THE DL POLY 2 USER MANUAL - KIST computational science

THE DL POLY 2 USER MANUAL - KIST computational science
THE DL POLY 2 USER MANUAL
W. Smith and T.R. Forester,
CCLRC, Daresbury Laboratory,
Daresbury,
Warrington WA4 4AD,
England
Version 2.12 Dec 1999
c CCLRC
1
ABOUT DL POLY
DL POLY is a parallel molecular dynamics simulation package developed at Daresbury
Laboratory by W. Smith and T.R. Forester under the auspices of the former Engineering
and Physical Sciences Research Council (EPSRC) for the EPSRC's Collaborative Computational Project for the Computer Simulation of Condensed Phases (CCP5) and the
Advanced Research Computing Group (ARCG) at Daresbury Laboratory. The package is
the property of The Council for the Central Laboratory of the Research Councils (CCLRC).
DL POLY is issued free under licence to academic institutions pursuing scientic
research of a non-commercial nature. Commercial organisations may be permitted a licence
to use the package after negotiation with the owners. Daresbury Laboratory is the sole
centre for distribution of the package. Under no account is it to be redistributed to third
parties without consent of the owners.
The purpose of the DL POLY package is to provide software for academic research that
is inexpensive, accessible and free of commercial considerations. Users have direct access
to source code for modication and inspection. In the spirit of the enterprise, contributions
in the form of working code are welcome, provided the code is compatible with DL POLY
in regard to its interfaces and programming style and it is adequately documented.
c CCLRC
2
DISCLAIMER
Neither the CCLRC, EPSRC, CCP5 nor any of the authors of the DL POLY 2 package
or its derivatives guarantee that the package is free from error. Neither do they accept
responsibility for any loss or damage that results from its use. Use of the DL POLY 2
package without charge is conned to academic research only. Commercial use is only
permissible following negotiation with Daresbury Laboratory. Users are not entitled to
redistribute the program to third parties.
c CCLRC
3
ACKNOWLEDGEMENTS
DL POLY 2 was developed under the auspices of the Council for the Central Laboratory
of the Research Councils, the Engineering and Physical Sciences Research Council, and the
former Science and Engineering Research Council, under grants from the Computational
Science Initiative and the Science and Materials Computing Committee. The package is
the property of the Council for the Central Laboratory of the Research Councils of the
United Kingdom.
Advice, assistance and encouragement in the development of DL POLY 2 has been given
by many people. We gratefully acknowledge the following:
D. Tildesley, M.J. Gillan, J. Goodfellow, D. Fincham, M. Rodger, W.C. Mackrodt,
J.H.R. Clarke, D. Brown, S. Price, P.J. Durham, P. Sherwood, G.D. Price, S.C. Potter, S.
Melchionna, F. Muller-Plathe, G. Ciccotti, M.W. Smith, A. Simpson, J. Geronowicz, the
HPCI Materials Consortium, the Edinburgh Parallel Computing Centre, the HPCI Centre
at Southampton and the CCP5 community.
We also thank users of previous versions of DL POLY who have passed on helpful
comments.
c CCLRC
4
Manual Notation
In the DL POLY Manual and Reference Manual specic fonts are used to convey specic
meanings:
1. directories - indicates unix le directories
2. routines - indicates subroutines, functions and programs.
3. macros - indicates a macro (le of unix commands)
4. directive - indicates directives or keywords
5. variables - indicates named variables and parameters
6. FILE - indicates lenames.
Contents
1 Introduction
1.1 The DL POLY Package . . . . . . . . . . . . . .
1.2 Functionality . . . . . . . . . . . . . . . . . . . .
1.2.1 Molecular Systems . . . . . . . . . . . . .
1.2.2 Force Field . . . . . . . . . . . . . . . . .
1.2.3 Boundary Conditions . . . . . . . . . . .
1.2.4 Algorithms . . . . . . . . . . . . . . . . .
1.3 Programming Style . . . . . . . . . . . . . . . . .
1.3.1 Programming Language . . . . . . . . . .
1.3.2 Memory Management . . . . . . . . . . .
1.3.3 Target Computers . . . . . . . . . . . . .
1.3.4 Version Control System (CVS) . . . . . .
1.3.5 Required Program Libraries . . . . . . . .
1.3.6 Internal Data Transfer . . . . . . . . . . .
1.3.7 Internal Documentation . . . . . . . . . .
1.3.8 Subroutine/Function Calling Sequences .
1.3.9 FORTRAN Parameters . . . . . . . . . .
1.3.10 Arithmetic Precision . . . . . . . . . . . .
1.3.11 Units . . . . . . . . . . . . . . . . . . . .
1.3.12 Error Messages . . . . . . . . . . . . . . .
1.4 The DL POLY 2 Directory Structure . . . . . . .
1.4.1 The source Sub-directory . . . . . . . . .
1.4.2 The utility Sub-directory . . . . . . . . . .
1.4.3 The data Sub-directory . . . . . . . . . .
1.4.4 The bench Sub-directory . . . . . . . . . .
1.4.5 The execute Sub-directory . . . . . . . . .
1.4.6 The build Sub-directory . . . . . . . . . .
1.4.7 The public Sub-directory . . . . . . . . . .
1.4.8 The respa Sub-directory . . . . . . . . . .
1.4.9 The sdk Sub-directory . . . . . . . . . . .
1.5 Obtaining the Source Code . . . . . . . . . . . .
1.6 DLPROTEIN . . . . . . . . . . . . . . . . . . . .
1.7 Other Information . . . . . . . . . . . . . . . . .
5
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
9
11
12
12
12
13
13
15
15
15
15
16
16
16
16
17
17
17
18
18
19
19
19
19
19
20
20
20
20
20
21
22
22
c CCLRC
2 DL POLY 2 Force Fields and Algorithms
2.1 The DL POLY 2 Force Field . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2 The Intramolecular Potential Functions . . . . . . . . . . . . . . . . . . . .
2.2.1 Bond Potentials . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2.2 Distance Restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2.3 Valence Angle Potentials . . . . . . . . . . . . . . . . . . . . . . . . .
2.2.4 Angular Restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2.5 Dihedral Angle Potentials . . . . . . . . . . . . . . . . . . . . . . . .
2.2.6 Improper Dihedral Angle Potentials . . . . . . . . . . . . . . . . . .
2.2.7 Inversion Angle Potentials . . . . . . . . . . . . . . . . . . . . . . . .
2.2.8 Tethering Forces . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2.9 Frozen Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3 The Intermolecular Potential Functions . . . . . . . . . . . . . . . . . . . .
2.3.1 Short Ranged (van der Waals) Potentials . . . . . . . . . . . . . . .
2.3.2 Metal Potentials . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.3 Three Body Potentials . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.4 Four Body Potentials . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.5 External Fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.4 Long Ranged Electrostatic (Coulombic) Potentials . . . . . . . . . . . . . .
2.4.1 Atomistic and Charge Group Implementation . . . . . . . . . . . . .
2.4.2 Direct Coulomb Sum . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.4.3 Truncated and Shifted Coulomb Sum . . . . . . . . . . . . . . . . .
2.4.4 Coulomb Sum with Distance Dependent Dielectric . . . . . . . . . .
2.4.5 Ewald Sum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.4.6 Smooth Particle Mesh Ewald . . . . . . . . . . . . . . . . . . . . . .
2.4.7 Reaction Field . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.4.8 Dynamical Shell Model . . . . . . . . . . . . . . . . . . . . . . . . .
2.5 Integration algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.5.1 Bond Constraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.5.2 Potential of Mean Force (PMF) Constraints and the Evaluation of
Free Energy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.5.3 Thermostats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.5.4 Gaussian Constraints . . . . . . . . . . . . . . . . . . . . . . . . . .
2.5.5 Barostats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.5.6 Rigid Bodies and Rotational Integration Algorithms . . . . . . . . .
2.5.7 The DL POLY 2 Multiple Timestep Algorithm . . . . . . . . . . . .
2.5.8 The DL POLY 2 RESPA Multiple Timestep Implementation . . . .
2.6 DL POLY Parallelisation . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.6.1 The Replicated Data Strategy . . . . . . . . . . . . . . . . . . . . . .
2.6.2 Distributing the Intramolecular Bonded Terms . . . . . . . . . . . .
2.6.3 Distributing the Nonbonded Terms . . . . . . . . . . . . . . . . . . .
2.6.4 Modications for the Ewald Sum . . . . . . . . . . . . . . . . . . . .
2.6.5 Three Body Forces . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.6.6 Metal Potentials . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6
23
25
27
27
29
29
31
32
35
35
38
39
39
39
42
43
44
45
46
46
47
48
49
50
52
53
54
56
57
59
60
61
62
65
70
71
72
72
73
73
75
75
75
c CCLRC
7
2.6.7 Summing the Atomic Forces . . . . . . . . . . . . . . . . . . . . . . . 75
2.6.8 The RD-SHAKE and Parallel QSHAKE Algorithms . . . . . . . . . 76
3 DL POLY 2 Construction and Execution
3.1 Constructing DL POLY 2 : an Overview . . . . . . . . . . . . . . .
3.1.1 Constructing the Standard Version . . . . . . . . . . . . . .
3.1.2 Constructing Nonstandard Versions . . . . . . . . . . . . .
3.2 Compiling and Running DL POLY 2 . . . . . . . . . . . . . . . .
3.2.1 Compiling the Source Code . . . . . . . . . . . . . . . . . .
3.2.2 Assisting Compilation with the Utility Program parset . .
3.2.3 Running DL POLY 2 . . . . . . . . . . . . . . . . . . . . .
3.2.4 Restarting DL POLY 2 . . . . . . . . . . . . . . . . . . . .
3.3 A Guide to Preparing Input Files . . . . . . . . . . . . . . . . . . .
3.3.1 Inorganic Materials . . . . . . . . . . . . . . . . . . . . . . .
3.3.2 Macromolecules . . . . . . . . . . . . . . . . . . . . . . . . .
3.3.3 Adding Solvent to a Structure . . . . . . . . . . . . . . . .
3.3.4 Analysing Results . . . . . . . . . . . . . . . . . . . . . . .
3.3.5 Choosing Ewald Sum Variables . . . . . . . . . . . . . . . .
3.4 DL POLY 2 Error Processing . . . . . . . . . . . . . . . . . . . . .
3.4.1 The DL POLY 2 Internal Error Facility . . . . . . . . . . .
4 DL POLY 2 Data Files
4.1 The INPUT les . . . . . . .
4.1.1 The CONTROL File .
4.1.2 The CONFIG File . .
4.1.3 The FIELD File . . .
4.1.4 The REVOLD File . .
4.1.5 The TABLE File . . .
4.2 The OUTPUT Files . . . . .
4.2.1 The HISTORY File .
4.2.2 The OUTPUT File . .
4.2.3 The REVCON File . .
4.2.4 The REVIVE File . .
4.2.5 The RDFDAT File . .
4.2.6 The ZDNDAT File . .
4.2.7 The STATIS File . . .
5 DL POLY 2 Examples
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
..
..
..
..
..
..
..
..
..
..
..
..
..
..
.
.
.
.
.
.
.
.
.
.
.
.
.
.
..
..
..
..
..
..
..
..
..
..
..
..
..
..
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
..
..
..
..
..
..
..
..
..
..
..
..
..
..
.
.
.
.
.
.
.
.
.
.
.
.
.
.
..
..
..
..
..
..
..
..
..
..
..
..
..
..
.
.
.
.
.
.
.
.
.
.
.
.
.
.
..
..
..
..
..
..
..
..
..
..
..
..
..
..
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
..
..
..
..
..
..
..
..
..
..
..
..
..
..
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
..
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
..
..
..
..
..
..
..
..
..
..
..
..
..
..
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
78
80
80
81
85
85
89
90
91
91
92
92
93
93
93
96
96
97
99
99
107
110
121
123
125
125
128
131
131
131
132
132
138
5.1 DL POLY Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
5.1.1 Test Cases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
5.1.2 Benchmark Cases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
c CCLRC
8
6 DL POLY 2 Utilities
144
7 DL POLY 2 Subroutines and Functions
150
A The DL POLY 2 Makele
159
B Periodic Boundary Conditions in DL POLY
170
C DL POLY Error Messages and User Action
176
6.1 Miscellaneous Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
6.1.1 parset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
6.1.2 Useful Macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
7.1 Subroutine and Function Specications . . . . . . . . . . . . . . . . . . . . . 152
7.1.1 dl params.inc: The DL POLY Parameters (Include) File . . . . . 152
Chapter 1
Introduction
9
c CCLRC
10
Scope of Chapter
This chapter describes the concept, design and directory structure of DL POLY 2 and how
to obtain a copy of the source code.
c CCLRC
11
1.1 The DL POLY Package
DL POLY 2 (DL POLY [1]) is a package of subroutines, programs and data les, designed
to facilitate molecular dynamics simulations of macromolecules, polymers, ionic systems
and solutions on a distributed memory parallel computer. The rst version was written
on behalf of CCP5 [2] in the eighteen months preceding September 1993 when the (beta)
release appeared. The principal authors at that stage were Bill Smith and Tim Forester at
Daresbury Laboratory. For want of a more imaginative acronym the package was named
DL POLY. The entire DL POLY project was given a major boost by the provision of a
grant in January 1993 from the SERC's Computational Science Initiative. An additional
grant was made by the EPSRC in June 1994 to continue developments in the period 199597. In April 1995 the project came under the Council for the Central Laboratory of the
Research Councils.
There were many reasons for writing the package. The rst reason being to exploit
parallel computing for molecular simulation in the UK. There were several worthy packages
available to the academic community including GROMOS [3], AMBER [4] and X-PLOR
[5], but none of these were designed (as far as we were able to tell) with parallel computers
in mind, (though parallel versions of these programs now exist). We decided then that
the eort involved in devising a new code which had parallelism built into it from the
start would be well spent. This we thought would allow us to adapt the code to new
architectures with greater ease. The second reason was to bring to fruition the high level of
parallel programming expertise at Daresbury Laboratory, and generally within the CCP5
community, stretching back several years, in the area of molecular dynamics. We therefore
thought it worthwhile to tap into this expertise to produce a new package. The third reason
was that we thought it would be valuable to produce a package that was entirely free from
commercial constraints, by which we mean the source code would be available to academic
institutions for adaptation and extension. There would be no restriction preventing users
from examining (and verifying!) the source code. DL POLY was not to be a \black box".
Of course, in a rapidly developing subject area, we cannot guarantee we have everything
a potential user may need. However since this is very much a project endorsed by CCP5,
which serves the UK (and World-Wide) academic community, we are also hopeful that our
users will be inclined to contribute any extensions of the package they devise and so accelerate its development. As it stands, the package has some nice features we believe. While
it is designed for distributed memory parallel machines, we have taken care to ensure that
it can, with minimum modication, be run on the popular workstations. Scaling up a simulation from a small workstation to a massively parallel machine remains straightforward.
This ought to encourage novices to take up parallel computing!
Users are reminded that we are interested in hearing what other features could be
usefully incorporated. We obviously have ideas of our own and CCP5 strongly inuences
developments, but other input would be welcome nevertheless. We also request that our
users respect the integrity of DL POLY 2 source and not pass it on to third parties. We
require that all users of the package register with us, not least because we need to keep
everyone abreast of new developments and discovered bugs. We have developed various
forms of licence, which we hope will ward o litigation (from both sides), without denying
c CCLRC
12
access to genuine scientic users.
In the next section we outline the capabilities of DL POLY 2 as briey as possible. This
is followed by a description of the DL POLY 2 directory structure and how to obtain the
source code from Daresbury Laboratory. Much more information is to be found later in
this manual. Access to all this information and more can be gained via out WWW page:
http://www.dl.ac.uk/TCSC/Software/DL POLY/main.html
1.2 Functionality
The following is a list of the features DL POLY 2 . It is worth reminding users that
DL POLY 2 represents a package rather than a single program, so users should consider
piecing together their own program with the desired functionality. We will however, supply
a consolidated program in the distributed source.
1.2.1 Molecular Systems
DL POLY 2 will simulate the following molecular species:
1. Simple atomic systems and mixtures e.g. Ne, Ar, Kr, etc.
2. Simple unpolarisable point ions e.g. NaCl, KCl, etc.
3. Polarisable point ions and molecules e.g. MgO, H O etc.D
4. Simple rigid molecules e.g. CCl , SF , Benzene, etc.
5. Rigid molecular ions with point charges e.g. KNO , (NH ) SO , etc.
6. Polymers with rigid bonds e.g. CnH n
7. Polymers with rigid bonds and point charges e.g. proteins
8. Macromolecules and biological systems
9. Molecules with exible bonds
10. Silicate glasses and zeolites
11. Simple metals e.g. Al, Ni, Cu etc.
2
4
6
3
2 +2
1.2.2 Force Field
The DL POLY 2 force eld includes the following features:
1. All common forms of non-bonded atom-atom potential;
2. Atom-atom (site-site) Coulombic potentials;
3. Valence angle potentials;
4 2
4
c CCLRC
13
4. Dihedral angle potentials;
5. Inversion potentials;
6. Improper dihedral angle potentials;
7. 3-body valence angle and hydrogen bond potentials;
8. 4-body inversion potentials;
9. Sutton-Chen density dependent potentials (for metals) [6].
The parameters describing these potentials may be obtained, for example, from the
GROMOS [3], DREIDING [7] or AMBER [4] forceeld, which share functional forms. It is
relatively easy to adapt DL POLY 2 to user specic force elds.
1.2.3 Boundary Conditions
DL POLY 2 will accommodate the following boundary conditions;
1. None e.g. isolated polymer in space.
2. Cubic periodic boundaries.
3. Orthorhombic periodic boundaries.
4. Parallelepiped periodic boundaries.
5. Truncated octahedral periodic boundaries.
6. Rhombic dodecahedral periodic boundaries.
7. Slab (x,y periodic, z nonperiodic).
8. Hexagonal prism periodic boundaries.
These are describe in detail in Appendix B.
1.2.4 Algorithms
1.2.4.1 Parallel Algorithms
DL POLY 2 exclusively employs the Replicated Data parallelisation strategy [8, 9].
c CCLRC
1.2.4.2 Molecular Dynamics Algorithms
14
The DL POLY 2 MD algorithms are all couched in the form of the Verlet Leapfrog integration algorithm [10]. NVE, NVT, NPT and NT ensembles are available, with a selection
of thermostats and barostats. A parallel version of the SHAKE algorithm [11] called RDSHAKE is used for bond constraints [9]. Fincham's implicit quaternion algorithm (FIQA)
[12] is available for rigid molecular species. Rigid molecular species linked by rigid bonds
are handled with an algorithm of our own devising, called the QSHAKE algorithm [13].
The following MD algorithms are available:
1. Verlet leapfrog;
2. Verlet leapfrog with RD-SHAKE;
3. Rigid molecules with FIQA and RD-SHAKE;
4. Linked rigid molecules with QSHAKE [13];
5. Berendsen constant T algorithm with Verlet or RD-SHAKE [14];
6. Evans constant T algorithm with Verlet or RD-SHAKE [15];
7. Hoover constant T algorithm with Verlet or RD-SHAKE [16];
8. Berendsen constant T algorithm with FIQA and RD-SHAKE [14];
9. Berendsen constant T algorithm with QSHAKE [14];
10. Hoover constant T algorithm with FIQA and RD-SHAKE [16];
11. Hoover constant T algorithm with QSHAKE [16];
12. Berendsen constant T,P algorithm with RD-SHAKE [14];
13. Berendsen constant T, algorithm with RD-SHAKE [14];
14. Hoover constant T,P algorithm with RD-SHAKE [16];
15. Hoover constant T, algorithm with RD-SHAKE [16];
16. Berendsen constant T,P algorithm with FIQA and RD-SHAKE [14];
17. Berendsen constant T,P algorithm with QSHAKE [14];
18. Berendsen constant T, algorithm with FIQA and RD-SHAKE [14];
19. Berendsen constant T, algorithm with QSHAKE [14];
20. Hoover constant T,P algorithm with FIQA and RD-SHAKE [16];
21. Hoover constant T,P algorithm with QSHAKE [16];
c CCLRC
15
22. Hoover constant T, algorithm with FIQA and RD-SHAKE [16];
23. Hoover constant T, algorithm with QSHAKE [16];
A variant of DL POLY 2 that handles the time reversible, multiple timestep RESPA
algorithm [17, 18] is also available for atomic systems and rigid ion systems [19], but it is
not applicable to systems which have rigid body molecules or constraints.
1.3 Programming Style
The programming style of DL POLY 2 is intended to be as uniform as possible. The
following stylistic rules apply throughout. Potential contributors of code are requested to
note the stylistic convention.
1.3.1 Programming Language
Versions of DL POLY 2 prior to 2.11 are written exclusively in FORTRAN 77. Versions of
DL POLY 2 from 2.11 contain extensions written in FORTRAN 90.
