Computer Modelling of Fluids Polymers and Solids

542 Pages·1989·14.1 MB·English

by  C. R. A. Catlow (auth.), C. R. A. Catlow, S. C. Parker, M. P. Allen (eds.)

Computer Modelling of Fluids Polymers and Solids
NATO ASI Series
Advanced Science Institutes Series
A Series presenting the results of activities sponsored by the NA TO Science Committee,
which aims at the dissemination of advanced scientific and technological knowledge,
with a view to strengthening links between scientific communities.
The Series is published by an international board of publishers in conjunction with the
NATO Scientific Affairs Division
A Life Sciences Plenum Publishing Corporation
B Physics London and New York
C Mathematical Kluwer Academic Publishers
and Physical Sciences Dordrecht, Boston and London
D Behavioural and Social Sciences
E Applied Sciences
F Computer and Systems Sciences Springer-Verlag
G Ecological Sciences Berlin, Heidelberg, New York, London,
H Cell Biology Paris and Tokyo
Series C: Mathematical and Physical Sciences - Vol. 293
Computer Modelling of Fluids
Polymers and Solids
edited by
C.R.A. Catlow
Davy Faraday Research Laboratory,
The Royal Institution,
London, United Kingdom
s.c. Parker
Department of Chemistry,
University of Bath,
Bath, United Kingdom
and
M.P. Allen
H.H. Wills Physics Laboratory,
University of Bristol,
Bristol, United Kingdom
Kluwer Academic Publishers
Dordrecht / Boston / London
Published in cooperation with NATO Scientific Affairs Division
Proceedings of the NATO Advanced Study Institute on
Computer Modelling of Fluids Polymers and Solids
Bath, United Kingdom
September 4-17, 1988
Library of Congress Cataloging in Publication Data
NATO Advanced Study Institute on Computer Modelling of Flulds Polymers
and Solids (1988 University of Bath. U.K.)
Computer model ling of flulds polymers and sol ids: proceedings of
the NATO Advanced Study Institute on Computer Model ling of Fluids
Polymers and Solids. held at the University of Bath. U.K .• Sept.
4-17th.1988 / edited by C.R.A. Catlow. S.C.Parker. M.P. Allen.
p. em. -- (NATO ASI series. Series C. Mathetical and physical
sciences; vol. 293)
1. Condensed matter--Mathematical models--Congresses.
2. Condensed matter--Computer simulation--Congresses. 3. Polymers-
-Congresses. 4. Amorphous substances--Congresses. I. Catlow. C.
R. A. (Charles Richard Arthur). 1947- II. Parker. S.C.
III. Al len. M.P. IV. Title. V. Series: NATO ASI series. Series C.
Mathematical and physical sciences; no. 293.
aC173.4.C65N374 1988
530.4·1--dc20 89-28175
ISBN-13: 978-94-010-7621-0 e-ISBN-13: 978-94-009-2484-0
001: 10.1007/978-94-009-2484-0
Published by Kluwer Academic Publishers,
P.O. Box 17,3300 AA Dordrecht, The Netherlands.
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TABLE OF CONTENTS v
Preface and Acknowledgements vii
Lecturers ix
1 • AN INTRODUCTION TO ca1PUTER t-UDELLING OF CONDENSED MA'ITER 1
C.R.A. Catlow
2. TOWARDS REALISTIC t-UDEL INTERIDLECULAR POTENTIALS 29
S.L. Price
3. t-ULECULAR DYNAMICS 55
A.J .C. Ladd
4. t-UNTE CARLO SIMULATIONS 83
D. Frenkel
5. NON-EQUILIBRIUM STATISTICAL MECHANICS AND t-ULECULAR 125
DYNAMICS COMPUTATIONS
D.J. Evans
6. THE PATH -INTEGRAL SIMULATION OF QUANTUM SYSTEMS 155
M.J. Gillan
7. THE METHOD OF CONSTRAINTS: APPLICATION TO A SIMPLE 189
N-ALKANE t-UDEL
J.P. Ryckaert
8. t-ULECULAR DYNAMICS OF CHAIN t-ULECULES 203
J.H.R. Clarke
vi
9. CXX1PUTER IDDELLING OF OXIDE SURFACES AND INTERFACES 219
P.J. Lawrence and S. C.Parker
10. HARDWARE ISSUES IN IDLECULAR DYNAMICS ALGORITHM 249
DESIGN
D. C. Rapaport
11 • PARALLEL CXX1PUTERS AND THE SIMULATION OF SOLIDS 269
AND LIQUIDS
D. Fincham
12. IDLECULAR SIMULATIONS OF PRal'EIN STRUCTURE, 289
DYNAMICS AND THERMODYNAMICS
C.L. Brooks
13. SIMULATION OF PLASTIC CRYSTALS 335
M. Meyer
14. IDLECULAR DYNAMICS SIMULATIONS OF AQUEOUS 357
SYSTEMS
K. Heinzinger
15. COMPUTER SIMULATION OF INORGANIC MATERIALS 395
R.A. Jackson
16. Ca1PUTER IDDELLING OF THE STRUCTURE AND 405
THERMODYNAMIC PROPERTIES OF SILICATE
MINERALS
S.C. Parker and G.D. Price
APPENDIX: COMPUTER SIMULATION EXERCISES 431
M.P. Allen, D.M. Heyes, M. Leslie, S.L. Price,
W. Smith and D.J. Tildesley
SUBJECT INDEX 537
PREFACE
Computer Modelling techniques have developed very rapidly
during the last decade, and interact with many contemporary scientific
disciplines. One of the areas of greatest activity has concerned the
modelling of condensed phases, including liquids solids and amorphous
systems, where simulations have been used to provide insight into
basic physical processes and in more recent years to make reliable
predictions of the properties of the systems simulated. Indeed the
predictive role of simulations is increasingly recognised both in
academic and industrial contexts. Current active areas of application
include topics as diverse as the viscosity of liquids, the conformation
of proteins, the behaviour of hydrogen in metals, the diffusion of
molecules in porous catalysts and the properties of micelles.
