic Press, UK, 2004
ISBN-10: 0121641376 | ISBN-13: 978-0121641375
Density-Functional Theory of Atoms and Molecules
Oxford University Press, USA, 1994
ISBN-10: 0195092767 | ISBN-13: 978-0195092769
Essentials of Computational Chemistry: Theories and Models
Wiley, 2nd edition, UK, 2004
ISBN-10: 0470091827 | ISBN-13: 978-0470091821
Introduction to the Theory and Applications of Molecular and Quantum Mechanics
Springer, 2nd edition, The Netherlands, 2011
ISBN-10: 9048138612 | ISBN-13: 978-9048138616
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