1.3.2 Memory Management
Since version 2.11 of DL POLY 2 , the major array dimensions are calculated at the time of
execution and the associated arrays created through the dynamic array allocation features
of FORTRAN 90. In versions prior to 2.11, array dimensions are xed at compilation time
and dened by FORTRAN PARAMETER statements
1.3.3 Target Computers
DL POLY 2 is targeted towards distributed memory parallel computers. However, versions
of the program for serial computers are easily produced. To facilitate this all machine
specic calls are located in dedicated FORTRAN routines, to permit substitution by appropriate alternatives, or even deletion.
DL POLY 2 will run on the the following computers:
1. Cray T3D
2. Cray T3E
3. DEC Alpha
4. HP 9000 Series
5. Hitachi SR2201
6. IBM RS6000
7. IBM SP/2
c CCLRC
16
8. Intel iPSC/860
9. SUN SPARC and ULTRA SPARC.
10. Silicon Graphics machines (all kinds).
Porting of DL POLY 2 to these and other machines requires PVM or MPI message
passing tools, with the exception of Intel distributed memory machines.
1.3.4 Version Control System (CVS)
DL POLY 2 was developed with the aid of the CVS version control system. We strongly
recommend that users of DL POLY 2 adopt this system for code development, particularly
where several users access the same source code. For information on CVS please contact:
info cvs [email protected]:ai:mit:edu
1.3.5 Required Program Libraries
DL POLY 2 is, for the most part, self contained and does not require access to many
additional program libraries. The required program libraries for parallel execution are
either PVM or MPI (we recommend the latter). The other exception is the need for 3D
Fast Fourier Transform (FFT) routines in the Smooth Particle Mesh Ewald (SPME) method
introduced in Version 2.12. For applications on Cray T3E/D and IBM SP/2 computers the
required routines are readily available in the scientic subroutine libraries (routines cct3d
and dcft3 respectively). For other machines however, we have assumed the public domain
FFT routine twnd t is available. The standard Ewald sum remains available for users
without access to a suitable substitute.
1.3.6 Internal Data Transfer
As a general policy, there should be NO COMMON blocks in DL POLY 2 . All nonlocal
and large local arrays are passed as subroutine arguments. It follows that there should be
no BLOCK DATA.
However the introduction of the FORTRAN 90 dynamic array allocation features in
DL POLY 2 version 2.11 has required the creation of a named COMMON block (/params/)
to facilitate the passing of the array dimensions between subroutines. (Formerly the dimensions had been dened as FORTRAN parameters and incorporated in each subroutine
through the include le dl params.inc.) The COMMON block /params/ is dened in the
new version of the include le dl params.inc and is included in almost all subroutines.
Additional COMMON blocks are also required to facilitate inter-node communication
via MPI and PVM.
1.3.7 Internal Documentation
All subroutines are supplied with a header block of FORTRAN COMMENT records giving:
c CCLRC
17
1. The name of the author and/or modifying author
2. The version number or date of production
3. A brief description of the function of the subroutine
4. A copyright statement
5. A CVS revision number and associated data.
Elsewhere FORTRAN COMMENT cards are used liberally.
1.3.8 Subroutine/Function Calling Sequences
The variables in the subroutine arguments are specied in the order:
1. logical and logical arrays
2. character and character arrays
3. integer
4. real and complex
5. integer arrays
6. real and complex arrays
This is admittedly arbitrary, but it really does help with error detection.
1.3.9 FORTRAN Parameters
All parameters dened by the FORTRAN parameter statements are specied in the include
le: dl params.inc, which is included at compilation time in all subroutines requiring the
parameters. All parameters specied in dl params.inc are described by one or more
comment cards.
Note that since the implementation of FORTRAN 90 memory management in Version
2.11, the dl params.inc le also contains the COMMON block /params/, described above.
1.3.10 Arithmetic Precision
All real variables and parameters are specied in 64-bit precision (i.e real*8).
c CCLRC
18
1.3.11 Units
Internally all DL POLY 2 subroutines and functions assume the use of the following dened
molecular units:
1. The unit of time (to) is 1 10 seconds (i.e. picoseconds).
2. The unit of length (`o ) is 1 10 metres (i.e. Angstroms).
3. The unit of mass (mo) is 1:6605402 10 kilograms (i.e. atomic mass units).
4. The unit of charge (qo) is 1:60217733 10 coulombs (i.e. unit of proton charge).
5. The unit of energy (Eo = mo(`o =to) ) is 1:6605402 10 Joules (10 kJ mol ).
6. The unit of pressure (Po = Eo`o ) is 1:6605402 10 Pascal (166:05402 bar).
7. Planck's constant (h) which is 6:350780668 Eoto.
In addition the following conversion factors are used:
The coulombic conversion factor (o) is:
"
#
1
qo
o =
= 138935:4835
Eo 4o `o
such that:
UMKS = Eo o UInternal
Where U represents the conguration energy.
The Boltzmann factor (kB ) is 0:831451115 EoK , such that:
T = Ekin=kB
represents the conversion from kinetic energy (in internal units) to temperature (in Kelvin).
Note: In the DL POLY 2 OUTPUT le, the print out of pressure is in units of kbars at
all times. The unit of energy is either DL POLY 2 units specied above, or in other units
specied by the user at run time. The default is DL POLY units.
12
10
27
19
2
23
3
1
7
2
1
1.3.12 Error Messages
All errors detected by DL POLY 2 during run time initiate a call to the subroutine error,
which prints an error message in the standard output le and terminates the program. All
terminations of the program are global (i.e. every node of the parallel computer will be
informed of the termination condition and stop executing.)
In addition to terminal error messages, DL POLY 2 will sometimes print warning messages. These indicate that the code has detected something that is unusual or inconsistent.
The detection is non-fatal, but the user should make sure that the warning does represent
a harmless condition.
c CCLRC
19
1.4 The DL POLY 2 Directory Structure
The entire DL POLY 2 package is stored in a Unix directory structure. The topmost
directory is named dl poly nn, where nn is a generation number. Beneath this directory
are several sub-directories named: source; utility; data; bench; execute; build, public, respa,
and sdk. Briey, the content of each sub-directory is as follows:
sub-directory
contents
source
utility
data
bench
execute
build
public
sdk
respa
primary subroutines for the DL POLY 2 package
subroutines, programs and example data for all utilities
example input and output les for DL POLY 2
large test cases suitable for benchmarking
the DL POLY 2 run-time directory
makeles to assemble and compile DL POLY 2 programs
directory of routines donated by DL POLY 2 users
directory of routines used to construct the DL POLY 2 GUI
directory of routines used to construct the DL POLY 2 RESPA program
A more detailed description of each sub-directory follows.
1.4.1 The source Sub-directory
In this sub-directory all the essential source code for DL POLY 2 , excluding the utility
software. In keeping with the `package' concept of DL POLY 2 , it does not contain any
complete programs; these are assembled at compile time using an appropriate makele.
The subroutines in this sub-directory are documented in chapter 7.
1.4.2 The utility Sub-directory
This sub-directory stores all the utility subroutines, functions and programs in DL POLY 2
, together with examples of data. The various routines in this sub-directory are documented
in chapter 6 of this manual. Users who devise their own utilities are advised to store them
in the utility sub-directory.
1.4.3 The data Sub-directory
This sub-directory contains examples of input and output les for testing the released
version of DL POLY 2 . The examples of input data are copied into the execute subdirectory when a program is being tested. The test cases are documented in chapter 5.
1.4.4 The bench Sub-directory
This directory contains examples of input and output data for DL POLY 2 that are suitable
for benchmarking DL POLY 2 on large scale computers. These are described in chapter 5.
c CCLRC
20
1.4.5 The execute Sub-directory
In the supplied version of DL POLY 2 , this sub-directory contains only a few macros for
copying and storing data from and to the data sub-directory and for submitting programs
for execution. (These are decribed in section 6.1.2.) However when a DL POLY 2 program
is assembled using its makele, it will be placed in this sub-directory and will subsequently
be executed from here. The output from the job will also appear here, so users will nd
it convenient to use this sub-directory if they wish to use DL POLY 2 as intended. (The
experienced user is not absolutely required to use DL POLY 2 this way however.)
1.4.6 The build Sub-directory
This sub-directory contains the standard makeles for the creation (i.e. compilation and
linking) of the DL POLY 2 simulation programs. The makeles supplied select the appropriate subroutines from the source sub-directory and deposit the executable program in
the execute directory. The user is advised to copy the appropriate makele into the source
directory, in case any modications are required. The copy in the build sub-directory will
then serve as a backup.
1.4.7 The public Sub-directory
This sub-directory contains assorted routines donated by DL POLY users. Potential users
should note that these routines are unsupported and come without any guarantee
or liability whatsoever. They should be regarded as potentially useful resources to be
hacked into shape as needed by the user. This directory is available from the CCP5 Program
Library by direct FTP(see below).
1.4.8 The respa Sub-directory
This sub-directory rst appeared in Version 2.12, when the RESPA subroutines were separated from the source directory to make construction of the RESPA program simpler.
The respa sub-directory consists of the subroutines unique to the RESPA application. The
RESPA makele (Makele respa in the build sub-directory has been designed to gather the
additional subroutines required from the source sub-directory at compile time. It is not
necessary for the user to copy them over.
1.4.9 The sdk Sub-directory
The DL POLY 2 Graphical User Interface (GUI) is based on the CERIUS Visualiser from
Molecular Simulations Inc. The subroutines written by Daresbury Laboratory are to be
found in this sub-directory. However, alone they are insuÆcient to create a working GUI,
but DL POLY 2 users who have access to MSI's SDK (Software Development Kit) will
be able to use these subroutines as a starting place for constructing, and modifying, the
DL POLY 2 GUI. For DL POLY 2 users without this resource, a compiled version of the
GUI is available for Silicon Graphics computers running the CERIUS Visualiser (version
3.5). See the document \The DL POLY 2 Graphical User Interface", by W. Smith [20].
2
2
c CCLRC
21
1.5 Obtaining the Source Code
To obtain a copy of DL POLY 2 it is rst necessary to obtain a licence from Daresbury
Laboratory. A copy of the licence form may be obtained in two ways: either by selecting
the licence button on the World Wide Web page:
(http://www.dl.ac.uk/TCSC/Software/DL POLY/main.html)
and downloading and printing the le; or by using FTP to copy the postscript le from the
CCP5 Program Library at Daresbury Laboratory in the following manner:
1. move to the desired directory on YOUR machine,
2. type: ftp ftp.dl.ac.uk
3. enter userid: anonymous
4. enter passwd: (use your name and site)
5. change to the CCP5 directory: cd ccp5
6. change to the DL POLY directory: cd DL POLY
7. type: binary
8. type: get LICENCE.ps.Z
9. type: quit
The licence le will need to be uncompressed (using the unix uncompress command) before
printing. Note that there are two versions of the licence available; one for single academic
users (with perhaps one or two postgraduate students); and one for academic groups (with
perhaps several research sta, including postdoctoral and permanent sta.) Choose the
one most suitable for you.
Once you have obtained the licence form you should sign it and return it to the following
address.
Dr. W. Smith
DL_POLY Program Library
Computational Science and Engineering Department
CCLRC Daresbury Laboratory
Daresbury
Warrington WA4 4AD
England
Please return the licenceby post please; FAXes are not acceptable to our Contracts Department. When the signed licence has been received DL POLY 2 source code will be sent
by ftp. We will need to contact you about this procedure, so please supply your e-mail
address. Please note we cannot create accounts on any of our machines for this purpose.
c CCLRC
22
The DL POLY 2 User Manual is freely available via World Wide Web or ftp, in the
same manner as the licence form. The much larger DL POLY 2 Reference Manual will be
available by the above ftp procedure only.
Daresbury Laboratory is the sole centre for the distribution of DL POLY 2 and copies
obtained from elsewhere will be regarded as illegal and will not be supported.
1.6 DLPROTEIN
DLPROTEIN is a further development of DL POLY that was written by S. Melchionna
and S. Cozzini (with assistance from M. Venturoli and Antonella Luise), specically to
handle protein simulations. In agreement with the authors the package is also available
from Daresbury Laboratory under the same terms as DL POLY . Though having much in
common with DL POLY it represents a major rewrite, with many features not present in
the original code (and with many original features missing). It is therefore documented
separately from DL POLY and users should consult the appropriate manual: \The DLPROTEIN User Manual" by S. Melchionna and S. Cozzini [21], which also available from
Daresbury Laboratory.
Our thanks go to S. Melchionna and S. Cozzini and their collaborators for generously
making DLPROTEIN available to us and for extending that availablity to DL POLY 2
users.
1.7 Other Information
The DL POLY 2 web page: http://ftp.dl.ac.uk/TCS/Software/DL POLY/main.html provides additional information in the form of
1. Access to all documentation (including licences);
2. Frequently asked questions;
3. Bug reports.
Daresbury Laboratory also maintains two DL POLY 2 associated electronic mailing lists:
1. dl poly news - to which all registered DL POLY 2 users are automatically subscribed.
It is via this list that error reports and announcements of new versions are made. If
you are a DL POLY 2 user, but not on this list you may request to be added. Contact
[email protected]
2. dl poly mail - is a group list which is available to DL POLY 2 users by request. Its
purpose is to allow DL POLY 2 users to broadcast information and queries to each
other. To subscribe to this list send a mail message to [email protected] with the
one-line message:
subscribe dl poly mail
Subsequent messages may be broadcast by e-mailing to the address: dl poly [email protected]
Chapter 2
DL POLY 2 Force Fields and
Algorithms
23
c CCLRC
24
Scope of Chapter
This chapter describes the interaction potentials and simulation algorithms coded into
DL POLY 2 .
c CCLRC
25
2.1 The DL POLY 2 Force Field
The force eld is the set of functions needed to dene the interactions in a molecular system.
These may have a wide variety of analytical forms, with some basis in chemical physics,
which must be parameterised to give the correct energy and forces. A huge variety of
forms is possible and for this reason the DL POLY 2 force eld is designed to be adaptable.
While it is not supplied with its own force eld parameters, many of the functions familiar
to GROMOS [3] DREIDING [7] and AMBER [4] users have been coded in the package,
as well as less familiar forms. In addition DL POLY 2 retains the possibility of the user
dening additional potentials.
In DL POLY 2 the total conguration energy of a molecular system may be written as:
U (r 1 ; r 2 ; : : : ; r N )
=
NX
bond
(
)
Ubond ibond ; ra ; rb
ibond =1
NX
angle
Uangle iangle ; ra ; rb ; rc
iangle =1
NX
dihed
Udihed idihed ; ra ; rb ; rc ; rd
idihed =1
NX
inv
Uinv iinv ; ra ; rb ; rc ; rd
iinv =1
NX1 X
N
Upair i; j; jr i rj j
i=1 j>i
NX2 NX1 X
N
U3 body i; j; k; r i ; rj ; rk
i=1 j>i k>j
NX3 NX2 NX1 X
N
U4 body i; j; k; n; r i ; rj ; rk ; rn
i=1 j>i k>j n>k
N
X
Uextn i; r i ; v i
i=1
+
(
+
(
+
)
)
(
+
)
(
)
(
+
+
+
)
(
(
)
)
(2.1)
where Ubond ; Uangle; Udihed; Uinv , Upair , U body and U body are empirical interaction
functions representing chemical bonds, valence angles, dihedral angles, inversion angles,
pair-body, three-body and four-body forces respectively. The rst four are regarded by
DL POLY 2 as intra-molecular interactions and the next three as inter-molecular interactions. The nal term Uextn represents an external eld potential. The position vectors
ra ; rb ; rc and rd refer to the positions of the atoms specically involved in a given interaction. (Almost universally, it is the dierences in position that determine the interaction.)
The numbers Nbond ; Nangle, Ndihed and Ninv refer to the total numbers of these respective
interactions present in the simulated system, and the indices ibond ; iangle; iinv and idihed
uniquely specify an individual interaction of each type. It is important to note that there is
3
4
c CCLRC
26
no global specication of the intramolecular interactions in DL POLY 2 - all bonds, valence
angles and dihedrals must be individually cited.
The indices i, j (and k, n) appearing in the pair-body (and three or four-body) terms
indicate the atoms involved in the interaction. There is normally a very large number
of these and they are therefore specied according to atom types rather than indices. In
DL POLY 2 it is assumed that the pair-body terms arise from van der Waals and/or electrostatic (Coulombic) forces. The former are regarded as short ranged interactions and the
latter as long ranged. Long range forces require special techniques to evaluate accurately
(see section 2.4.) In DL POLY 2 the three-body terms are restricted to valence angle and
H-bond forms. The nonbonded, three-body and four-body interactions are globally specied
according to the types of atoms involved. DL POLY 2 also has the ability to handle metals
via density dependent functions (see below). Though essentially many-body potentials they
are handled in DL POLY 2 as special forms of pair potential.
In DL POLY 2 the intramolecular bonded terms are handled using bookkeeping arrays,
which specify the atoms involved in a particular interaction and point to the appropriate
arrays of parameters that dene the potential. The calculation of bonded forces therefore
follows the simple scheme:
1. Every atom in the simulated system is assigned a unique index number from 1 to N ;
2. Every intramolecular bonded term Utype in the system has a unique index number
itype : from 1 to Ntype where type represents a bond, angle or dihedral.
3. A pointer array keytype (ntype; itype ) carries the indices of the specic atoms involved
in the potential term labelled itype . The dimension ntype will be 2; 3 or 4, if the term
represents a bond, valence angle, dihedral/inversion.
4. The array keytype(ntype; itype ) is used to identify the atoms in a bonded term and the
appropriate form of interaction and thus to calculate the energy and forces.
DL POLY 2 calculates the nonbonded pair interactions using a Verlet neighbour list
[10] which is reconstructed at intervals during the simulation. This list records the indices
of all `secondary' atoms within a certain radius of each `primary' atom; the radius being
the cut-o radius (rcut) normally applied to the nonbonded potential function, plus an
additional increment (rcut ). The neighbour list removes the need to scan over all atoms
in the simulation at every timestep. The larger radius (rcut + rcut) means the same list
can be used for several timesteps without requiring an update. The frequency at which the
list must be updated depends on the thickness of the region rcut. DL POLY 2 has two
methods for constructing the neighbour list: the rst is based on the Brode-Ahlrichs scheme
[22] and is used when rcut is large in comparison with the simulation cell; the second uses
the link-cell algorithm [23] when rcut is relatively small. The potential energy and forces
arising from the nonbonded interactions are calculated using interpolation tables.
A complication in the construction of the Verlet neighbour list for macromolecules is
the concept of excluded atoms, which arises from the need to exclude certain atom pairs
from the overall list. Which atom pairs need to be excluded is dependent on the precise
c CCLRC
27
nature of the force eld model, but as a minimum atom pairs linked via extensible bonds
or constraints and atoms (grouped in pairs) linked via valence angles are probable candidates. The assumption behind this requirement is that atoms that are formally bonded in
a chemical sense, should not participate in nonbonded interactions. (However this is not
a universal requirement of all force elds.) The same considerations are needed in dealing
with charged excluded atoms.DL POLY 2 has several subroutines available for constructing
the Verlet neighbour list, while taking care of the excluded atoms (see chapters 3 and 7 for
further information.)
Three- and four-body nonbonded forces are assumed to be short ranged and therefore
calculated using the link-cell algorithm [23]. They ignore the possibility of there being any
excluded interactions involving the atoms concerned.
Throughout this section the description of the force eld assumes the simulated system
is described as an assembly of atoms. This is for convenience only and readers should
understand that DL POLY 2 does recognise molecular entities, dened either through constraint bonds or rigid bodies. In the case of rigid bodies, the atomic forces are resolved into
molecular forces and torques. These matters are discussed in greater detail later in sections
2.5.1 and 2.5.6).
Note that the subroutines mentioned in the subsections of this chapter are described in
greater detail in chapter 7.
2.2 The Intramolecular Potential Functions
In this section we catalogue and describe the forms of potential function available in
DL POLY 2 The key words required to select potential forms are given in brackets ()
before each denition. The derivations of the atomic forces, virial and stress tensor are also
outlined.
2.2.1 Bond Potentials
i
j
r
ij
The interatomic bond vector.
The bond potentials describe explicit bonds between specied atoms. They are functions
of the interatomic distance only. The potential functions available are as follows.
1. Harmonic bond: (harm)
1
(2.2)
U (rij ) = k(rij ro ) ;
2
2
c CCLRC
28
2. Morse potential: (mors)
U (rij ) = Eo [f1 exp( k(rij
3. 12-6 potential bond: (12-6)
A
rij12
U (rij ) =
!
B
rij6
4. Restrained harmonic: (rhrm)
1
U (rij ) = k(rij ro )
jrij
2
1
U (rij ) = krc + krc (jrij ro j
2
5. Quartic potential: (quar)
rc )
2
k
2 (rij
ro )2 +
k0
3 (rij
!