This book, which is based on a NATO ASI held at the University
of Bath, UK, from September 5th-17th, 1988, aims to give a general
survey of this field, with detailed discussions both of methodologies
and of applications. The earlier chapters of the book are devoted
mainly to techniques and the later ones to recent simulation studies of
fluids, polymers (including biological molecules) and solids. Special
attention is paid to the role of interatomic potentials which are the
fundamental physical input to simulations. In addition, developments in
computer hardware are considered in depth, owing to the crucial role
which such developments are playing in the expansion of the horizons
of computer modelling studies.
An important feature of this book is the exercises and problems
in the Appendix. These proved to be one of the most successful
aspects of the ASI, and they provide an introduction to and
illustrations of most of the current techniques in the field.
The ASI was made possible by a generous grant from the NATO
Scientific Affairs Division. We are also grateful for the additional
support that was provided by the SERC Collaborative Computer Project
CCP5 and by Chemical Design Ltd. We would further like to
acknowledge the enormous contribution made to the success of the ASI
by the organising committee, including Maurice Leslie, Bill Smith, David
Fincham and David Heyes, by the University of Bath Computing Service
and by graduate students from both Bristol and Bath.
The success of the ASI was also enhanced by the loan of 16
Inmos T800 transputers, and an Active Memory Technology Distributed
Array Processor WAPI. Thanks are due to Andy Jackson, Tony Hey,
Dave Nicolaides and John Alcock.
Finally, we would like to thank Mrs. H. Hitchen for her invaluable
help in the organisation of the meeting and in the preparation of the
proceedings.
C. R. A. Catlow, S. C. Parker, M. P. Allen
vii
Lecturers
Dr. C. L. Brooks, Department of Chemistry, Carnegie-Mellon University,
Pittsburgh, PA 15213, U.S.A.
Prof. C. R. A. Catlow, Department of Chemistry, University of Keele,
Keele, Staffordshire. ST5 5BG, U.K.
Dr. J. Clarke, Department of Chemistry, UMIST, Sackville Street,
Manchester, M60 1QD, U.K.
Dr. D. Evans, Research School of Chemistry, Australian National
University, P.O.Box 4, Canberra, ACT 2600, Australia.
Dr. D. Fincham, Computer Centre, University of Keele, Keele, Staffs
ST5 5BG, U.K.
Dr. D. Frenkel, Fysisck Laboratorium, Rijksuniversiteit, Sorbonnelaan 4,
Utrecht, Netherlands.
Dr. M. J. Gillan, Department of Physics, University of Keele, Keele
Staffs. ST5 5BG,. U.K.
Dr. K. Heinzinger, 6500 Mainz, Mainz Saarstrasse 23, Postfach 3060, \Vest
Germany.
Dr. R. A. Jackson, Department of Chemistry, University of Keele, Keele,
Staffs. ST5 5BG., U.K.
Dr. A.J.C.Ladd, Lawrence Livermore National Laboratory, University of
California, P.O.Box 808, Livermore, California 94550
U.S.A.
Dr. Guilia de Lorenzi, Consiglio Nazionale delle Richerche, Centro di
Fisica Stati Aggregati ed Impianto Ionico, 38050
Povo,Trento Italia.
Dr. M. Meyer, Laboratoire de Physique des Materiaux, Centre National
de la Recherche Scientifique, 1 Place Aristide-Briand,
Bellevue, 92195 Meudon Principal Cedex, France.
Dr. S. C. Parker, Department of Chemistry, University of Bath,
Claverton Down, Bath. BA2 7AY, U.K.
Dr. S. Price, University of Cambridge, University Chemical Laboratory
Lensfield Rd, Cambridge, CB2 lEW, U.K.