1];
(2.3)
;
(2.4)
ro j rc;
2
U (rij ) =
ro ))g2
ro )3 +
jrij roj > rc;
k00
(2.5)
(2.6)
(2.7)
4 (rij ro ) :
In these formulae rij is the distance between atoms labelled i and j :
rij = jrj ri j;
(2.8)
where r` is the position vector of an atom labelled `.
The force on the atom j arising from a bond potential is obtained using the general
formula:
"
#
1
@
U (rij ) r ;
(2.9)
f =
4
1
j
rij @rij
ij
The force f i acting on atom i is the negative of this.
The contribution to be added to the atomic virial is given by
W = rij f j ;
(2.10)
with only one such contribution from each bond.
The contribution to be added to the atomic stress tensor is given by
= rij fj ;
(2.11)
where and indicate the x; y; z components. The atomic stress tensor derived in this
way is symmetric.
In DL POLY 2 bond forces are handled by the routine bndfrc.
1
Note: some DL POLY 2 routines may use the convention that rij = ri
rj .
c CCLRC
29
2.2.2 Distance Restraints
In DL POLY 2 distance restraints, in which the separation between two atoms, is maintained around some preset value r is handled as a special case of bond potentials. As a
consequence distance restraints may be applied only between atoms in the same molecule.
Unlike with application of the \pure" bond potentials, the electrostatic and van der Waals
interactions between the pair of atoms are still evaluated when distance restraints are applied. All the potential forms of the previous section are avaliable as distance restraints,
although they have dierent key words:
1. Harmonic potential: (-hrm)
2. Morse potential: (-mrs)
3. 12-6 potential bond: (-126)
4. Restrained harmonic: (-rhm)
5. Quartic potential: (-qur)
In DL POLY 2 distance restraints are handled by the routine bndfrc.
0
2.2.3 Valence Angle Potentials
j
k
rij
θ
rik
i
The valence angle and associated vectors
The valence angle potentials describe the bond bending terms between the specied
atoms. They should not be confused with the three body potentials described later, which
are dened by atom types rather than indices.
1. Harmonic: (harm)
k
(2.12)
U (jik ) = (jik ) ;
2
2. Quartic: (quar)
0
U (jik ) =
k
2 (jik
0 )2 +
k0
3 (jik
2
0 )3 +
k00
4 (jik
0 )4 ;
(2.13)
c CCLRC
30
3. Truncated harmonic: (thrm)
k
0 )2 exp[ (rij8 + rik8 )=8 ];
(2.14)
2 (jik
0 )2 exp[ (rij =1 + rik =2 )];
(2.15)
U (jik ) =
2 (jik
4. Screened harmonic: (shrm)
U (jik ) =
k
5. Screened Vessal[24]: (bvs1)
U (jik )
h
= 8( k ) ( ) (jik
jik
exp[ (rij = + rik = )];
0
2
)2
2
1
i2 (2.16)
2
6. Truncated Vessal[25]: (bvs2 )
a (
U (jik ) = k[jik
2) a2 a
jik ) (jik + (jik ) ( ) ]exp[ (rij + rik )= ]:
0
0
2
2
2
0
0
3
8
1
8
8
(2.17)
7. Harmonic cosine: (hcos)
U (jik ) =
8. Cosine: (cos)
k
2 (cos(jik )
cos(0 ))2
U (jik ) = A[1 + cos(mjik
Æ)]
(2.18)
(2.19)
In these formulae jik is the angle between bond vectors rij and rik :
jik = cos
(
1
rij rik
rij rik
)
(2.20)
In DL POLY 2 the most general form for the valence angle potentials can be written
U (jik ; rij ; rik ) = A(jik )S (rij )S (rik )
(2.21)
where A() is a purely angular function and S (r) is a screening or truncation function. All
the function arguments are scalars. With this reduction the force on an atom derived from
the valence angle potential is given by:
as:
f` =
@
U ( ; r ; r );
@r` jik ij ik
(2.22)
c CCLRC
31
with atomic label ` being one of i; j; k and indicating the x; y; z component. The derivative
is
@
@
U (jik ; rij ; rik ) = S (rij )S (rik ) A(jik )
@r
@r
`
`
A(jik )S (rik )(Æ`j
rij @
S (r )
rij @rij ij
r @
S (r );
Æ`i ) ik
rik @rik ik
Æ`i )
(2.23)
with Æab = 1 if a = b and Æab = 0 if a 6= b. In the absence of screening terms S (r), this
formula reduces to:
@
@
U (jik ; rij ; rik ) =
A( )
(2.24)
@r`
@r` jik
The derivative of the angular function is
(
)
(
)
@
1
@
@ rij rik
A( ) =
(2.25)
@r` jik
sin(jik ) @jik A(jik ) @r` rij rik ;
with
(
)
rij
@ rij rik
rik
=
(
Æ
Æ
)
+
(
Æ
Æ
)
`j
`i
`k
`i
@r r r
r r
r r
A(jik )S (rij )(Æ`k
j
ij ik
(
ij ik
cos(jik ) (Æ`j
Æ`i )
rij
ij ik
r
Æ`i ) ik
2
rik
)
+ (Æ`k
(2.26)
The atomic forces are then completely specied by the derivatives of the particular functions
A() and S (r).
The contribution to be added to the atomic virial is given by
W = (rij f j + rik f k )
(2.27)
It is worth noting that in the absence of screening terms S(r), the virial is zero [26].
The contribution to be added to the atomic stress tensor is given by
f
= rij fj + rik
(2.28)
k
and the stress tensor is symmetric.
In DL POLY 2 valence forces are handled by the routine angfrc.
2.2.4 Angular Restraints
rij2
In DL POLY 2 angle restraints, in which the angle subtended by a triplet of atoms, is
maintained around some preset value is handled as a special case of angle potentials. As
a consequence angle restraints may be applied only between atoms in the same molecule.
Unlike with application of the \pure" angle potentials, the electrostatic and van der Waals
interactions between the pair of atoms are still evaluated when distance restraints are
applied. All the potential forms of the previous section are avaliable as angular restraints,
although they have dierent key words:
0
c CCLRC
1.
2.
3.
4.
5.
6.
7.
8.
32
Harmonic: (-hrm)
Quartic: (-qur)
Truncated harmonic: (-thm)
Screened harmonic: (-shm)
Screened Vessal[24]: (-bv1)
Truncated Vessal[25]: (-bv2)
Harmonic cosine: (-hcs)
Cosine : (-cos)
2.2.5 Dihedral Angle Potentials
i
n
r ij
Φ
rkn
k
j
r jk
The dihedral angle and associated vectors
The dihedral angle potentials describe the interaction arising from torsional forces in
molecules. (They are sometimes referred to as torsion potentials.) They require the specication of four atomic positions. The potential functions available in DL POLY 2 are as
follows.
1. Cosine potential: (cos)
U (ijkn ) = A [1 + cos(mijkn Æ)]
(2.29)
2. Harmonic: (harm)
1
2
U (ijkn) = k(ijkn 0 )2
3. Harmonic cosine: (hcos)
U (ijkn) =
k
2 (cos(ijkn)
cos(0 ))2
(2.30)
(2.31)
c CCLRC
33
4. Triple cosine: (cos3)
1
1
1
U () = A (1 + cos()) + A (1 cos(2)) + A (1 + cos(3))
(2.32)
2
2
2
In these formulae ijkn is the dihedral angle dened by
ijkn = cos fB (rij ; rjk ; rkn)g;
(2.33)
with
)
(
(
rij rjk ) (rjk rkn)
(2.34)
B (rij ; rjk ; rkn ) =
jrij rjk jjrjk rknj :
With this denition, the sign of the dihedral angle is positive if the vector product (rij rjk ) (rjk rkn ) is in the same direction as the bond vector rjk and negative if in the
opposite direction.
The force on an atom arising from the dihedral potential is given by
1
2
3
1
f` =
@
U (ijkn );
@r`
(2.35)
with ` being one of i; j; k; n and one of x; y; z. This may be expanded into
(
)
1
@
@
@
U (ijkn) =
U (ijkn) B (rij ; rjk ; rkn ):
@r`
sin(ijkn) @ijkn
@r`
The derivative of the function B (rij ; rjk ; rkn) is
@
@
1
B (r ; r ; r ) =
f(r r ) (r r )g
@r`
with
ij
jk kn
jrij rjk jjrjk rknj @r`
(
ij
jk
jk
kn
(2.36)
(2.37)
)
cos(ijkn)
1
2
jrij rjk j
@
jrij rjk j2 + jr 1 r j2 @[email protected] jrjk rknj2 ;
2 @r jk
kn
`
`
@
f(r r ) (rjk rkn)g
@r` ij jk
@
jr r j2
@r` ij jk
=
rij ([rjk rjk ] (Æ`k
Æ`n ) + [rjk rkn ] (Æ`k
Æ`j )) +
([r r ] (Æ
rjk
ij jk `n Æ`k ) + [r jk rkn ] (Æ`j
Æ`i )) +
([r r ] (Æ
rkn
ij jk `k
Æ`j ) + [rjk rjk ] (Æ`i Æ`j )) +
2rjk [rij rkn](Æ`j
Æ`k );
= 2rij ([rjk rjk ] (Æ`j
2rjk ([rij rij ] (Æ`k
Æ`i ) + [rij rjk ] (Æ`j
(2.38)
Æ`k )) +
Æ`j ) + [rij rjk ] (Æ`i Æ`j ));
(2.39)
c CCLRC
@
jr r j2
@r` jk kn
34
([r r ] (Æ
= 2rkn
jk jk `n
2rjk ([rknrkn] (Æ`k
Æ`k ) + [rjk rkn ] (Æ`j
Æ`j ) + [rjk rkn ] (Æ`k
Where we have used the the following denition:
X
[a b] = (1 Æ )a b :
Æ`k )) +
Æ`n )):
(2.40)
(2.41)
Formally, the contribution to be added to the atomic virial is given by
W=
4
X
i=1
(2.42)
ri f i
However it is possible to show (by tedious algebra using the above formulae, or more
elegantly by thermodynamic arguments [26],) that the dihedral makes no contribution to
the atomic virial.
The contribution to be added to the atomic stress tensor is given by
p + r p
= rij pi + rjk
(2.43)
kn n
jk
n
o
cos(ijkn) r g + r g + r h + r h ;
ij i
jk k
jk j
kn n
2
with
[r r ]
pi = (rjk
(2.44)
jk kn rkn [r jk rjk ] )=(jr ij rjk jjr jk r kn j)
pn = (rjk [rij rjk ] rij [rjk rjk ] )=(jr ij rjk jjrjk rkn j)
(2.45)
pjk = (rij [rjk rkn] + rkn[rij rjk ] 2rjk [rij rkn] )=(jr ij rjk jjrjk rknj) (2.46)
[r r ] )=jr r j
(2.47)
gi = 2(rij [rjk rjk ] rjk
ij jk ij
jk
gk = 2(rjk [rij rij ] rij [rij rjk ] )=jrij rjk j
(2.48)
[r r ]
hj = 2(rjk
(2.49)
kn kn rkn [r jk rkn ] )=jr jk r kn j
hn = 2(rkn [rkn rkn ] rjk [rjk rkn ] )=jr jk rknj
(2.50)
The sum of the diagonal elements of the stress tensor is zero (since the virial is zero) and
the matrix is symmetric.
Lastly, it should be noted that the above description does not take into account the
possible inclusion of distance-dependent 1-4 interactions, as permitted by some force elds.
Such interactions are permissible in DL POLY 2 and are described in the section on pair
potentials below. DL POLY 2 also permits scaling of the 1-4 interactions by a numerical
factor. 1-4 interactions do, of course, contribute to the atomic virial.
In DL POLY 2 dihedral forces are handled by the routine dihfrc.
2
2
2
2
c CCLRC
35
2.2.6 Improper Dihedral Angle Potentials
Improper dihedrals are used to restrict the geometry of molecules and as such need not
have a simple relation to conventional chemical bonding. DL POLY 2 makes no distinction
between dihedral angle functions and improper dihedrals (both are calculated by the same
subroutines) and all the comments made in the preceeding section apply.
An important example of the use of the improper dihedral is to conserve the structure
of chiral centres in molecules modelled by united-atom centres. For example -amino acids
such as alanine (CH CH(NH )COOH), in which it is common to represent the CH and
CH groups as single centres. Conservation of the chirality of the carbon is achieved
by dening a harmonic improper dihedral angle potential with an equilibrium angle of
35.264o . The angle is dened by vectors r , r and r , where the atoms 1,2,3 and 4 are
shown in the following gure. The gure denes the D and L enantiomers consistent with
the international (IUPAC) convention. When dening the dihedral, the atom indices are
entered in DL POLY 2 in the order 1-2-3-4.
3
2
3
12
23
34
N
C
3
3
C
N
2
2
α
α
1
1
H
H
4
4
β
β
L
D
L=α-N-C-β
1 2 3 4
D=α-C-N-β
1 2 3 4
The L and D enantiomers and dening vectors
In DL POLY 2 improper dihedral forces are handled by the routine dihfrc.
2.2.7 Inversion Angle Potentials
c CCLRC
36
j
n
φ
i
k
The inversion angle and associated vectors
The inversion angle potentials describe the interaction arising from a particular geometry of three atoms around a central atom. The best known example of this is the
arrangement of hydrogen atoms around nitrogen in ammonia to form a trigonal pyramid.
The hydrogens can `ip' like an inverting umbrella to an alternative structure, which in
this case is identical, but in principle causes a change in chirality. The force restraining the
ammonia to one structure can be described as an inversion potential (though it is usually
augmented by valence angle potentials also). The inversion angle is dened in the gure
above - note that the inversion angle potential is a sum of the three possible inversion angle terms. It resembles a dihedral potential in that it requires the specication
of four atomic positions.
The potential functions available in DL POLY 2 are as follows.
1. Harmonic: (harm)
1
(2.51)
U (ijkn) = k(ijkn )
2
2. Harmonic cosine: (hcos)
k
U (ijkn) = (cos(ijkn ) cos( ))
(2.52)
2
0
2
0
3. Planar potential: (plan)
U (ijkn) = A [1
cos(ijkn)]
In these formulae ijkn is the inversion angle dened by
ijkn = cos
with
and the unit vectors
(
1
)
rij wkn
;
rij wkn
wkn = (rij u^kn )^ukn + (rij v^kn )^vkn
u^kn
v^kn
= (^rik + r^in)=jr^ik + r^inj
= (^rik r^in)=jr^ik r^inj:
2
(2.53)
(2.54)
(2.55)
(2.56)
c CCLRC
37
As usual, rij = rj ri etc. and the hat r^ indicates a unit vector in the direction of r. The
total inversion potential requires the calculation of three such angles, the formula being
derived from the above using the cyclic permutation of the indices j ! k ! n ! j etc.
Equivalently, the angle ijkn may be written as
(
)
[(
rij u^kn ) + (rij v^kn) ] =
= cos
(2.57)
ijkn
2
1
2 1 2
rij
Formally, the force on an atom arising from the inversion potential is given by
@
U (ijkn );
(2.58)
f` =
@r`
with ` being one of i; j; k; n and one of x; y; z. This may be expanded into
(
)
@
1
@
U (ijkn ) =
@r`
sin(ijkn) @ijkn U (ijkn) (
)
@ [(rij u^kn) + (rij v^kn ) ] =
:
(2.59)
@r
rij
2
2 1 2
`
Following through the (extremely tedious!) dierentiation gives the result:
(
)
1
@
f` =
(2.60)
sin(ijkn) @ijkn U (ijkn) (
1
cos(ijkn) g
(Æ`j Æ`i ) r rij + rij w (Æ`j Æ`i)f(rij u^kn)^ukn + (rij v^kn)^vkn
kn
ij
(
)
rij u^kn rik
+(Æ Æ )
r (r u^ )^u
(r r (r u^ )(r u^ ))
2
`k
+(Æ`k
+(Æ`n
+(Æ`n
`i
ukn rik ij
(
rij v^kn Æ`i )
r
vknrik ij
(
rij u^kn Æ`i )
r
ukn rin ij
(
rij v^kn Æ`i )
r
vknrin ij
ij
kn
kn
ij
ik
(rij v^kn)^vkn
(rij rik
(rij u^kn)^ukn (rij rin
(rij v^kn)^vkn
(rij rin
ij
kn
ik
kn
rik2
)
rik
(rij v^kn)(rik v^kn)) r2
ik
)
rin
(rij u^kn)(rin u^kn)) r2
in
)#)
rin
(rij v^kn)(rin v^kn)) r2
in
This general formula applies to all atoms ` = i; j; k; n. It must be remembered however, that
these formulae apply to just one of the three contributing terms (i.e. one angle ) of the
full inversion potential: specically the inversion angle pertaining to the out-of-plane vector
rij . The contributions arising from the other vectors rik and rin are obtained by the cyclic
permutation of the indices in the manner described above. All these force contributions
must be added to the nal atomic forces.
Formally, the contribution to be added to the atomic virial is given by
W=
4
X
i=1
ri f i
(2.61)
c CCLRC
38
However it is possible to show by thermodynamic arguments (cf [26],) or simply from
the fact that the sum of forces on atoms j,k and n is equal and opposite to the force on
atom i, that the inversion potential makes no contribution to the atomic virial.
If the force components f` for atoms ` = i; j; k; n are calculated using the above formulae, it is easily seen that the contribution to be added to the atomic stress tensor is given
by
f + r f = rij fj + rik
(2.62)
in n
k
The sum of the diagonal elements of the stress tensor is zero (since the virial is zero) and
the matrix is symmetric.
In DL POLY 2 inversion forces are handled by the routine invfrc.
2.2.8 Tethering Forces
DL POLY 2 also allows atomic sites to be tethered to a xed point in space, r taken as their
position at the beginning of the simulation. This is also known as position restraining. The
specication, which comes as part of the molecular description, requires a tether potential
type and the associated interaction parameters.
Note, rstly, that application of tethering potentials means that momentum will no
longer be a conserved quantity of the simulation. Secondly, in constant pressure simulations,
where the MD cell changes size or shape, the reference position is scaled with the cell vectors.
The potential functions available in DL POLY 2 are as follows, in each case ri is the
distance of the atom from its position at t = 0:
1. harmonic potential: (harm)
1
U (ri ) = k(ri ) ;
(2.63)
2
2. restrained harmonic :(rhrm)
1
U (ri ) = k(ri )
ri rc;
(2.64)
2
1
U (ri ) = krc + krc(ri rc )
ri > rc ;
(2.65)
2
3. Quartic potential: (quar)
0
0
0
0
0
0
2
0
2
0
0
0
0
00
k
k
(
ri ) + (ri ) + (ri ) :
(2.66)
2
3
4
The force on the atom i arising from a tether potential is obtained using the general
formula:
1
@
f =
U (ri ) r ;
(2.67)
U (ri0 ) =
i
k
2
0
2
0
ri0 @ri0
0
3
0
i0
The contribution to be added to the atomic virial is given by
W = ri f i ;
0
4
(2.68)
c CCLRC
39
The contribution to be added to the atomic stress tensor is given by
= ri fi ;
(2.69)
where and indicate the x; y; z components. The atomic stress tensor derived in this
way is symmetric.
In DL POLY 2 bond forces are handled by the routine tethfrc.
0
2.2.9 Frozen Atoms
DL POLY 2 also allows atoms to be completely immobilised (i.e. \frozen" at a xed point
in the MD cell). This is achieved by setting all forces and velocities associated with that
atom to zero during each MD timestep. Frozen atoms are signalled by assigning an atom a
non-zero value for the freeze parameter in the FIELD le. DL POLY 2 does not calculate
contributions to the virial or the stress tensor arising from the constraints required to freeze
atomic positions. In DL POLY 2 the frozen atom option cannot be used for sites in a rigid
body. As with the tethering potential, the reference position is scaled with the cell vectors
in constant pressure simulations.
In DL POLY 2 the frozen atom option is handled by the subroutine freeze.
2.3 The Intermolecular Potential Functions
In this section we outline the pair-body, three-body and four-body potential functions
available in DL POLY 2 . An important distinction between these and intramolecular
(bond) forces in DL POLY 2 is that they are specied by atom types rather than atom
indices.
2.3.1 Short Ranged (van der Waals) Potentials
The short ranged pair forces available in DL POLY 2 are as follows.
1. 12 - 6 potential: (12-6)
!
!
A
B
U (rij ) =
;
r
r
12
2. Lennard-Jones: (lj)
2
U (rij ) = 4 4
rij
(2.70)
6
ij
ij
!12
rij
!6 3
5
;
(2.71)
3. n - m potential [27]: (nm)
U (rij ) =
"
Eo
r
m o
(n m)
rij
!n
r
n o
rij
!m #
;
(2.72)
c CCLRC
40
4. Buckingham potential: (buck)
U (rij ) = A
exp
rij C
;
rij6
(2.73)
5. Born-Huggins-Meyer potential: (bhm)
U (rij ) = A
exp[B (
C
rij6
rij )]
6. Hydrogen-bond (12 - 10) potential: (hbnd)
U (rij ) =
A
rij12
7. Shifted force n - m potential [27]: (snm)
U (rij )
=
=
(
!n
B
rij10
)
!
rcut
ro
m+1
n+1
(2.74)
;
n
Eo
ro
1
m n
n m
(n m)
rij
n
m o rij ro
+ (nmE
n m)
ro
=
with
"
!
D
;
rij8
(2.75)
(
ro
rij
!m
m )#
1
(2.76)
(2.77)
1
1
!
1
n m
(2.78)
)
= [n m(1 + (m= m 1)=(mn ) mm
n (1 + (n= n 1)= n )] (2.79)
This peculiar form has the advantage over the standard shifted n-m potential in that
both Eo and r (well depth and location of minimum) retain their original meaning
after the shifting process.
8. Tabulation: (tab). The potential is dened numerically only.
The parameters dening these potentials are supplied to DL POLY 2 at run time (see
the description of the FIELD le in section 4.1.3). Each atom type in the system is specied
by a unique eight-character label dened by the user. The pair potential is then dened
internally by the combination of two atom labels.
As well as the numerical parameters dening the potentials, DL POLY 2 must also
be provided with a cuto radius rcut, which sets a range limit on the computation of the
interaction. Together with the parameters, the cuto is used by the subroutine forgen
(or forgen rsq) to construct an interpolation array vvv for the potential function over
0
c CCLRC
41
the range 0 to rcut. A second array ggg is also calculated, which is related to the potential
via the formula:
@
G(rij ) = rij
U ( r );
(2.80)
@rij ij
and is used in the calculation of the forces. Both arrays are tabulated in units of energy.
The use of interpolation arrays, rather than the explicit formulae, makes the routines for
calculating the potential energy and atomic forces very general, and enables the use of
user dened pair potential functions. DL POLY 2 also allows the user to read in the
interpolation arrays directly from a le (see the description of the fortab routine (chapter
7) and the TABLE le (section 4.1.5). This is particularly useful if the pair potential
function has no simple analytical description (e.g. spline potentials).
The force on an atom j derived from one of these potentials is formally calculated with
the standard formula:
"
#
1
@
fj =
U (r ) r ;
(2.81)
rij @rij ij ij
where rij = rj ri. The force on atom i is the negative of this.
The contribution to be added to the atomic virial (for each pair interaction) is
W = rij f j :
(2.82)
The contribution to be added to the atomic stress tensor is given by
= rij fj ;
(2.83)
where and indicate the x; y; z components. The atomic stress tensor derived from the
pair forces is symmetric.
Since the calculation of pair potentials assumes a spherical cuto (rcut ) it is necessary to
apply a long range correction to the system potential energy and virial. Explicit formulae
are needed for each case and are derived as follows. For two atom types a and b, the
correction for the potential energy is calculated via the integral
Z 1
ab = 2 Na Nb
Ucorr
g (r)Uab (r)r dr
(2.84)
V r ab
where Na ; Nb are the numbers of atoms of types a and b, V is the system volume and gab (r)
and Uab (r) are the appropriate pair correlation function and pair potential respectively. It
is usual to assume gab (r) = 1 for r > rcut. DL POLY 2 sometimes makes the additional
assumption that the repulsive part of the short ranged potential is negligible beyond rcut.
The correction for the system virial is
Na Nb Z 1
@
ab
Wcorr = 2 V
gab (r) Uab (r)r dr;
(2.85)
@r
r
where the same approximations are applied. Note that these formulae are based on the
assumption that the system is reasonably isotropic beyond the cuto.
In DL POLY 2 the short ranged forces are calculated by one of the routines srfrce,
srfrce rsq, and srfrceneu. The long range corrections are calculated by routine lrcorrect. The calculation makes use of the Verlet neighbour list described above.
2
cut
3
cut
c CCLRC
42
2.3.2 Metal Potentials
DL POLY 2 includes density dependent potentials suitable for calculating the properties of
metals. The basic model is due to Finnis and Sinclair [28] as implemented by Sutton and
Chen [6]. The form of the potential is: (stch)
Usc =
2
X
4
i<j
!n
a
rij
where the local density i is given by
i =
a
rij
X
j
C
X
i
3
(2.86)
1i =2 5 ;
!m
(2.87)
The Sutton-Chen potential has the advantage that it is decomposable into pair contributions
and thus falls within the general tabulation scheme of DL POLY 2 , where it is treated as
a short ranged interaction. The same form of potential may be used in alloys, through the
appropriate choice of parameters and a. The parameters n and m however must be the
same for all component elements. DL POLY 2 calculates this potential in two stages: the
rst calculates the local density i for each atom; and the second calculates the potential
energy and forces. Interpolation
arrays are used in both these stages.
The total force f tot
on
an
atom
j derived from this potential is calculated in the standard
j
way:
(2.88)
f tot
j = rj Usc ;
which gives
!n
!m #
!
"
X
Cm
a
1
a
=
=
tot
fj = r ;
n
(2.89)
rij
2 (j + i ) rij
rij ij
i6 j
which is recognisable as a sum of pair forces, for example the force on atom j due to the
atom i:
!n
!m #
"
!
a
Cm
a
1
=
=
r ;
(2.90)
fj = n
rij
2 (j + i ) rij
rij ij
where rij = rj ri. The force on atom i is the negative of this.
With the pair forces thus dened the contribution to be added to the atomic virial from
each atom pair is then
W = rij f j :
(2.91)
The contribution to be added to the atomic stress tensor is given by
= rij fj ;
(2.92)
where and indicate the x; y; z components. The atomic stress tensor is symmetric.
1 2
1 2
2
=
1 2
1 2
2
c CCLRC
43
The long range correction for the system potential is in two parts. Firstly by analogy
with the short ranged potentials the correction to the local density is obtained by
i = oi + 4
1 a m
Z
rcut
r
(2.93)
r2 dr;
where oi is the uncorrected local density and is the mean particle density. Evaluating the
integral yields
a a m
(2.94)
Æ = 4
(m 3) rcut
which is the local density correction and is identical for all atoms. The correction is applied
immediately after the local density is calculated. The density term of the Sutton Chen
potential needs no further correction. The pair term correction is obtained by analogy with
the short ranged potentials and is
Na a n
Ucorr = 2
:
(2.95)
(n 3) rcut
The correction to the local density having already been applied.
To estimate the virial correction we assume the corrected local densities are constants
(i.e. independent of distance - at least beyond the range rcut). This allows the virial
correction to be computed by the methods used in the short ranged potentials. The result
is:
)
(
N
m C a m X
nN a n
=
i
(2.96)
Wcorr = 2a (n 3) r
(m 3) rcut
cut
i
This correction may be used as it stands, or with the further approximation:
3
3
3
3
3
3
N
X
i
2
i 1=2 =
2
3
N
< 1i =2 >
1 2
(2.97)
where < i = > is regarded as a constant of the system.
In DL POLY 2 the metal forces are handled by the routine suttchen. The local density
is calculated by routines scdens and denloc. The long range corrections are calculated
by lrcmetal.
1 2
2.3.3 Three Body Potentials
The three-body potentials in DL POLY 2 are mostly valence angle forms. (They are primarily included to permit simulation of amorphous materials e.g. silicate glasses.) However,
these have been extended to include the DREIDING [7] hydrogen bond. The potential
forms available are as follows.
1. Truncated harmonic: (thrm)
U (jik ) =
k
2 (jik
0 )2 exp[ (rij8 + rik8 )=8 ];
(2.98)
c CCLRC
44
2. Screened Harmonic: (shrm)
U (jik ) =
k
2 (jik
0 )2 exp[ (rij =1 + rik =2 )];
(2.99)
3. Screened Vessal[24]: (bvs1)
U (jik )
h
k
= 8( ) ( ) (jik
jik
exp[ (rij = + rik = )];
0
2
)
2
1
2
i2 (2.100)
2
4. Truncated Vessal[25]: (bvs2)
a (
U (jik ) = k[jik
2) a2 a
jik ) (jik + (jik ) ( ) ]exp[ (rij + rik )= ]:
(2.101)
5. DREIDING hydrogen bond [7]: (hbnd
U (jik ) = Dhb cos (jik )[5(Rhb =rjk )
(2.102)
0
0
2
2
2
0
0
4
3
8
1
8
8
6(Rhb =rjk ) ]
12
10
Note that for the hydrogen bond, the hydrogen atom must be the central atom. Several
of these functions are identical to those appearing in the intra-molecular valenceangle descriptions above. There are signicant dierences in implementation however, arising from
the fact that the three-body potentials are regarded as inter-molecular. Firstly, the atoms
involved are dened by atom types, not specic indices. Secondly, there are no excluded
atoms arising from the three body terms. (The inclusion of pair potentials may in fact be
essential to maintain the structure of the system.)
The three body potentials are very short ranged, typically of order 3 A. This property,
plus the fact that three body potentials scale as N , where N is the number of particles,
makes it essential that these terms are calculated by the link-cell method [29].
The calculation of the forces, virial and stress tensor as described in the section valence
angle potentials above.
DL POLY 2 applies no long range corrections to the three body potentials. The three
body forces are calculated by the routine thbfrc.
3
2.3.4 Four Body Potentials
The four-body potentials in DL POLY 2 are entirely inversion angle forms, primarily included to permit simulation of amorphous materials (particularly borate glasses). The
potential forms available in DL POLY 2 are as follows.
1. Harmonic: (harm)
1
U (ijkn) = k(ijkn )
(2.103)
2
0
2
c CCLRC
45
2. Harmonic cosine: (hcos)
U (ijkn) =
3. Planar potential: (plan)
k
2 (cos(ijkn)
cos(0 ))2
(2.104)
U (ijkn) = A[1
cos(ijkn)]
(2.105)
These functions are identical to those appearing in the intra-molecular inversion angle
descriptions above. There are signicant dierences in implementation however, arising
from the fact that the four-body potentials are regarded as inter-molecular. Firstly, the
atoms involved are dened by atom types, not specic indices. Secondly, there are no
excluded atoms arising from the four-body terms. (The inclusion of other potentials, for
example pair potentials, may in fact be essential to maintain the structure of the system.)
The four body potentials are very short ranged, typically of order 3 A. This property,
plus the fact that four body potentials scale as N , where N is the number of particles,
makes it essential that these terms are calculated by the link-cell method [29].
The calculation of the forces, virial and stress tensor described in the section on inversion
angle potentials above.
DL POLY 2 applies no long range corrections to the four body potentials. The fourbody forces are calculated by the routine fbpfrc.
4
2.3.5 External Fields
In addition to the molecular force eld, DL POLY 2 allows the use of an external force
eld. Examples of eld available include:
1. Electric eld: (elec)
Fi = Fi + qi :H
(2.106)
2. Oscillating shear: (oshm)
(2.107)
F x = A cos(2n:z=Lz )
3. Continuous shear: (shrx)
1 jzj
vx = A
: jzj > z
(2.108)
2 z
4. Gravitational eld: (grav)
Fi = Fi + mi :H
(2.109)
5. Magnetic eld: (magn)
Fi = Fi + qi :(vi ^ H )
(2.110)
6. Containing sphere: (sphr)
: r > Rcut
(2.111)
F = A(R r) n
0
0
c CCLRC
46
It is recommended that the use of an external eld should be accompanied by a thermostat
(this does not apply to example 6, since this is a conservative eld).
In DL POLY 2 external eld forces are handled by the routine extnfld.
2.4 Long Ranged Electrostatic (Coulombic) Potentials
DL POLY 2 incorporates several techniques for dealing with long ranged electrostatic potentials. These are as follows.
1. Atomistic and charge group implementation.
2. Direct Coulomb sum;
3. Truncated and shifted Coulomb sum;
4. Coulomb sum with distance dependent dielectric;
5. Ewald sum;
6. Smooth Particle Mesh Ewald (SPME);
7. Reaction eld;
8. Dynamical shell model.
Some of these techniques can be combined. For example 1, 3 and 4 can be used in conjunction with 7. The Ewald sum and SPME are restricted to periodic (or pseudo-periodic)
systems only, though DL POLY 2 can handle a broad selection of periodic boundary conditions, including cubic, orthorhombic, parallelepiped, truncated octahedral, hexagonal prism
and rhombic dodecahedral. The Ewald sum is the method of choice for periodic systems.
The other techniques can be used with either periodic or non-periodic systems, though in
the case of the direct Coulomb sum, there are likely to be problems of convergence.
DL POLY 2 will correctly handle the electrostatics of both molecular and atomic species.
However it is assumed that the system is electrically neutral. A warning message is printed
if the system is found to be charged, but otherwise the simulation proceeds as normal. No
correction for non-neutrality is applied.
2
2.4.1 Atomistic and Charge Group Implementation
The Ewald sum is an accurate method for summing long-ranged potentials, such as the
Coulomb potential, in periodic systems. This can be a very cpu intensive calculation and
the use of more eÆcient, but less accurate methods, is common. Invariably this involves
truncation of the potential at some nite distance r . If an atomistic scheme is used for
the truncation criterion there is no guarantee that the interaction sphere will be neutral
and spurious \charging" eects will almost certainly be seen in a simulation. This arises
cut
2
Unlike the other elements of the force eld, the electrostatic forces are NOT specied in the input
FIELD le, but by setting appropriate directives in the CONTROL le. See section 4.1.1.
c CCLRC
47
because the potential being truncated is long-ranged (1=r for charge-charge interactions).
However if the cuto scheme is based on neutral groups of atoms, then at worst, at long
distance the interaction will be a dipole-dipole interaction and vary as 1=r . The truncation
eects at the cuto are therefore much less severe than if an atomistic scheme is used. In
DL POLY 2 the interaction is evaluated between all atoms of both groups if any site of
the rst group is within the cuto distance of any site of the second group. The groups
are known interchangeably as \charge groups" or \neutral groups" in the documentation which serves as a reminder that the advantages of using such a scheme are lost if the groups
carry an overall charge. There is no formal requirement in DL POLY 2 that the groups
actually be electrically neutral.
The charge group scheme is more cpu intensive than a simple atomistic cuto scheme as
more computation is required to determine whether or not to include a set of interactions.
However the size of the Verlet neighbourhood list (easily the largest array in DL POLY 2
) is considerably smaller with a charge group scheme than an atomistic scheme as only a
list of interacting groups need be stored as opposed to a list of interacting atoms.
3
2.4.2 Direct Coulomb Sum
Use of the direct Coulomb sum is sometimes necessary for accurate simulation of isolated
(nonperiodic) systems. It is not recommended for periodic systems.
The interaction potential for two charged ions is
1 qiqj
(2.112)
U (rij ) =
4 rij
with q` the charge on an atom labelled `, and rij the magnitude of the separation vector
rij = rj ri .
The force on an atom j derived from this force is
1 qiqj
fj =
(2.113)
4 rij rij
with the force on atom i the negative of this.
The contribution to the atomic virial is
1 qiqj
(2.114)
W = 4
rij
0
3
0
0
which is simply the negative of the potential term.
The contribution to be added to the atomic stress tensor is
= rij fj ;
(2.115)
where ; are x; y; z components. The atomic stress tensor is symmetric.
In DL POLY 2 these forces are handled by the routines coul0 and coul0neu.
c CCLRC
48
2.4.3 Truncated and Shifted Coulomb Sum
This form of the Coulomb sum has the advantage that it drastically reduces the range of
electrostatic interactions, without giving rise to a violent step in the potential energy at the
cuto. Its main use is for preliminary preparation of systems and it is not recommended
for realistic models.
The form of the potential function is
(
)
qi qj 1
1
U (rij ) =
(2.116)
4 rij rcut
with q` the charge on an atom labelled `, rcut the cuto radius and rij the magnitude of
the separation vector rij = rj ri.
The force on an atom j derived from this potential, within the radius rcut, is
1 qiqj r
fj =
(2.117)
4 rij ij
with the force on atom i the negative of this.
The contribution to the atomic virial is
W = rij f j
(2.118)
which is not the negative of the potential term in this case.
The contribution to be added to the atomic stress tensor is given by
= rij fj ;
(2.119)
where ; are x; y; z components. The atomic stress tensor is symmetric.
In DL POLY 2 these forces are handled by the routine coul1.
A further renement of this approach is to truncate the 1=r potential at r and add
a linear term to the potential in order to make both the energy and the force zero at the
cuto. The potential is thus
"
#
qi qj 1
rij
2
U (rij ) =
(2.120)
4 rij + r
r
with the force on atom j given by
"
#
qi qj 1
1
fj =
(2.121)
4 rij r rij
with the force on atom i the negative of this.
This removes the heating eects that arise from the discontinuity in the forces at the
cuto in the simple truncated and shifted potential. The physics of this potential however
are little better. It is only recommended for very crude structure optimizations.
0
0
3
cut
2
cut
0
0
2
2
cut
cut
c CCLRC
49
The contribution to the atomic virial is
W = rij f j
which is not the negative of the potential term.
The contribution to be added to the atomic stress tensor is given by
= rij fj ;
where ; are x; y; z components. The atomic stress tensor is symmetric.
In DL POLY 2 these forces are handled by the routine coul4.
2.4.4 Coulomb Sum with Distance Dependent Dielectric
(2.122)
(2.123)
This potential attempts to address the diÆculties of applying the direct Coulomb sum,
without the brutal truncation of the previous case. It hinges on the assumption that the
electrostatic forces are eectively `screened' in real systems - an eect which is approximated
by introducing a dielectic term that increases with distance.
The interatomic potential for two charged ions is
1 qiqj
U (rij ) =
(2.124)
4 (rij ) rij
with q` the charge on an atom labelled `, and rij the magnitude of the separation vector
rij = rj ri . (r) is the distance dependent dielectric function. In DL POLY 2 it is assumed
that this function has the form
(r) = r
(2.125)
where is a constant. Inclusion of this term eectively accelerates the rate of convergence
of the Coulomb sum.
The force on an atom j derived from this potential is
1 qiqj
(2.126)
fj =
2 rij rij
with the force on atom i the negative of this.
The contribution to the atomic virial is
W = rij f j
(2.127)
which is 2 times the potential term.
The contribution to be added to the atomic stress tensor is given by
= rij fj ;
(2.128)
where ; are x; y; z components. The atomic stress tensor is symmetric.
In DL POLY 2 these forces are handled by the routines coul2 and coul2neu.
0
0
4
c CCLRC
50
2.4.5 Ewald Sum
The Ewald sum [10] is the best technique for calculating electrostatic interactions in a
periodic (or pseudo-periodic) system.
The basic model for a neutral periodic system is a system of charged point ions mutually
interacting via the Coulomb potential. The Ewald method makes two amendments to this
simple model. Firstly each ion is eectively neutralised (at long range) by the superposition
of a spherical gaussian cloud of opposite charge centred on the ion. The combined assembly
of point ions and gaussian charges becomes the Real Space part of the Ewald sum, which
is now short ranged and treatable by the methods described above (section 2.1). The
second modication is to superimpose a second set of gaussian charges, this time with the
same charges as the original point ions and again centred on the point ions (so nullifying
the eect of the rst set of gaussians). The potential due to these gaussians is obtained
from Poisson's equation and is solved as a Fourier series in Reciprocal Space. The complete
Ewald sum requires an additional correction, known as the self energy correction, which
arises from a gaussian acting on its own site, and is constant. Ewald's method therefore
replaces a potentially innite sum in real space by two nite sums: one in real space and
one in reciprocal space; and the self energy correction.
For molecular systems, as opposed to systems comprised simply of point ions, additional
modications are necessary to correct for the excluded (intra-molecular) Coulombic interactions. In the real space sum these are simply omitted. In reciprocal space however, the
eects of individual gaussian charges cannot easily be extracted, and the correction is made
in real space. It amounts to removing terms corresponding to the potential energy of an ion
` due to the gaussian charge on a neighbouring charge m (or vice versa). This correction
appears as the nal term in the full Ewald formula below. The distinction between the
error function erf and the more usual complementary error function erfc found in the real
space sum, should be noted.
The total electrostatic energy is given by the following formula.
1 exp( k =4 ) X
N
N
1 X
1 X
qj qn
Uc =
j
qj exp( ik rj )j +
erfc(rnj )
2Vo k6 0
k
4
j
n<j rnj
(
)
M
1 X X
erf (r`m )
q`qm Æ`m p +
;
(2.129)
Æ
4
3
2
0
2
2
=
0
molecules `m
2
0
1
`m
r`m
where N is the number of ions in the system and N the same number discounting any
excluded (intramolecular) interactions. M represents the number of excluded atoms in a
given molecule and includes the atomic self correction. Vo is the simulation cell volume and
k is a reciprocal lattice vector dened by
k = `u + mv + nw
(2.130)
3
Strictly speaking, the real space sum ranges over all periodic images of the simulation cell, but in the
DL POLY 2 implementation, the parameters are chosen to restrict the sum to the simulation cell and its
nearest neighbours i.e. the minimum images of the cell contents.
c CCLRC
51
where `; m; n are integers and u; v; w are the reciprocal space basis vectors. Both Vo and
u; v; w are derived from the vectors (a; b; c) dening the simulation cell. Thus
Vo = ja b cj
(2.131)
and
bc
u = 2
abc
ca
v = 2
(2.132)
abc
= 2 a a bb c :
With these denitions, the Ewald formula above is applicable to general periodic systems.