Dr. J.P. Ryckaert, Pool de Physique, Faculte de Science, Universite
Libre de Bruxelles, C.P. 223, Bruxelles B 1050 Belgium.
ix
AN INTRODUCTION TO COMPUTER MODELLING OF CONDENSED MATTER
C. R. A. CAT LOW
Department of Chemistry, University of Keele, Keele, Staffs. ST5 5BG.
1. INTRODUCTION
This book is concerned with the computer simulation of condensed
matter at the atomic and molecular levels. Indeed, we can define this
area of simulation as the attempt to model and predict the structural and
dynamical properties of matter using interatomic force models; the latter
clearly play a central role in the field which is reflected by their
extensive coverage in this book.
There are two broad philosophies in contemporary simulation studies.
First, simulations may be used to provide insight and to illuminate the
range and limitations of analytical theories. Much of the earlier work in
this field, especially that concerned wi~h the modelling of hard sphere
systems, is in this category. And there have been impressive
achievements notably the discovery of the long-time tail in the velocity
auto-correlation function in dense fluids, a detailed discussion of which
is given by Ladd in Chapter (3). The second approach uses simulation
as a technique to predict the properties of real systems. One of the
best examples here is the work of Parker and Price (summarised in
Chapter (16» concerning the mantle mineral Mg2Si04 for which there
have been successful predictive simulations of the behaviour of the
material at high temperatures and pressures. This type of application
makes high demands on the quality of the interatomic potential used.
The principle techniques used in the simulation field are energy
minimisation, molecular dynamics and Monte-Carlo methods, all of which
are reviewed in detail in this book. The great majority of calculations
are based on a classical description of the system, but we should note
that the incorporation of quantum effects into simulations is now
possible; and in Chapter (6) Gillan reviews this important development.
Hybrid methods which combine simulation with electronic structure
techniques (for example, the recent work of Car and Parrinello ( 1» are
also of growing importance. In addition, in solid state studies the
embedding of quantum mechanical cluster calculations by a simulated
surrounding structure is becoming increasingly common, as in the recent
studies of Harding et al(2) and Vail et al(3).
A brief introduction to the main features of each simulation
technique is given later in this Chapter; and in the final section we
give a short review of the applications of energy minimisation
C.R.A. Callow et al. (eds.), Computer Modelling of Fluids Polymers and Solids, 1-28.
© 1990 by Kluwer Academic Publishers.
2
techniques, the use of which has been one of the most productive areas
in the simulation field. However, to demonstrate the scope and extent of
the field, we first present a general summary of the more important
areas of application of simulations, which include the following:
(i) Structure and d namics of molecular li uids and solids, where, for
example, in recent studies of diatomic !iquids (e.g. 012)' impressive
agreement between theoretical and experimental properties - both
structural and dynamical - has been achieved. In addition, several
successful studies are reported on phase transitions and dynamical
properties of molecular solids.
(U) Aqueous solutions and electrolytes, for which, as discussed in
Chapter (14), simulations can now yield adequate models for the
structure of water and have given considerable insight into the
structures of hydrated ions.
(iii) Simulation of micelles and colloids where valuable qualitative insight
has been gained into the behaviour of these complex systems.
(iv) Simulation of the structures, mechanical properties and dynamics of
polymers - a very active field in recent years in which simulations using
supercomputers have allowed phenomena such as polymer reptation to be
modelled.
(v) Simulation of complex crystal structures, where energy minimisation
methods can now make very detailed predictions of the structures and
properties of crystals with very large unit cells, e.g. the microporous
zeolites discussed in Chapter (15).
(vi) Defect structures and energies in solids, for which very detailed
predictions are now available for a wide variety of materials as discussed
later in this Chapter.
(vii) Sorption in porous media - an area where there is currently rapid
progress in topics ranging from capillary action to the location by
simulation of reactive molecules in zeolite pores.
(vii) Properties of surfaces, surface defects and impurities and of
surface layers, where calculations have made realistic predictions of
surface structural properties (5), and of the segregation of impurities and
defects to surfaces(6). In addition, elegant dynamical simulation studies
of the behaviour of sorbed layers have also been performed(7).
Simulation studies of grain boundaries and interfaces is also a field of
growing importance.
(ix) Structural properties of metal hydrides where work discussed by
Gillan in Chapter (6), has shown the valuable role of quantum simulation
techniques.
(x) Studies of liquid crystals where simulations have improved our
understanding of the phase diagrams of these systems and of the nature
of order-disorder transitions.
(xi) Structure and dynamics of glasses, for which simulation studies
have been performed on both oxide and halide materials yielding
structural models in good agreement with experiment.
(xii) Studies of viscosity and shear thinning where there have been
several successful studies of the atomic processes responsible for these
macroscopic phenomena.
(xiii) Investigation of protein dynamics, in which there has been an
explosion of work over the past five years which is discussed in detail
in Chapter (12).