(A small additional modication is necessary for rhombic dodecahedral and truncated octahedral simulation cells [30].)
In practice the convergence of the Ewald sum is controlled by three variables: the
real space cuto rcut; the convergence parameter and the largest reciprocal space vector
kmax used in the reciprocal space sum. These are discussed more fully in section 3.3.5.
DL POLY 2 can provide estimates if requested (see CONTROL le description 4.1.1.
The force on an atom j is obtained by dierentiation and is
1
N
qj X
exp( k =4 ) X
fj =
ik exp(k rj )
qn exp( ik rn )
Vo 6 0
k
n
k
N q qj X
pnj exp( rnj ) rnj
+ 4 r n erfc(rnj ) + 2r
(2.133)
w
2
0
2
2
=
0
2 2
3
nj
n
2pr`j exp(
M q qj X
`
40 ` r`j3 erf (r`j )
r`j ) r`j
2 2
The electrostatic contribution to the system virial can be obtained as the negative of the
Coulombic energy. However in DL POLY 2 this formal equality can be used as a check on
the convergence of the Ewald sum. The actual electrostatic virial is obtained during the
calculation of the diagonal of the stress tensor.
The electrostatic contribution to the stress tensor is given by
1
N
X
1
1
1
exp( k =4 ) j X
=
1 2
+
K
qj exp( ik rj )j
2Vo k6 0
4 k
k
j
N q q X
1
2
rnj
j n
+ 4
(2.134)
erfc(rnj ) + p exp( rnj ) R
r
2
0
2
2
2
2
2
=
0
2 2
3
j<n nj
M q q X
j `
4
0
j<` r`j
3
erf (r`j )
2pr`j exp(
nj
2 r`j2 ) R`j ;
c CCLRC
52
where matrices K and R` are dened as follows.
j
= k k
(2.135)
= r`j r`j
(2.136)
In DL POLY 2 the full Ewald sum is handled by several routines: ewald1 and ewald1a
handle the reciprocal space terms; ewald2, ewald2 2pt, ewald2 rsq and ewald4,
ewald4 2pt handle the real space terms (with the same Verlet neighbour list routines
that are used to calculate the short range forces); and ewald3 calculates the self interaction corrections. It should be noted that the Ewald potential and force interpolation arrays
in DL POLY 2 are erc and fer respectively.
K R`j
2.4.6 Smooth Particle Mesh Ewald
As its name implies the Smooth Particle Mesh Ewald (SPME) method is a modication
of the standard Ewald method. DL POLY 2 implements the SPME method of Essmann
et al. [31]. Formally this method is capable of treating van der Waals forces also, but
in DL POLY 2 it is conned to electrostatic forces only. The main dierence from the
standard Ewald method is in its treatment of the the reciprocal space terms. By means
of an interpolation procedure involving (complex) B-splines, the sum in reciprocal space is
represented on a three dimensional rectangular grid. In this form the Fast Fourier Transform (FFT) may be used to perform the primary mathematical operation, which is a 3D
convolution. The eÆciency of these procedures greatly reduces the cost of the reciprocal
space sum when the range of k vectors is large. The method (briey) is as follows (for full
details see [31]):
1. Interpolation of the exp( ik rj ) terms (given here for one dimension):
X
exp(2iuj k=L) b(k)
1Mn (uj `)exp(2ik`=K )
(2.137)
`=
1
in which k is the integer index of the k vector in a principal direction, K is the total
number of grid points in the same direction and uj is the fractional coordinate of ion
j scaled by a factor K (i.e. uj = Ksxj). Note that the denition of the B-splines
implies a dependence on the integer K , which limits the formally innite sum over
`. The coeÆcients Mn (u) are B-splines of order n and the factor b(k) is a constant
computable from the formula:
b(k) = exp(2i(n
1)k=K )
"
nX2
`=0
Mn (` + 1)exp(2ik`=K )
2. Approximation of the structure factor S (k):
S (k) b (k )b (k )b (k )Qy (k ; k ; k )
1
1
2
2
3
3
1
2
3
#
1
(2.138)
(2.139)
c CCLRC
53
where Qy(k ; k ; k ) is the discrete Fourier transform of the charge array Q(` ; ` ; ` )
dened as
1
2
Q(`1 ; `2 ; `3 ) =
3
N
X
j =1
1
qj
X
n1 ;n2 ;n3
2
3
Mn (u1j `1 n1 L1 )Mn (u2j `2 n2 L2 )Mn (u3j `3 n3 L3 )
(2.140)
(in which the sums over n ; ; etc are required to capture contributions from all
relevant periodic cell images, which in practice means the nearest images.)
3. Approximating the reciprocal space energy Urecip:
1 X Gy(k ; k ; k )Q(k ; k ; k )
Urecip =
(2.141)
2Vo k ;k ;k
123
0
1
1
2
2
3
1
2
3
3
in which Gy is the discrete Fourier transform of the function
exp( k =4 ) B (k ; k ; k )(Qy(k ; k ; k ))
G(k ; k ; k ) =
2
1
2
3
and where
k
2
1
2
2
3
1
2
3
(2.142)
B (k1 ; k2 ; k3 ) = jb1 (k1 )j2 jb2 (k2 )j2 jb3 (k3 )j2
(2.143)
and (Qy(k1 ; k2 ; k3 )) is the complex conjgate of Qy(k1 ; k2 ; k3 ). The function G(k1; k2 ; k3 )
is thus a relatively simple product of the gaussian screening term appearing in the
conventional Ewald sum, the function B (k ; k ; k ) and the discrete Fourier transform
of Q(k ; k ; k )
4. Calculating the atomic forces, which are given formally by:
X
@Urecip
@Q(k ; k ; k )
f =
= 1
Gy(k ; k ; k )
(2.144)
1
1
2
2
3
3
j
@rj
Vo 0 k1 ;k2;k3
1
2
3
1
2
@rj
3
Fortunately, due to the recursive properties of the B-splines, these formulae are easily
evaluated.
The virial and the stres tensor are calculated in the same manner as for the conventional
Ewald sum.
2.4.7 Reaction Field
In the reaction eld method it is assumed that any given molecule is surrounded by a
spherical cavity of nite radius within which the electrostatic interactions are calculated
explicitly. Outside the cavity the system is treated as a dielectric continuum. The occurence
of any net dipole within the cavity induces a polarisation in the dielectric, which in turn
interacts with the given molecule. The model allows the replacement of the innite Coulomb
sum by a nite sum plus the reaction eld.
c CCLRC
54
The reaction eld model coded into DL POLY 2 is the implementation of Neumann
based on charge-charge interactions [32]. In this model, the total Coulombic potential is
given by
"
#
X
B rnj
1
1
(2.145)
Uc =
4 qj qn rnj + 2R
0
0
2
3
c
j<n
where the second term on the right is the reaction eld correction to the explicit sum, with
Rc the radius of the cavity. The constant B is dened as
2( 1) ;
B =
(2.146)
(2 + 1)
with the dielectric constant outside the cavity. The eective pair potential is therefore
"
#
B rnj
1
1
U (rnj ) =
(2.147)
4 qj qn rnj + 2Rc :
This expression unfortunately leads to large uctuations in the system Coulombic energy,
due to the large `step' in the function at the cavity boundary. In DL POLY 2 this is
countered by subtracting the value of the potential at the cavity boundary from each pair
contribution. The term subtracted is
1 qj qn 1 + B :
(2.148)
4 R
2
0
1
0
1
1
0
2
3
0
0
c
0
The eective pair force on an atom j arising from another atom n within the cavity is
given by
"
#
qj qn 1 B
fj =
(2.149)
4 rnj Rc rnj :
The contribution of each eective pair interaction to the atomic virial is
W = rnj f j
(2.150)
and the contribution to the atomic stress tensor is
f :
= rnj
(2.151)
j
In DL POLY 2 the reaction eld is handled by the routines coul3 and coul3neu.
0
0
2.4.8 Dynamical Shell Model
3
3
An atom or ion is polarisable if it develops a dipole moment when placed in an electric
eld. It is commonly expressed by the equation
= E;
(2.152)
where is the induced dipole and E is the electric eld. The constant is the polarisability.
c CCLRC
55
The dynamical shell model is a method of incorporating polarisability into a molecular
dynamics simulation. The method used in DL POLY 2 is that devised by Fincham et al
[33] and is known as the adiabatic shell model. An alternative model is presented in [34].
In the static shell model a polarisable atom is represented by a massive core and massless
shell, connected by a harmonic spring, hereafter called the core-shell unit. The core and
shell carry dierent electric charges, the sum of which equals the charge on the original
atom. There is no electrostatic interaction (i.e. self interaction) between the core and shell
of the same atom. Non-Coulombic interactions arise from the shell alone. The eect of
an electric eld is to separate the core and shell, giving rise to a polarisation dipole. The
condition of static equilibrium gives the polarisability as:
= (2qs qc )=k
(2.153)
where qs and qc are the shell and core charges and k is the force constant of the harmonic
spring.
In the adiabatic method, a fraction of the atomic mass is assigned to the shell to permit
a dynamical description. The fraction of mass is chosen to ensure that the natural frequency
of vibration of the harmonic spring (i.e.
=
1
k
=
(2.154)
2 x(1 x)m ;
with m the atomic mass,) is well above the frequency of vibration of the whole atom in the
bulk system. Dynamically the core-shell unit resembles a diatomic molecule with a harmonic
bond, however the high vibrational frequency of the bond prevents eective exchange of
kinetic energy between the core-shell unit and the remaining system. Therefore, from an
initial condition in which the core-shell units have negligible internal vibrational energy,
the units will remain close to this condition throughout the simulation. This is essential if
the core shell unit is to maintain a net polarisation. (In practice there is a slow leakage of
kinetic energy into the core-shell units, but this should should not amount to more than a
few percent of the total kinetic energy.)
The calculation of the virial and stress tensor in this model is based on that for a
diatomic molecule with charged atoms. The electrostatic and short ranged forces are calculated as described above. The forces of the harmonic springs are calculated as described
for intramolecular harmonic bonds. The relationship between the kinetic energy and the
temperature is dierent however, as the core-shell unit is permitted only three translational
degrees of freedom, and the degrees of freedom corresponding to rotation and vibration of
the unit are discounted (the kinetic energy of these is regarded as zero).
In DL POLY 2 the shell forces are handled by the routine shlfrc. The kinetic energy is calculated by corshl and the routine shqnch performs the temperature scaling.
The dynamical shell model is used in conjunction with the methods for long range forces
described above.
2
2
1 2
c CCLRC
56
2.5 Integration algorithms
DL POLY integration algorithms are based around the Verlet leapfrog scheme, which is
both simplectic (time reversible) and simple in nature [10]. It generates trajectories in the
microcanonical (NVE) ensemble in which the total energy (kinetic plus potential energy)
is conserved. If this property drifts or uctuates signicantly in the course of a simulation
it indicates that the timestep is too large or the potential cutos too small (relative r.m.s.
uctuations in the total energy of 10 are typical with this algorithm).
The algorithm requires values of position (r) and force (f ) at time t while the velocities
(v) are half a timestep behind. The rst step is to advance the velocities to t + (1=2)t by
integration of the force:
1
1 t) + t f (t)
v (t + t) v(t
(2.155)
2
2
m
where m is the mass of a site and t is the timestep.
The positions are then advanced using the new velocities:
1
r(t + t) r(t) + t v (t + t)
(2.156)
2
Molecular dynamics simulations normally require properties that depend on position
and velocity at the same time (such as the sum of potential and kinetic energy). The
velocity at time t is obtained from the average of the velocities half a timestep either side
of time t:
1
1
1
(2.157)
v(t) = v(t
2
2 t) + v(t + 2 t)
The instantaneous temperature, for example can then be obtained from the atomic
velocities assuming the system has no net momentum:
PN
T = i mivi (t)
(2.158)
5
=1
kB f
2
where i labels particles (which can be atoms or rigid molecules), N the number of particles
in the system, kB Boltzmanns constant and f the number of degrees of freedom in the
system (3N 3 if the system is periodic and without constraints).
The routine nve 0 implements the Verlet leapfrog algorithm and calculates the instantaneous temperature. The conserved quantity is the total energy of the system
H = U + KE
(2.159)
where U is the potential energy of the system and KE the kinetic energy at time t.
The full selection of integrration algorithms within DL POLY 2 is as follows:
NVE
nve 0
nve 1
Verlet leapfrog
Verlet leaprog with RD-SHAKE
c CCLRC
nveq 1
nveq 2
nvt b0
nvt b1
nvt e0
nvt e1
nvt h0
nvt h1
nvtq b1
nvtq b2
nvtq h1
nvtq h2
npt b0
npt b1
npt b3
npt h0
npt h1
npt h3
nptq b1
nptq b2
nst b0
nst h0
nptq b3
nptq b4
nptq h1
nptq h2
nptq h3
nptq h4
57
Rigid units with FIQA and RD-SHAKE
Linked rigid units with QSHAKE
Constant T (Berendsen [14]) with Verlet leapfrog
Constant T (Berendsen [14]) with RD-SHAKE
Constant T (Evans [15]) with Verlet leapfrog
Constant T (Evans [15]) with RD-SHAKE
Constant T (Hoover [16]) with Verlet leapfrog
Constant T (Hoover [16]) with RD-SHAKE
Constant T (Berendsen [14]) with FIQA and RD-SHAKE
Constant T (Berendsen [14]) with QSHAKE
Constant T (Hoover [16]) with FIQA and RD-SHAKE
Constant T (Hoover [16]) with QSHAKE
Constant T,P (Berendsen [14]) with Verlet leapfrog
Constant T,P (Berendsen [14]) with FIQA and RD-SHAKE
Constant T, (Berendsen [14]) with RD-SHAKE
Constant T,P+ (Hoover [16]) with Verlet leapfrog
Constant T,P+ (Hoover [16]) with RD-SHAKE
Constant T, (Hoover [16]) with RD-SHAKE
Constant T,P (Berendsen [14]) with FIQA and RD-SHAKE
Constant T,P (Berendsen [14]) with QSHAKE
Constant T, (Berendsen [14]) with Verlet leapfrog
Constant T, (Hoover [16]) with Verlet leapfrog
Constant T, (Berendsen [14]) with FIQA and RD-SHAKE
Constant T, (Berendsen [14]) with QSHAKE
Constant T,P (Hoover [16]) with FIQA and RD-SHAKE
Constant T,P (Hoover [16]) with QSHAKE
Constant T, (Hoover [16]) with FIQA and RD-SHAKE
Constant T, (Hoover [16]) with QSHAKE
In the above table the FIQA algorithm is Fincham's Implicit Quaternion Algorithm [12]
and QSHAKE is the DL POLY 2 algorithm combining rigid bonds and rigid bodies in the
same molecule [13].
2.5.1 Bond Constraints
The SHAKE algorithm for bond constraints was devised by Ryckaert et al. [11] and is widely
used in molecular simulation. It is a two stage algorithm based on the Verlet integration
scheme [10]. DL POLY 2 employs a leapfrog variant. In the rst stage the Verlet leapfrog
algorithm calculates the motion of the atoms in the system assuming a complete absence of
the rigid bond forces. The positions of the atoms at the end of this stage do not conserve
the distance constraint required by the rigid bond and a correction is necessary. In the
second stage the deviation in the length of a given rigid bond is used retrospectively to
compute the constraint force needed to conserve the bondlength. It is relatively simple to
c CCLRC
58
show that the constraint force has the form
ij (dij d0ij ) o
Gij (2.160)
2t doij d0ij dij
where: ij is the reduced mass of the two atoms connected by the bond; doij and d0ij are the
original and intermediate bond vectors; dij is the constrained bondlength; and t is the
Verlet integration time step. It should be noted that this formula is an approximation only.
2
2
2
G12
1’
1
d
2
12
G21
2’
1
o
d
12
2
The SHAKE algorithm calculates the constraint force G = G that conserves the
bondlength d between atoms 1 and 2, following the initial movement to positions 10 and
20 under the unconstrained forces F and F .
12
21
12
1
2
For a system of simple diatomic molecules, computation of the constraint force will, in
principle, allow the correct atomic positions to be calculated in one pass. However in the
general polyatomic case this correction is merely an interim adjustment, not only because
the above formula is approximate, but the successive correction of other bonds in a molecule
has the eect of perturbing previously corrected bonds. The SHAKE algorithm is therfore
iterative, with the correction cycle being repeated for all bonds until each has converged to
the correct length, within a given tolerance. The tolerance may be of the order 10 A to
10 A depending on the precision desired.
The procedure may be summarised as follows:
1. All atoms in the system are moved using the Verlet algorithm, assuming an absence
of rigid bonds (constraint forces). (This is stage 1 of the SHAKE algorithm.)
4
8
c CCLRC
59
2. The deviation in each bondlength is used to calculate the corresponding constraint
force (2.160) that (retrospectively) `corrects' the bond length.
3. After the correction (2.160) has been applied to all bonds, every bondlength is checked.
If the largest deviation found exceeds the desired tolerance, the correction calculation
is repeated.
4. Steps 2 and 3 are repeated until all bondlengths satisfy the convergence criterion
(This iteration constitutes stage 2 of the SHAKE algorithm).
The parallel version of this algorithm, as implemented in DL POLY 2 , is known as
RD SHAKE [9] (see section 2.6.8). The subroutine nve 1 implements the Verlet leapfrog
algorithm with bond constraints. The routine rdshake 1 is called to apply the SHAKE
corrections to position.
It should be noted that the fully converged constraint forces Gij make a contribution
to the system virial and the stress tensor.
The contribution to be added to the atomic virial (for each constrained bond) is
(2.161)
W = dij Gij :
The contribution to be added to the atomic stress tensor is given by
= dij Gij ;
(2.162)
where and indicate the x; y; z components. The atomic stress tensor derived from the
pair forces is symmetric.
2.5.2 Potential of Mean Force (PMF) Constraints and the Evaluation of
Free Energy
A generalization of bond constraints can be made to constrain a system to some point along
a reaction coordinate. A simple example of such a reaction coordinate would be the distance
between two ions in solution. If a number of simulations are conducted with the system
constrained to dierent points along the reaction coordinate then the mean constraint force
may be plotted as a function of reaction coordinate and the function integrated to obtain the
free energy for the overall process [35]. The PMF constraint force, virial and contributions
to the stress tensor are obtained in a manner analagous to that for a bond constraint
(see previous section). The only dierence is that the constraint is now applied between
the centres of two groups which need not be atoms alone. DL POLY 2 reports the PMF
constraint virial, W, for each simulation. Users can convert this to the PMF constraint
force from
G
= W =d
where d is the constraint distance between the two groups used to dene the reaction
coordinate.
PMF
PMF
PMF
PMF
c CCLRC
60
2.5.3 Thermostats
The system may be coupled to a heat bath to ensure that the average system temperature
is maintained close to the requested temperature, T . When this is done the equations
of motion are modied and the system no longer samples the microcanonical ensemble.
Instead trajectories in the canonical (NVT) ensemble, or something close to it are generated.
DL POLY 2 comes with three dierent thermostats: Nose-Hoover [16], Berendsen [14], and
Gaussian constraints [15]. Of these only the Nose-Hoover algorithm generates trajectories
in the canonical (NVT) ensemble. The other methods will produce properties that typically
dier from canonical averages by O(1=N ) [10]
ext
2.5.3.1 Nose- Hoover Thermostat
In the Nose-Hoover algorithm [16] Newton's equations of motion are modied to read:
dr(t)
= v ( t)
dt
dv(t)
(2.163)
= f (t) (t)v(t)
dt
m
(2.164)
The friction coeÆcient, , is controlled by the rst order dierential equation
d(t) 1 T
=
1
dt
T2 Text
(2.165)
where T is a specied time constant (normally in the range [0.5, 2] ps). In DL POLY 2
is stored at half timesteps as it has dimensions of (1/time). The integration takes place
as:
1
1
t T
(t + t)
(t
2
2 t) + T T 1 1 (t 1 t) + (t + 1 t)
(t)
2
2
2
#
"
f (t)
1
1
v(t + t)
v (t
t) + t m (t)v(t)
2
2
1 v(t 1 t) + v(t + 1 t)
v (t)
2
2
2
1
r(t + t)
(2.166)
r(t) + t v(t + t)
2
2
ext
Since v(t) is required to calculate T and itself, the algorithm requires several iterations to
obtain self consistency. In DL POLY 2 the number of iterations is set to 3 (4 if the system
has bond constraints). The iteration procedure is started with the standard Verlet leapfrog
prediction of v(t) and T . The conserved quantity is derived from the extended Hamiltonian
c CCLRC
61
for the system which, to within a constant, is the Helmholtz free energy:
!
T (t) Z t
H = H + fkB T
(2.167)
2 + o (s)ds
If bond constraints are present an extra iteration is required due to the call to the
SHAKE routine. Note that the SHAKE corrections need only be applied during the rst
iteration as subsequent to this the velocities, relative to the bond c.o.m. velocity, will be
orthogonal to the bond vectors. The velocity scaling imposed by the thermostat is isotropic
so does not destroy this orthogonality. The algorithm is implemented in the DL POLY
routines nvt h0 and nvt h1, the latter being for systems with bond constraints.
2
NVT
NVE
2
ext
2.5.3.2 Berendsen Thermostat
In the Berendsen algorithm the instantaneous temperature is pushed towards the desired
temperature by scaling the velocities at each step:
t T
1+
"
T
ext
T
1
1=2
#
1 t) + t f (t) v(t
2
m
1 v(t 1 t) + v(t + 1 t)
2
2
2
1
r(t) + t v(t + t)
r(t + t)
(2.168)
2
As with the Nose-Hoover thermostat iteration is required to obtain self consistency of ,
v(t) and T , although it should be noted has dierent roles in the two thermostats. The
Berendsen algorithm conserves total momentum but not energy.
As with the Nose-Hoover algorithm the presence of constraint bonds requires an additional iteration with one application of SHAKE corrections. The algorithm is implemented
in the DL POLY routines nvt b0 and nvt b1, the latter being for systems with bond
constraints.
1
v(t + t)
2
v(t)
2.5.4 Gaussian Constraints
Kinetic temperature can be made a constant of the equations of motion by imposing an
additional constraint on the system. If one writes the equations of motions as :
dr(t)
= v ( t)
dt
dv(t)
= f (t) (t)v(t)
(2.169)
dt
m
(2.170)
c CCLRC
62
with the temperature constraint
dT
dt
/
d
dt
!
X
i
then choosing
X
(mivi) /
2
i
m2i v i (t) f i (t) = 0
(2.171)
(t):f i(t)
(2.172)
i mi vi (t)
minimizes the \least squares" dierences between the Newtonian and constrained trajectories. Following Brown and Clarke [36] the algorithm is implemented by calculating
= 1=(1 + t=2)
=
P
i mi v i
P
s
2 2
Text
T
1 t)
1 t) + t f (t)
(2
1)v (t
2
2
m
1
r(t) + t v (t + t)
r(t + t)
(2.173)
2
where T is obtained from standard Verlet leapfrog integration. Only one iteration is needed
(two if the system has bond constraints) to constrain the instantaneous temperature to
exactly T however energy is not conserved by this algorithm.
The algorithm is implemented in the DL POLY routines nvt e0 and nvt e1. The
latter is for systems with bond constraints.
v (t +
ext
2.5.5 Barostats
The size and shape of the simulation cell may be dynamically adjusted by coupling the
system to a barostat in order to obtain a desired average pressure (P ) and/or isotropic
stress tensor (). DL POLY 2 has two such algorithms: a Hoover type barostat and the
Berendsen barostat. Only the former has a well dened conserved quantity.
ext
2.5.5.1 The Hoover Barostat
DL POLY 2 uses the Melchionna modication of the Hoover algorithm [37] in which the
equations of motion involve a Nose - Hoover thermostat and a barostat in the same spirit.
Cell size variation
For isotropic uctuations the equations of motion are:
dr(t)
= v(t) + (r(t) R )
dt
dv (t)
= f (t) [(t) + (t)] v(t)
0
dt
m
c CCLRC
63
d(t)
dt
d(t)
dt
dV (t)
dt
= 1
T
1
Text
2
T
= N k T1 V (t)(P P )
B
P
= [3(t)]V (t)
(2.174)
where is the barostat friction coeÆcient, R the system centre of mass, P a specied time
constant for pressure uctuations, P the instantaneous pressure and V the system volume.
The conserved quantity is, to within a constant, the Gibbs free energy of the system:
HNP T = HNV T + P V (t) + 3N k2B T (t) P
(2.175)
The algorithm is readily implemented in the leapfrog scheme:
1
1 t) + t T 1
(t + t)
(t
2
2
T T
1
1
1
(t)
2 (t 2 t) + (t + 2 t)
1 t) + tV (t) (P P )
1
(t
(t + t)
2
2
N kB T P 1
1
1
(t)
(t
t) + (t + t)
2
2
2
"
#
f ( t)
1
1
v (t + t)
v (t
t) + t m [(t) + (t)] v(t)
2
2
1
1
1
v (t)
2 v(t 2t) + v(t + 2 t)
1
1
1
r(t + t)
r(t) + t v (t + t) + (t + t) r(t + t) R
2
2
2
1
1
r(t + t)
(2.176)
2
2 [r(t) + r(t + t)]
Like the Nose-Hoover thermostat, several iterations are required to obtain self consistency.
DL POLY 2 uses 4 iterations (5 if bond constraints are present) with the standard Verlet
leapfrog predictions for the initial estimates of T , P , v(t) and r(t + t). Note also that
the change in box size requires the SHAKE algorithm to be called each iteration with the
new cell vectors obtained from:
1
V (t + t)
V (t)exp 3t (t + t)
2 1
H(t)exp t (t + t)
(2.177)
H(t + t)
2
where H is the cell matrix whose columns are the three cell vectors a; b; c.
ext
ext
2
0
ext
ext
2
2
2
ext
ext
2
ext
0
1
2
c CCLRC
64
The isotropic changes to cell volume are implemented in the DL POLY routine npt h1
which allows for systems containing bond constraints.
Cell size and shape variation
The isotropic algorithm may be extended to allowing the cell shape to vary by dening
The equations of motion are implemented as:
1
1
t T
(t + t)
(t
2
2 t) + T T 1 1 (t 1 t) + (t + 1 t)
(t)
2
2
2
1
1
tV (t) (t + t)
(t
t) +
P 1
2
2
N kB T P 1 (t 1 t) + (t + 1 t)
(t)
2
2
2
"
#
i
f ( t) h
1
1
v (t + t)
v (t
t) + t m (t)1 + (t) v(t)
2
2
1 v(t 1 t) + v(t + 1 t)
v (t)
2
2
2
1
1
1
r(t + t)
r(t) + t v (t + t) + (t + t) r(t + t) R
2
2
2
1
1
r(t + t)
(2.178)
2
2 [r(t) + r(t + t)]
where 1 is the identity matrix and the pressure tensor. The new cell vectors are calculated
from
1
H(t + t)
H(t)exp t (t + t)
(2.179)
2
as a tensor, .
2
ext
ext
2
ext
0
DL POLY 2 uses a power series expansion truncated at the quadratic term to approximate
the exponential of the tensorial term. The new volume is found from
h
i
(2.180)
V (t + t) V (t)exp t tr( )
The conserved quantity is
HNP T = HNV T + P V (t) + 3N k2B T tr[(t)] P
(2.181)
This algorithm is implemented in the routines nst h0 (nonbonded systems) and npt h3
(with bond constraints).
ext
ext
2
2
c CCLRC
65
2.5.5.2 Berendsen Barostat
With the Berendsen barostat the system is made to obey the equation of motion
dP
dt
= (P
ext
P )=P
(2.182)
Cell size variations
In the isotropic implementation, at each step the MD cell volume is scaled by by a
factor and the coordinates, and cell vectors, by = where
t
=1
(P P )
(2.183)
1 3
P
ext
and is the isothermal compressibility of the system. The Berendesen thermostat is applied
at the same time. In practice is a specied constant which DL POLY 2 takes to be the
isothermal compressibility of liquid water. The exact value is not critical to the algorithm
as it relies on the ratio P = . P is specied by the user.
This algorithm is implemented in npt b1 with 4 or 5 iterations used to obtain self
consistency in the v(t).
Cell size and shape variations
The extension of the isotropic algorithm to anisotropic cell variations is straightforward.
The tensor is dened by
t
(P 1 )
(2.184)
=1
P
and the new cell vectors given by
H(t + t) H(t)
(2.185)
As in the isotropic case the Berendsen thermostat is applied simultaneously and 4 or 5 iterations are used to obtain convergence. The algorithm is implemented in nst b0 (nonbonded
systems) and npt b3 (with bond constraints).
ext
2.5.6 Rigid Bodies and Rotational Integration Algorithms
2.5.6.1 Description of Rigid Body Units
A rigid body unit is a collection of point atoms whose local geometry is time invariant.
One way to enforce this in a simulation is to impose a suÆcient number of bond constraints
between the atoms in the unit. However, in many cases this is may be either problematic
or impossible. Examples in which it is impossible to specify suÆcient bond constraints are
1. linear molecules with more than 2 atoms (e.g. CO )
2. planar molecules with more than three atoms (e.g. benzene).
2
c CCLRC
66
Even when the structure can be dened by bond constraints the network of bonds produced
may be problematic. Normally, they make the iterative SHAKE procedure slow, particularly if a ring of constraints is involved (as occurs when one denes water as a constrained
triangle). It is also possible, inadvertently, to over constrain a molecule (e.g. by dening a
methane tetrahedron to have 10 rather than 9 bond constraints) in which case the SHAKE
procedure will become unstable. In addition, massless sites (e.g. charge sites) cannot be
included in a simple constraint approach making modelling with potentials such as TIP4P
water impossible. All these problems may be circumvented by dening rigid body units in
terms of a center of mass (c.o.m) and an orientation and solving the resultant rigid body
equations of motion.
A rigid body has associated with it a rotational inertia matrix I, whose components are
given by I = 1=2 P mr r where the r are the distance to the centre of mass and the
m are the site masses. In DL POLY 2 we dene the local body frame to be that in which
the rotational inertia tensor ^I is diagonal and the components satisfy Ixx Iyy Izz . These
three components are stored in the arrays rotinx, rotiny and rotinz for each unique type
of rigid body in the system. The total mass of the rigid body unit, M , is stored in the
array gmass and the location of sites with respect to the local body axes are stored in the
arrays gxx, gyy and gzz.
The orientation of a local body frame with respect to the space xed frame is described
via a four dimensional unit vector, the quaternion q = [q ; q ; q ; q ]T . The Rotational
matrix to transform from the local body frame to the space xed frame is the unitary
matrix
0
q +q q q
2(q q q q ) 2(q q + q q ) 1
2(q q q q ) A
(2.186)
R = @ 2(q q + q q ) q q + q q
2(q q q q ) 2(q q + q q ) q q q + q
so that if d^ is the position of a site in the local body frame with respect to its centre of
mass, its position in the space xed frame (w.r.t. its centre of mass) is given by
d = R d^
(2.187)
4
sites
0
2
0
2
1
2
2
1 2
0 3
1 3
0 2
2
3
2
0
1 2
2
1
0 3
2
2
2 3
0 1
2
3
2
0
1
2
1 3
0 2
2 3
2
1
0 1
2
2
3
2
3
2.5.6.2 Integration of the Rigid Body Equations of Motion
The net translational force acting upon the rigid unit is
X
F = f
(2.188)
where f is the force on a rigid unit site, and the sum includes all sites in the body. The
translational motion can be integrated by the standard leapfrog algorithm.
t
t ) + t M F (t)
V (t + ) = V (t
(2.189)
2
2
1
4
An alternative approach is to dene \basic" and \secondary" particles. The basic particles are the
minimun number needed to dene a local body axis system. The remaining particle positions are expressed
in terms of the c.o.m. and the basic particles. Ordinary bond constraints can then be applied to the basic
particles provided the forces and torques arising from the secondary particles are transferred to the basic
particles in a physically meaningful way.
c CCLRC
67
t )
(2.190)
2
where M is the mass of the rigid unit, V is the rigid bodies c.o.m. velocity and X is the
c.o.m. position. The cartesian components of these quantitites are stored in the arrays:
gvxx, gvyy, and gvzz for c.o.m. velocity; and gcmx, gcmy, and gcmz for c.o.m. position.
The torque acting upon the body in the space xed frame is
X
= d f :
(2.191)
X (t + t) = X (t) + t V (t +
Transformed to the local body frame (and including the centrifugal terms) this is
^ = RT + eta:
(2.192)
where
x = (^(I )yy ^(I )zz )^!y !^ z
(2.193)
plus cyclic permutations for y and z components. The angular velocity transformed to the
local body frame, !^ , can then be integrated using the leapfrog algorithm and the diagonal
rotational inertia tensor.
t ) + t ^I ^(t)
t
!^ (t + ) = !^ (t
(2.194)
2
2
The new quaternions cannot be found so simply. DL POLY 2 uses Fincham's implicit
quaternion algorithm (FIQA) to do this [12]. In this algorithm the new quaternions are
found by solving the implicit equation
t Q[q(t)]^w(t) + Q[q(t + t)]^w(t + t)
q(t + t) = q(t) +
(2.195)
2
where w^ = [0; !^ ]T and Q[q] is
1
0
Q=
q0
1 BB q1
2 @ q2
q3
q1
q0
q3
q2
q2
q3
q0
q1
q3 1
q2 C
C
q1 A
q0
(2.196)
The above equation is solved iteratively with
q(t + t) = q(t) + t Q[q(t)]^w(t)
(2.197)
as the rst guess. Typically no more than 3 or 4 iterations are needed for convergence. At
each step the constraint
kq(t + t)k = 1
(2.198)
is imposed.
The quaternions are stored in the arrays q0, q1, q2 and q3. The angular velocity
(transformed to the body xed frame) is stored in the arrays omx, omy and omx, while
c CCLRC
68
the work arrays opx, opy, opz, oqx, oqy, oqz hold values of !^ (t) and !^ (t + t). The
torques, ^(t) are held in the work arrays tqx, tqy and tqz.
The NVE algorithm is implemented in nveq 1 which allows for a system containing a
mixture of rigid bodies and atomistic species, provided the rigid bodies are not linked to
other species by constraint bonds.
Thermostats and Barostats
It is straightforward to couple the rigid body equations of motion to a thermostat
and/or barostat. The thermostat is coupled to both the translational and rotational degrees
of freedom and so both the translational and rotational velocities are propagated in an
analogous manner to the thermostated atomic velocities. The barostat, however, is coupled
only to the translational degrees of freedom, not to the rotational ones.DL POLY 2 supports
both Hoover type and Berendsen thermostats and barostats for systems containing rigid
bodies. The Hoover thermostat is implemented in nvtq h1, the Hoover isotropic barostat
(plus themostat) in nptq h1 and the anisotropic barostat in nptq h3. The analogous
routines for the Berendsen algorithms are nvtq b1, nptq b1 and nptq b3.
2.5.6.3 Linked Rigid Bodies
The above integration algorithm can be used for rigid bodies in a system containing
\atomic" species (whose equations of motion are integrated with the standard leapfrog
algorithm). These rigid bodies may even be linked to other species (including other rigid
bodies) by extensible bonds. However if a rigid body is linked to an atom or another rigid
body by a bond constraint the above algorithm is not adequate. The reason is that the
constraint will introduce an additional force and torque onto the body that can only be
found after the integration of the unconstrained unit. DL POLY 2 has a suite of integration algorithms to cope with this situation in which both the constraint conditions and the
quaternion equations are solved similtaneously using an extension of the SHAKE algorithm
called \QSHAKE" [13].
The QSHAKE algorithm proceeds as follows: Consider the gure in which two rigid
bodies are linked by a constraint bond. We seek to choose F so that at the end of the
integration step the two sites in the constraint bond are a distance r apart. The integration
of the bodies as free units leaves the sites r0 apart. Since the constraint force produces
both a force and torque on the rigid units the correction to the constrained sites position
must include both the translation and rotation of the body as a whole. The translational
contribution is
1
xT = (t) F
(2.199)
M
The torque induced by the constraint force is
= da F
(2.200)
so the correction to the angular velocity of the body is
! = t I :
(2.201)
const
2
const
const
const
1
const
c CCLRC
69
The \rotational" correction to the position of the site is thus
(2.202)
xR = t (! da)
which in general will not be in the same direction as F and xT . If we denote the
components of xR parallel and perpendicular to F by xkR and x?R the correction
to the site position is
x = (xT + xkR) + x?R
(2.203)
Clearly the presence of the constraint force and torque will mean the positions and velocities
of the remaining sites in the rigid body will also have to be corrected. We proceed by seeking
an approximation to F then reintegrating the rigid body equations of motion with the
improved total forces and torques on the body. A few iterations are normally suÆcient
to achieve convergence: If we assume the bond distance r is large in comparison to the
correction then after the correction is made the bond length is
const
const
const
r
= p r0 + xk + (x?)
h
i
= p (r0) + 2r0 xk + xk + x?
h
i
p (r0) + 2r0 xk
2
2
2
2
2
2
(2.204)
(2.205)
x?R . Thus a rst order correction
where xk = P xT + xkR and x? = P
to the position of the constrained site is
x = xT + xkR
1 + hI (d e) d i e = (t) F
a
a
M
bodies
bodies
2
1
const
(2.206)
where e is the unit vector Fh =kF k. Theiterm in the f: : :g denes an eective mass,
M: where 1=M = 1=M + I (da e) da e.
The eective reduced mass for the two linked bodies, a and b, is = MaMb =(Ma +Mb).
As in the standard SHAKE algorithm, the reduced mass can then be used to predict the
constraint force
0
(2.207)
F
= t (r 2r r )
Note that each prediction of the constraint force requires the rigid body equations of motion
to be reintegrated accurately. If two bodies are linked by one constraint bond only two or
three iterations are necessary for convergence. However convergence may be slower if an
extended network of linked bodies is involved. Note also that the reduced mass needs to
be re-evaluated every time-step because it depends on the relative orienation of the two
bodies. Finally, we note the algorithm reduces to the standard SHAKE algorithm if the
rigid bodies are replaced by point atoms. In such a case, even though da is zero, care must
be taken to avoid the singularity arising from I .
const
1
const
2
2
const
2
2
1
c CCLRC
70
This \linked rigid body" algorithm is implemented in nveq 2 with the QSHAKE corrections to the forces applied in qshake. Again it is straightforward to couple these systems
to a Hoover type or Berendsen thermostat and/or barostat. The Hoover and Berendsen
thermostated versions are found in nvtq h2 and nvtq b2 respectively. The isotropic constant pressure implementations are found in nptq h2 and nptq b2, while the anisotropic
constant pressure routines are found in nptq h4 and nptq b4. An outline of the parallel
version of QSHAKE is given in section 2.6.8.
2.5.7 The DL POLY 2 Multiple Timestep Algorithm
For simulations employing a large spherical cuto rcut in the calculation of the interactions
DL POLY 2 oers the possibility of using a multiple timestep algorithm to improve the
eÆciency. The method is based on that described by Streett et al [38, 39] with extension
to Coulombic systems by Forester et al [40].
In themultiple timestep algorithm there are two cutos for the pair interactions: a
relatively large cuto (rcut) which is used to dene the standard Verlet neighbour list;
and a smaller cuto rprim which is used to dene a primary list within the larger cuto
sphere (see gure). Forces derived from atoms in the primary list are generally much
larger than those derived from remaining (so-called secondary) atoms in the neighbour list.
Good energy conservation is therefore possible if the forces derived from the primary atoms
are calculated every timstep, while those from the secondary atoms are calculated much
less frequently, and are merely extrapolated over the interval. DL POLY 2 handles this
procedure as follows.
DL POLY 2 updates the Verlet neighbour list at irregular intervals, determined by the
movement of atoms in the neighbour list (see section 2.1). The interval between updates
is usually of the order of 20 timesteps. Partitioning the Verlet list into primary and
secondary atoms always occurs when the Verlet list is updated, and thereafter at intervals
of multt timesteps (i.e. the multi-step interval specied by the user - see section 4.1.1).
Immediately after the partitioning, the force contributions from both the primary and
secondary atoms are calculated. The forces are again calculated in total in the subsequent
timestep. Thereafter, for multt-2 timesteps, the forces derived from the primary atoms
are calculated explicitly, while those derived from the secondary atoms are calculated by
linear extrapolation of the exact forces obtained in the rst two timesteps of the multi-step
interval. It is readily apparent how this scheme can lead to a signicant saving in execution
time.
Extension of this basic idea to simulations using the Ewald sum requires the following:
1. the reciprocal space terms are calculated only for the rst two timesteps of the multistep,
2. the contribution to the reciprocal space terms arising from primary interactions are
immediately subtracted, leaving only the long-range components. (This is done in
real space, by subtracting erf terms.);
3. the real space Coulombic forces arising from the secondary atoms are calculated in
c CCLRC
71
the rst two timesteps of the multi-step using the normal Ewald expressions (i.e. the
erfc terms).
4. the Coulombic forces arising from primary atoms are calculated at every timestep in
real space assuming the full Coulombic force;
In this way the Coulombic forces can be handled by the same multiple timestep scheme as
the van der Waals forces. The algorithm is described in detail in [40].
Note that the accuracy of the algorithm is a function of the multi-step interval multt,
and decreases as multt increases. Also, the algorithm is non-symplectic (i.e. it is not time
reversible) and is therefore susceptible to energy drift. Its use with a thermostat is therefore
advised.
rprim
rcut
dius rprim and secondary if outside this radius but within rcut. Interactions arising from primary atoms are evaluated every t
2.5.8 The DL POLY 2 RESPA Multiple Timestep Implementation
The DL POLY 2 RESPA Program is a variant of DL POLY 2 that handles the time reversible, multiple timestep RESPA algorithm due to Tuckerman and Berne [17, 18] as implemented by Procacci and Marchi for atomic and rigid ion systems[19]. However, it is not
applicable to systems which have rigid body molecules or constraints, and for this reason
the RESPA code is kept separate from the DL POLY 2 main source in the sub-directory
called respa.
The DL POLY 2 implementation allows the user to dene three concentric regions
around a given atom. Forces deriving from atoms in the innermost region are updated
more frequently (i.e. every timestep) than those in the immediate outer region, which in
turn are updated more frequently than those deriving from the outermost region. This
(depending on the relative sizes of each region and the frequency of the forces update)
c CCLRC
72
can represent a great computational saving. This is coupled with the advantage that the
algorithm is time reversible and therefore possesses long term stability.
The method is fully documented in [19]. A makele (Makele respa) is available in the
build sub-directory, which will build the RESPA program (DLRESPA.X). A test case may
be found in the data sub-directory.
2.6 DL POLY Parallelisation
DL POLY 2 is a distributed parallel molecular dynamics package based on the Replicated
Data parallelisation strategy [41, 42]. In this section we briey outline the basic methodology. Users wishing to add new features DL POLY 2 will need to be familiar with the
underlying techniques as they are described (in greater detail) in references [30, 42]).
2.6.1 The Replicated Data Strategy
The Replicated Data (RD) strategy [41] is one of several ways to achieve parallelisation
in MD. Its name derives from the replication of the conguration data on each node of a
parallel computer (i.e. the arrays dening the atomic coordinates ri, velocities vi and forces
f i , for all N atoms fi : i = 1; : : : ; N g in the simulated system, are reproduced on every
processing node). In this strategy most of the forces computation and integration of the
equations of motion can be shared easily and equally between nodes and to a large extent
be processed independently on each node. The method is relatively simple to program and
is reasonably eÆcient. Moreover, it can be \collapsed" to run on a single processor very
easily. However the strategy can be expensive in memory and have high communication
overheads, but overall it has proven to be successful over a wide range of applications.
These issues are explored in more detail in [41, 42].
Systems containing complex molecules present several diÆculties. They often contain
ionic species, which usually require Ewald summation methods [10, 43], and intra-molecular
interactions in addition to inter-molecular forces. These are handled easily in the RD
strategy, though the SHAKE algorithm [11] requires signicant modication [30].
The RD strategy is applied to complex molecular systems as follows:
1. Using the known atomic coordinates ri, each node calculates a subset of the forces
acting between the atoms. These are usually comprised of:
(a) atom-atom pair forces (e.g. Lennard Jones, Coulombic etc.);
(b) non-rigid atom-atom bonds;
(c) valence angle forces;
(d) dihedral angle forces;
(e) improper dihedral angle forces.
2. The computed forces are accumulated in (incomplete) atomic force arrays f i independently on each node;
c CCLRC
73
3. The atomic force arrays are summed globally over all nodes;
4. The complete force arrays are used to update the atomic velocities and positions.
It is important to note that load balancing (i.e. equal and concurrent use of all processors)
is an essential requirement of the overall algorithm. In DL POLY 2 this is accomplished
for the pair forces with an adaptation of the Brode-Ahlrichs scheme [22].
2.6.2 Distributing the Intramolecular Bonded Terms
DL POLY 2 handles the intramolecular in which the atoms involved in any given bond
term are explicitly listed. Distribution of the forces calculations is accomplished by the
following scheme:
1. Every atom in the simulated system is assigned a unique index number from 1 to N ;
2. Every intramolecular bonded term Utype in the system has a unique index number
itype : from 1 to Ntype where type represents a bond, angle or dihedral.
3. A pointer array keytype (ntype; itype ) carries the indices of the specic atoms involved
in the potential term labelled itype . The dimension ntype will be 2; 3 or 4, if the term
represents a bond, angle or dihedral.
4. The array keytype(ntype; itype ) is used to identify the atoms in a bonded term and
the appropriate form of interaction and thus to calculate the energy and forces. Each
processor is assigned the independent task of evaluating a block of (Int(Ntotal =Nnodes))
interactions.
The same scheme works for all types of bonded interactions. The global summation of
the force arrays does not occur until all the force contributions, including nonbonded forces
has been completed.
2.6.3 Distributing the Nonbonded Terms
In DL POLY 2 the nonbonded interactions are handled with a Verlet neighbour list [10]
which is reconstructed at intervals during the simulation. This list records the indices of all
`secondary' atoms within a certain radius of each `primary' atom; the radius being the cuto radius (rcut) normally applied to the nonbonded potential function, plus an additional
increment (rcut). The larger radius (rcut + rcut) permits the same list to be used for
several timesteps without requiring an update. The frequency at which the list must be
updated clearly depends on the thickness of the region rcut. In RD, the neighbour list is
constructed simultaneously on each node and in such a way as to share the total burden of
the work equally between nodes. Each node is responsible for a unique set of nonbonded
interactions and the neighbour list is therefore dierent on each node. DL POLY 2 uses
a method based on the Brode-Ahlrichs scheme [22] (see gure below) to construct the
neighbour list.
c CCLRC
74
Additional modications are necessary to handle the excluded atoms [42]. A distributed
excluded atoms list is constructed by DL POLY 2 at the start of the simulation. The list
is constructed so that the excluded atoms are referenced in the same order as they would
appear in the Verlet neighbour list if the bonded interactions were ignored, allowing for the
distributed structure of the neighbour list.
Brode Ahlrichs Algorithm
12 Atoms, 4 processors
1,2
1,3
1,4
1,5
1,6
1,7
2,3
2,4
2,5
2,6
2,7
2,8
3,4
3,5
3,6
3,7
3,8
3,9
4,5
4,6
4,7
4,8
4,9
4,10
5,6
5,7
5,8
5,9
5,10
5,11
6,7
6,8
6,9
6,10
6,11
6,12
7,8
7,9
7,10
7,11
7,12
8,9
8,10
8,11
8,12
8,1
9,10
9,11
9,12
9,1
9,2
10,11
10,12
10,1
10,2
10,3
11,12
11,1
11,2
11,3
11,4
12,1
12,2
12,3
12,4
12,5
Processor 0
Schematic diagram of the parallel implementation of the Brode-Ahlrichs algorithm.
The diagram illustrates the reordering of the upper triangular matrix of n(n-1)/2 pair
interactions so that the rows of the matrix are of approximately equally length. Each entry
in the table consists of a primary atom index (constant within a row) and a \neighbouring"
atom index. Rows are assigned sequentially to nodes. In the diagram node 0 deals with
rows 1, 5 and 9, node 1 to rows 2, 6, and 10 etc.
When a charge group scheme (as opposed to an atomistic scheme) is used for the
non-bonded terms, the group-group interactions are distributed using the Brode-Ahlrichs
approach. This makes the Verlet list considerably smaller, thus saving memory, but also
results in a more \coarse grain" parallelism. The consequence of which is that performance
c CCLRC
75
with a large number of processors will degrade more quickly than with the atomistic scheme.
Once the neighbour list has been constructed, each node of the parallel computer may
proceed independently to calculate the pair force contributions to the atomic forces.
2.6.4 Modications for the Ewald Sum
For systems with periodic boundary conditions DL POLY 2 employs the Ewald Sum to
calculate the Coulombic interactions (see section 2.4.5).
Calculation of the real space component in DL POLY 2 employs the algorithm for the
calculation of the nonbonded interactions outlined above. The reciprocal space component
is calculated using the schemes described in [43], in which the calculation can be parallelised by distribution of either k vectors or atomic sites. Distribution over atomic sites
requires the use of a global summation of the qi exp( ik rj ) terms, but is more eÆcient in
memory usage. Both strategies are computationally straightforward. Subroutine ewald1
distributes over atomic sites and is often the more eÆcient of the two approaches. Subroutine ewald1a distributes over the k vectors and may be more eÆcient on machines with
large communication latencies.
Other routines required to calculate the ewald sum include ewald2, ewald3 and
ewald4. The rst of these calculates the real space contribution, the second the self
interaction corrections, and the third is required for the multiple timestep option.
2.6.5 Three Body Forces
DL POLY 2 can calculate three body interactions of the valence angle type [44]. These are
not dealt with in the same way as the normal nonbonded interactions. They are generally
very short ranged and are most eectively calculated using a link-cell scheme [23]. No
reference is made to the Verlet neighbour list nor the excluded atoms list. It follows that
atoms involved in the same three-body term can interact via nonbonded (pair) forces and
ionic forces also. The calculation of the three-body terms is distributed over processors on
the basis of the identity of the central atom in the bond. A global summation is required
to specify the atomic forces fully.
2.6.6 Metal Potentials
The simulation of metals by DL POLY 2 makes use of density dependent potentials of the
Sutton-Chen type [6]. The dependence on the atomic density presents no diÆculty however,
as this class of potentials can be resolved into pair contributions. This permits the use of
the distributed Verlet neighbour list outlined above.
2.6.7 Summing the Atomic Forces
The nal stage in the RD strategy, is the global summation of the atomic force arrays. This
must be done After all the contributions to the atomic forces have been calculated. To do
this DL POLY 2 employs a global summation algorithm [41], which is generally a system
specic utility.
c CCLRC
76
Similarly, the total conguration energy and virial must be obtained as a global sum of
the contributing terms calculated on all nodes.
2.6.8 The RD-SHAKE and Parallel QSHAKE Algorithms
The RD-SHAKE algorithm is a parallel adaptation of SHAKE couched in the Replicated
Data strategy. The essentials of the RD-SHAKE method are as follows.
1. The bond constraints acting in the simulated system are shared equally between the
processing nodes.
2. Each node makes a list recording which atoms are bonded by constraints it is to
process. Entries are zero if the atom is not bonded.
3. A copy of the array is passed to each other node in turn. The receiving node compares
the incoming list with its own and keeps a record of the shared atoms and the nodes
which share them.
4. In the rst stage of the SHAKE algorithm, the atoms are updated through the usual
Verlet algorithm, without regard to the bond constraints.
5. In the second (iterative) stage of SHAKE, each node calculates the incremental correction vectors for the bonded atoms in its own list of bond constraints. It then sends
specic correction vectors to all neighbours that share the same atoms, using the
information compiled in step 3.
6. When all necessary correction vectors have been received and added the positions of
the constrained atoms are corrected.
7. Steps 5 and 6 are repeated until the bond constraints are converged.
8. After convergence the coordinate arrays on each node are passed to all the other
nodes. The coordinates of atoms that are not in the constraint list of a given node
are taken from the incoming arrays (an operation we term splicing).
9. Finally, the change in the atom positions is used to calculate the atomic velocities.
This scheme contains a number of non-trivial operations, which are described in detail
in [30]. However some general comments are worth making.
The compilation of the list of constrained atoms on each node, and the circulation
of the list (items 1 - 3 above) need only be done once in any given simulation. It also
transpires that in sharing bond contraints between nodes, there is an advantage to keeping
as many of the constraints pertaining to a particular molecule together on one node as is
possible within the requirement for load balancing. This reduces the data that need to
be transferred between nodes during the iteration cycle. It is also advantageous, if the
molecules are small, to adjust the load balancing between processors to prevent shared
atoms. The loss of balance is compensated by the elimination of communications during
the SHAKE cycle. These techniques are exploited by DL POLY 2 .
c CCLRC
77
The QSHAKE algorithm is an extension of the SHAKE algorithm for constraint bonds
between rigid bodies. The parallel strategy is very similar to that of RD-SHAKE. The only
signicant dierence is that increments to the atomic forces, not the atomic positions, are
passed between processors at the end of each iteration.
Chapter 3
DL POLY 2 Construction and
Execution
78
c CCLRC
79
Scope of Chapter
This chapter describes how to compile a working version of DL POLY 2 and how to run it.
c CCLRC
80
3.1 Constructing DL POLY 2 : an Overview
3.1.1 Constructing the Standard Version
DL POLY 2 was designed as a package of useful subroutines rather than a single program,
which means that users were to be able to construct a working simulation program of
their own design from the subroutines available, which is capable of performing a specic
simulation. However we recognise that many, perhaps most, users will be content with
creating a standard version that covers a wide variety (if not all) of the possible applications
and for this reason we have provided the necessary tools to assemble such a version. The
method of creating the standard version is described in detail in this chapter, however a
brief step-by-step description follows.
1. DL POLY 2 is supplied as a UNIX compressed tar le. This must uncompressed and
un-tared to create the DL POLY 2 directory (section 1.4).
2. In the build subdirectory you will nd the required DL POLY 2 makele (see section
3.2.1 and Appendix A, where the main Makele is listed). This must be copied into
the subdirectory containing the relevant source code. In most cases this will be the
source subdirectory.
3. The makele is executed with the appropriate keywords (section 3.2.1) which select for
specic computers and if a parallel machine is used, the appropriate communication
software.
4. The makele produces the executable version of the code, which as a default will be
named DLPOLY.X and located in the execute subdirectory.
5. To run the executable for the rst time you require the les CONTROL, FIELD and
CONFIG (and possibly TABLE if you have tabulated potentials). These must be
present in the directory from which the program is executed. (See section 4.1 for the
description of the input les.)
6. Executing the program will produce the les OUTPUT, REVCON and REVIVE (and
optionally STATIS, HISTORY, RDFDAT and ZDNDAT) in the executing directory.
(See section 4.2 for the description of the output les.)
This simple procedure is enough to create a standard version to run the supplied test
cases. (For versions preceeding 2.11, it will not run the larger benchmark cases however.)
Creating a larger executable, or one which is tailored to an application dierent from the
test cases is more complicated. The main diÆculty centres on assigning appropriate array
dimensions to meet the application's needs. In versions of DL POLY 2 after 2.11 these
dimensions are calculated by the subroutine parset.f and its support routines cfgscan.f,
conscan.f and fldscan.f. These support routines scan the CONFIG, CONTROL and
FIELD les at the start of a run and estimate the required array sizes. (A description of
the individual arrays found in DL POLY 2 is provided in Appendix C of the DL POLY 2
Reference Manual.)
c CCLRC
81
In versions preceeding 2.11, the size of the DL POLY 2 executable is determined by
the the dl params.inc (include) le (see section 7.1.1), which species all the FORTRAN
parameters of the code and is included in each subroutine at compile time. This le is found
in the source directory and is internally documented (it is also documented in chapter 7).
Reconstructing the dl params.inc for a new simulation is the most diÆcult aspect of
preparing a DL POLY 2 executable. If the parameters are not appropriate, DL POLY 2
will complain if any parameter is too small and abort in execution. Each such error will
entail a recompilation of the code, and DL POLY 2 generally detects only one error at a
time! Fortunately, the process of creating a new dl params.inc le is greatly assisted by
the utility program parset (see section 6.1.1). Provided the CONTROL, CONFIG and
FIELD les are available, parset will create a suitable parameters le for you. (See section
3.2.2).
3.1.2 Constructing Nonstandard Versions
In constructing a nonstandard DL POLY 2 simulation program, the rst requirement is for
the user to write a program to function as the root segment. The source directory contains
an example of such a root program: dlpoly. This root program calls the major routines
required to perform the simulation and also controls the normal \molecular dynamics cycle" which consists of forces calculation followed by integration of the equation of motion.
dlpoly also monitors the cpu usage and brings about a controlled termination of the program if the usage approaches the allotted job time within a pre-set closure time. Lastly,
dlpoly is the routine that rst opens the OUTPUT le (section 4.2.2), which provides
the summary of the job. Users are recommended to study the dlpoly root as a model for
other implementations of the package they may wish to construct. The dependencies and
calling hierarchies of all the DL POLY 2 subroutines can be found in the Appendix of the
DL POLY 2 Reference Manual.
If additional functionality is added to DL POLY 2 by the user, the parset.f routine
(and its support routines) will need modifying to allow specication of the dimensions of
any new arrays. (A description of the existing arrays found in DL POLY 2 is provided in
the Appendix of the DL POLY 2 Reference Manual.)
Any molecular dynamics simulation performs ve dierent kinds of operation: initialisation; forces calculation; integration of the equations of motion; calculation of system
properties; and job termination. It is worth considering these operations in turn and to indicate which DL POLY 2 routines are available to perform them. We do not give a detailed
description, but provide only a guide. Readers are recommended to examine the dierent
routines described in chapter 7 of the DL POLY 2 Reference Manual for further details
(particularly regarding further dependencies i.e. additional routines that must be called.)
The following outline assumes a system containing exible molecules held together by rigid
bonds, but without rigid bodies.
Initialisation requires rstly that the program determine what kind of parallel machine
it is running on. The routine machine determines how many processing nodes are being
used and also returns the node identity to each process. Next the job control information is
required; this is obtained by the routine simdef, which reads the CONTROL le (section
c CCLRC
82
4.1.1). The description of the system to be simulated: the types of atoms and molecules
present and the intermolecular forces; are obtained by the sysdef routine, which reads the
FIELD le (section 4.1.3). Lastly, the atomic positions and velocities must be provided.
These are obtained by the sysgen routine, which reads the CONFIG le (section 4.1.2)
and also generates the initial velocities if required to do so. If the system contains constraint bonds, the routine passcon is required to process molecular connectivity data and
establish the communication procedure between nodes, and the quench routine is required
to set the starting velocities correctly. Also needed in the initialisation, is the routine forgen, which constructs the interpolation arrays for the short-range forces calculations, and
the routine exclude which identies atoms that are explictly chemically bonded through
bonds, constraints or valence angles. The resulting list is known as the excluded atoms list.
The calculation of the pair forces represents the bulk of any simulation. A Verlet
neighbour list is used by DL POLY 2 in calculating the atomic forces. The routine that
constructs this this is called parlst. This routine builds the neighbour list taking into
account the occurrence of atoms in the excluded atoms list. The routine srfrce calculates
the short-range (van der Waals) forces, making use of the images routine to handle any
periodic boundary conditions. Coulombic forces are handled by a varity of routines: coul0,
coul1 and coul2 handle Coulombic forces without periodic boundaries; ewald1, ewald2
and ewald3 are used for systems with periodic boundaries (an additional routine: ewald4
is necessary for the multiple timestep algorithm). Intramolecular forces require the routines
angfrc, bndfrc and dihfrc. If the multiple timestep algorithm is required, the routine
multiple must be used to call the various forces routines. It also calls the primlst routine
to split the interaction list into primary and secondary neighbours. The decision to update
the neighbour list is handled by the routine vertest. The routine extnfld is required
if the simulated system has an external force eld (e.g. electrostatic eld) operating. To
help with equilibration simulations, the routine fcap is sometimes required to reduce the
magnitude of badly equilibrated forces. Since DL POLY 2 is based on the replicated data
strategy, a global sum routine (gdsum) is required to sum the atomic forces on all nodes.
Integration of the equations of motion is handled by one of the routines listed and
described in section 2.5. For example routines nve 0, nvt e0, nvt h0, nvt b0 etc. are
used if no constraint forces are present. These routines treat the NVE, Evans-NVT, HooverNose-NVT and NVT-Berendsen ensembles respectively. The corresponding versions of these
routines which handle constraint forces are nve 1, nvt e1, nvt h1 or nvt b1. These
versions call the routine rdshake 1 to handle the constraints. rdshake 1 itself calls
a number of additional routines: merge, shmove and splice. For ad hoc temperature
scaling, the routine vscaleg is required.
As mentioned elsewhere, DL POLY 2 does not contain many routines for computing
system properties during a simulation. Radial distributions may be calculated however,
using the routines rdf0 and rdf1. Similarly diffsn0 and diffsn1 calculate approximate
mean square displacements. Ordinary thermodynamic quantities are calculated by the
routine static, which also writes the STATIS le (section 4.2.7). Routine traject writes
the HISTORY (section 4.2.1) le for later analysis.
Job termination is handled by the routine result which writes the nal summaries in
the OUTPUT le and dumps the restart les REVIVE and REVCON (sections 4.2.4 and
c CCLRC
83
4.2.3 respectively).
An idea of the construction of a DL POLY 2 program can be obtained from the following
owchart. The example represents a DL POLY 2 program which uses the multiple timestep
algorithm, with bond constraints and the Nose-Hoover thermostat.
c CCLRC
MACHINE
SIMDEF
SYSDEF
SYSGEN
FORGEN
EXCLUDE
INTLIST
GAUSS
QUENCH
VERTEST
PARLST
84
PASSCON
SHMOVE
SPLICE
VSCALE
LRCORRECT
MULTIPLE
EWALD1
BNDFRC
PRIMLST
ANGFRC
SRFRCE
DLPOLY
DIHFRC
EWALD2,4
EXTNFLD
COUL0,1 or 2
GDSUM FORCES
EWALD3
FCAP
RDF0
NVT_H1
SHMOVE
VSCALE
RDSHAKE_1
SPLICE
STATIC
MERGE
REVIVE
DIFFSN0,1
TRAJECT
RESULT
REVIVE
RDF1
c CCLRC
85
3.2 Compiling and Running DL POLY 2
3.2.1 Compiling the Source Code
When you have obtained DL POLY 2 from Daresbury Laboratory and unpacked it, your
next task will be to compile it. To aid compilation a general makele (\Makele") has
been provided in the sub-directory build (see Appendix A to this document). The general
DL POLY 2 makele will build an executable with a wide range of functionality - suÆcient
for the test cases and for most users requirements. Other makeles are found in the build
sub-directory for variants of DL POLY 2 , such as the respa version. Users will need to
modify the makele if they are to add additional functionality to the code, or if it requires
adaptation for a non specied computer. Modications may also be necessary if the Smooth
Particle Mesh Ewald method is to be correctly incorporated (see below: \Modifying the
makele").
Copy the makele from the build sub-directory to the source sub-directory and run it
there - it will create the executable in the execute sub-directory. The compilation of the
program is initiated by typing the command:
make target
where target is the specication of the required machine (e.g. sp2-mpi). For many computer
systems this command is suÆcient to compile a working version of DL POLY 2 .
The full specication of the make command is as follows
make <TARGET= : : : > < STRESS=: : : > < TYPE=: : : > < EX=: : : > < BINROOT=: : : >
< PVM NODES=: : : >
where some (or all) of the keywords may be omitted. The keywords and their use are
described below. Note that keywords may also be set in the unix environment (e.g. with
the \setenv" command in a C-shell).
The makele rst takes each FORTRAN routine in turn and scans it with a C-preprocessor.
The purpose of this is to activate the required features in the code (and extract non-selected
features from the original source code). For example if MPI is specied, all other message
passing calls pertaining to PVM (for example) are removed. If NOSTRESS is specied, the
statements for calculating the stress tensor are removed. The result of the preprocessing
is a temporary FORTRAN le which is then compiled to produce the object code. If all is
well, the makele will combine the object code with the system libraries and produce the
executable.
3.2.1.1 Keywords for the Makele
1. TARGET
The TARGET keyword indicates which kind of computer the code is to be compiled for. This must be specifed - there is no default value. Valid targets can be
listed by the makele if the command make is typed, without arguments. The list
c CCLRC
86
frequently changes as more targets are added and redundant ones removed. Users are
encouraged to extend the Makele for themselves, using existing targets as examples.
2. STRESS
The STRESS keyword activates the code that calculates the stress tensor in the
DL POLY 2 code. The arguments are:
NOSTRESS - if the stress tensor is not required;
STRESS - if the stress tensor is required (default).
Calculation of the stress tensor is essential if \constant stress" (Rahman-Parrinello)
MD is required.
3. TYPE
The TYPE keyword creates variants of the DL POLY 2 code which determine which
scheme is to be used for the interpolation of the short-range potential and force arrays.
The arguments are:
3pt - compile with 3-point interpolation (default);
4pt - compile with 4-point interpolation;
rsq - compile with r interpolation.
A discussion of the merits of the dierent interpolation methods is given below (section
3.2.1.3).
4. EX
The EX keyword species the executable name. The default name for the executable
is \DLPOLY.X".
5. BINROOT
The BINROOT keyword species the directory in which the executable is to be stored.
The default setting is \../execute".
6. PVM NODES
The PVM NODES keywords species how many processes are to be invoked when
the code is run under PVM. There is no default value. If this is not set at compile
time the code will compile but produce an error message on execution. If you get this
error (error 1) delete the module initcomms.o and recompile with PVM NODES set
to a number consistent with a hypercube architecture (one of (1,) 2, 4, 8 etc).
2
c CCLRC
87
3.2.1.2 Modifying the Makele
1. Changing the TARGET
If you do not intend to run DL POLY 2 on one of the specied machines, you must
add appropriate lines to the makele to suit your circumstances. The safest way
to do this is to modify an existing TARGET option for your purposes. The makele
supplied with DL POLY 2 contains examples for serial, PVM, and MPI environments
as well as for Intel and Cray (T3E) parallel machines so you should nd one close to
your requirements. You must of course be familiar with the appropriate invocation
of the FORTRAN compiler for your local machine and also any alternatives to PVM
or MPI your local machine may be running. After DL POLY 2 Version 2.12, the
required C preprocessor is supplied with the source code, and is called dpp.c (written
by J. Genornowicz, Southampton University, 1999). If you wish to compile for MPI
or PVM systems remember to ensure the appropriate library directories are included
in the C-preprocessing ags (CPPFLAGS). If you intend the program for a single
processor machine use the ag -DSERIAL (see the \sun" example in the makele).
2. Enabling the Smooth Particle Mesh Ewald
Users of DL POLY 2 Version 2.12 (and above) should note that modications to
the makele may be required if the code is automatically to incorporate the Smooth
Particle Mesh Ewald (SPME) . Primarily this requires a specication of the system library location of the 3D Fast Fourier Transform (FFT) routine implicit in the method.
The default FFT routine for DL POLY 2 is the public domain code FFTW, but this
is not specied for all platforms represented in the makele. The user who wishes to
use the SPME feature should check the relevant part of the makele to make sure
this is enabled (this is generally made clear in the makele comments). The SPME
feature is enabled by setting the parameter FFTW LIBRARY to specify the location
of the FFTW software, and by inserting the ag -DFFTW in the CPFLAGS list (see
above). Note that for most parallel systems represented in the makele the appropriate FFT is already enabled (which is usually not FFTW). This is particularly the
case for Cray T3E, IBM SP/2 and parallel SGI machines.
3. MPI and PVM implementations
The implementation of MPI may dier between sites. On some systems the Fortran callable subroutine names are expected to end with an underscore (\ "). If this
is the case the ag -DMPIU must be included as part of the C-preprocessing ags
and the le \mpif.h" copied from the MPI library directory into the source directory.
Alternatively you can set the path to the MPI library either the \-I" option on the
C-preprocessing ags. The DL POLY 2 makele assumes you have copied the le
over (see the entry hp-mpi: in the makele). This appends an underscore to all MPI
subroutine names and to the name of the MPI common block. If the underscores are
not required the ag must be omitted (see the entry \sp2-mpi:).
c CCLRC
88
When using MPI you need a copy of the MPI include le \mpif.h" in the source
directory. On many machines this is stored in the /usr/include directory, in which
case the make procedure should nd it automatically (as it also does for IBM SP/2
and Cray T3E machines, where it is stored elsewhere). However, if the make reports
a failure to nd the \mpif.h" le, you must amend the makele to ensure that it
copied from the true location before C-preprocessing is attempted. There are several
examples in the makele of how this is done.
Similarly when using PVM you need to place a copy of the PVM include le \pvmf.h"
in the source directory or copy it in before C-preprocessing.
4. Problems with optimization ?
Some subroutines do not compile correctly when using optimization on some compilers. This is not the fault of the DL POLY 2 code, but of the compiler concerned.
This is circumvented by compiling the oending subroutines unoptimised. See the
entries for various machines in the makele to see how this is done if you experience
problems with other subroutines.
5. Changing the Timer
The only other routine likely to cause problems is timchk, which requires a machine specic timer. The makele should select the appropriate timer for you, but if
the timer routine you require is not included you will need to add the appropriate lines
of code. timchk returns the elapsed time in seconds. Note that the C routine etime
may be used on many unix systems. It is used as the default timer by DL POLY 2
on serial and PVM systems.
6. Adding new functionality
To include a new subroutine in the code simply add subroutine.o to the list of object
names in the makele. The simpliest way is to add names to the \OBJ ALL" list.
3.2.1.3 Note on Interpolation Schemes
In DL POLY 2 the short-range (Van der Waals) contributions to energy and force are
evaluated by interpolation of tables constructed at the beginning of execution. DL POLY 2
caters for three dierent interpolation schemes: 3-point and 4-point in r-space and linear
interpolation in r -space. Tabulation in r avoids the use of the square root function in
evaluation of the non-bonded interactions, and thus typically decreases execution time by
10-15 %. Note that tabulation in r usually requires more grid points (and hence more
memory) than tabulation in r. This is to ensure suÆcient accuracy is retained at small r.
A guide to the minimum number of grid points (mxgrid) required for interpolation in
r to give good energy conservation in a simulation is:
mxgrid 100(rcut=rmin)
2
2
2
c CCLRC
89
where rmin is the smallest position minimum of the non-bonded potentials in the system. The parameter mxgrid is dened in the dl params.inc le, and must be set before
compilation.
A guide to the minimum number of grid points required for interpolation in r is:
mxgrid 100(rcut=rmin)
where rmin is again the smallest position minimum of the non-bonded potentials in the
system.
For users in doubt as whether to use r or r -space interpolation we recommend the
former. This is because tabulation in r is less demanding on memory requirements and less
prone to inaccuracy should too small a value of mxgrid, or too large a value of rcut, be
used. Tabulation in r is therefore the default option for DL POLY, r interpolation can be
specied at compile time by `making' the executable with the directive TYPE=rsq.
The other issue of concern to users is the choice of 3 or 4 point schemes in r-space interpolation. The relative merits are as follows: 4 point interpolation may permit a smaller
number of grid points to be used in the interpolation tables thus saving on memory requirements. 3 point interpolation is quicker than 4 point interpolation and normally suÆciently
accurate. The choice involves decisions about speed, accuracy and memory requirements.
3-point interpolation is the default option.
A utility program tabchk is provided in the DL POLY utility sub-directory to help
users choose a suÆciently accurate interpolation scheme (including array sizes) for their
needs.
2
2
2
2
3.2.2 Assisting Compilation with the Utility Program parset
A particular diÆculty in creating a working version of DL POLY 2 prior to version 2.11 is
creating the dl params.inc le (section 7.1.1), which species (among other things) the
array sizes for the compiled code. The copy of dl params.inc supplied with DL POLY 2
contains settings appropriate for the test cases and some of the benchmarks but is not guaranteed to be appropriate for any user's specic requirements. Users must determine their
own requirements and so produce their own version of dl params.inc before compiling a
working version. While DL POLY 2 contains many error checks to prevent the arrays being
exceeded during a run, it is tedious to have to recompile the code each time an error is
detected. Furthermore the large number of parameters required to specify the entire code
makes it very unlikely that the code will run successfully rst time, or even after several
attempts.
To assist with this diÆculty, the utility program parset has been created (section
6.1.1). It can be used to create a dl params.inc le that is suitable for the simulation
being attempted. It works by scanning the DL POLY 2 input les (CONTROL, FIELD
and CONFIG) and then writing out a sample dl params.inc le, which has the name
new params.inc.
parset is not foolproof however. The user must prepare the correct input les beforehand, which can be diÆcult without the error checking the DL POLY 2 code aords.
Also, because of the complexity of the requirements, parset can only supply a reasonable
c CCLRC
90
estimate of some of the array dimensions, and these may not be quite right for every case.
(It will be reasonably close however). Notwithstanding the limitations of parset its use as
a labour saving device is recommended.
parset is described in detail in section 6.1.1. The program is found in the utility
subdirectory.
3.2.3 Running DL POLY 2
To run the DL POLY 2 executable (DLPOLY.X) you will initially require three, possibly
four, input data les, which you must create in the execute sub-directory, (or whichever
sub-directory you keep the executable program.) The rst of these is the CONTROL le
(section 4.1.1), which indicates to DL POLY 2 what kind of simulation you want to run,
how much data you want to gather and for how long you want the job to run. The second
le you need is the CONFIG le (section 4.1.2). This contains the atom positions and,
depending on how the le was created (e.g. whether this is a conguration created from
`scratch' or the end point of another run), the velocities also. The third le required is the
FIELD le (section 4.1.3), which species the nature of the intermolecular interactions, the
molecular topology and the atomic properties, such as charge and mass. Sometimes you
will require a fourth le: TABLE (section 4.1.5), which contains the potential and force
arrays for functional forms not available within DL POLY 2 (usually because they are too
complex e.g. spline potentials).
Examples of input les are found in the data sub-directory, which can be copied into
the execute subdirectory using the select macro found in the execute sub-directory.
A successful run of DL POLY 2 will generate several data les, which appear in the
execute sub-directory. The most obvious one is the le OUTPUT (section 4.2.2), which
provides an eective summary of the job run: the input information; starting conguration; instantaneous and rolling-averaged thermodynamic data; nal congurations; radial
distribution functions (RDFs); and job timing data. The OUTPUT le is human readable.
Also present will be the restart les REVIVE (section 4.2.4) and REVCON (section 4.2.3).
REVIVE contains the accumulated data for a number of thermodynamic quantities and
RDFs, and is intended to be used as the input le for a following run. It is not human
readable. The REVCON le contains the restart conguration i.e. the nal positions, velocities and forces of the atoms when the run ended and is human readable. The STATIS
le (section 4.2.7) contains a catalogue of instantaneous values of thermodynamic and other
variables, in a form suitable for temporal or statistical analysis. Finally, the HISTORY le
(section 4.2.1) provides a time ordered sequence of congurations to facilitate further analysis of the atomic motions. Depending on which version of the traject subroutine you
compiled in the code, this le may be either formatted (human readable) or unformatted.
You may move these output les back into the data sub-directory using the store macro
found in the execute sub-directory.
Note that versions of DL POLY 2 after 2.10 may also create the les RDFDAT and
ZDNDAT, containing the RDF and Z-density data respectively. They are both human
readable les.
c CCLRC
91
3.2.4 Restarting DL POLY 2
The best approach to running DL POLY 2 is to dene from the outset precisely the simulation you wish to perform and create the input les specic to this requirement. The program
will then perform the requested simulation, but may terminate prematurely through error,
inadequate time allocation or computer failure. Errors in input data are your responsibility, but DL POLY 2 will usually give diagnostic messages to help you sort out the trouble.
Running out of job time is common and provided you have correctly specied the job time
variables (using the close time and job time directives - see section 4.1.1) in the CONTROL le, DL POLY 2 will stop in a controlled manner, allowing you to restart the job as
if it had not been interrupted.
To restart a simulation after normal termination you will again require the CONTROL
le, the FIELD (and TABLE) le, and a CONFIG le, which is the exact copy of the
REVCON le created by the previous job. You will also require a new le: REVOLD
(section 4.1.4), which is an exact copy of the previous REVIVE le. If you attempt to restart
DL POLY 2 without this additional le available, the job will fail. Note that DL POLY 2
will append new data to the existing STATIS and HISTORY les if the run is restarted,
other output les will be overwritten.
In the event of machine failure, you should be able to restart the job in the same way
from the surviving REVCON and REVIVE les, which are dumped at intervals to meet
just such an emergency. In this case check carefully that the input les are intact and use
the HISTORY and STATIS les with caution - there may be duplicated or missing records.
The reprieve processing capabilities of DL POLY 2 are not foolproof - the job may crash
while these les are being written for example, but they can help a great deal. You are
advised to keep backup copies of these les, noting the times they were written, to help
you avoid going right back to the start of a simulation.
You can also extend a simulation beyond its initial allocation of timesteps, provided
you still have the REVCON and REVIVE les. These should be copied to the CONFIG
and REVOLD les respectively and the directive timesteps adjusted in the CONTROL
le to the new total number of steps required for the simulation. For example if you wish to
extend a 10000 step simulation by a further 5000 steps use the directive timesteps 15000
in the CONTROL le and include the restart directive. You can use the restart scale
directive if you want to reset the temperature at the restart, but note that this also resets
all internal accumulators (timestep included) to zero.
3.3 A Guide to Preparing Input Files
The CONFIG le and the FIELD le can be quite large and unwieldy particularly if a
polymer or biological molecule is involved in the simulation. This section outlines the paths
to follow when trying to construct les for such systems. The description of the DL POLY 2
force eld in chapter 2 is essential reading. The various utility routines mentioned in this
section are described in greater detail in chapter 6. Many of these have been incorporated
into the DL POLY 2 Graphical User Interface [20] and may be convenently used from there.
c CCLRC
92
3.3.1 Inorganic Materials
The utility genlat can be used to construct the CONFIG le for relatively simple lattice
structures. Input is interactive. The FIELD le for such systems are normally small and can
be constructed by hand. The utility genlat.to constructs the CONFIG le for truncatedoctahedral boundary conditions. Otherwise the input of force eld data for crystalline
systems is particularly simple, if no angular forces are required (notable exceptions to this
are zeolites and silicate glasses - see below). Such systems require only the specication of
the atomic types and the necessary pair forces. The reader is referred to the description of
the DL POLY 2 FIELD le for further details (section 4.1.3).
DL POLY 2 allows the simulation of zeolites and silicate (or other) glasses. Both these
materials require the use of angular forces to describe the local structure correctly. In both
cases the angular terms are included as three body terms, the forms of which are described
in chapter 2. These terms are entered into the FIELD le with the pair potentials. Note
that you cannot use truncated octahedral or rhombic dodecahedral boundary conditions in
conjunction with three body forces, due to the use of the link-cell algorithm for evaluating
the forces.
An alternative way of handling zeolites is to treat the zeolite framework as a kind of
macromolecule (see below). This was the suggested method for users of DL POLY 1.1, and
experience showed that this is quite adequate, provided it is remembered that the periodicity
of the system requires that \bonds" be described that cross the boundaries of the MD cell
and link with images of atoms from the opposite side. Specifying all this is tedious and is
best done computationally: what is required is to determine the nearest image neighbours
of all atoms and assign appropriate bond and valence angle potentials. (This may require
the denition of new bond forces in subroutine bndfrc, but this is easy.) What must be
avoided at all costs is specifying the angle potentials without specifying bond potentials. In
this case DL POLY 2 will automatically cancel the non-bonded forces between atoms linked
via valence angles and the system will collapse. The advantage of this method is that the
calculation is likely to be faster using three-body forces. This method is not recommended
for amorphous systems.
3.3.2 Macromolecules
Simulations of proteins are best tackled using the package DLPROTEIN [21] which is an
adaptation of DL POLY specic to protein modelling. However you may simulate proteins
and other macromolecules with DL POLY 2 if you wish. This is described below.
If you select a protein structure from a SEQNET le (e.g. from the Brookhaven
database), use the utility proseq to generate the le CONFIG. This will then function
as input for DL POLY 2 . Some caution is required here however, as the protein structure
may not be fully determined and atoms may be missing from the CONFIG le.
If you have the \edit.out" le produced by AMBER for your molecule use this as
the CONNECT DAT input le for the utility ambforce. ambforce will produce the
DL POLY 2 FIELD and CONFIG les for your molecule.
If you do not have the \edit.out" le things are a little more tricky, particularly in
c CCLRC
93
coming up with appropriate partial charges for atomic sites. However there are a series of
utilities that will at least produce the CONNECT DAT le for use with ambforce. We
now outline these utilities and the order in which they should be used.
If you have a structure from the Cambridge Structural database (CSDB) then use the
utility fraccon to take fractional coordinate data and produce a CONNECT DAT and
\ambforce.dat" le for use with ambforce. Note that you will need to modify fraccon to
get the AMBER names correct for sites in your molecule. The version of fraccon supplied
with DL POLY 2 is specic to the valinomycin molecule.
If you require an all atom force eld and the database le does not contain hydrogen
positions then use the utility fracfill in place of fraccon. fraccon produces an output
le HFILL which should then be used as input for the utility hfill. The hfill utility lls
out the structure with the missing hydrogens. (Note that you may need to know what the
atomic charges are in some systems, for example the AMBER charges from the literature.)
Note: with minor modications the utilities fracfill and fraccon can be used on
structures from databases other than the Cambridge structural database.
3.3.3 Adding Solvent to a Structure
The utility wateradd adds water from an equilibrated conguration of 256 SPC water
molecules at 300 K to ll out the MD cell. The utility solvadd lls out the MD box with
single-site solvent molecules from a f.c.c lattice. The FIELD les will then need to be edited
to account for the solvent molecules added to the le.
Hint: to save yourself some work in entering the non-bonded interactions variables
involving solvent sites to the FIELD le put two bogus atoms of each solvent type at the
end of the CONNECT DAT le (for AMBER force-elds) the utility ambforce will then
evaluate all the non-bonded variables required by DL POLY 2 . Remember to delete the
bogus entries from the CONFIG le before running DL POLY 2 .
3.3.4 Analysing Results
DL POLY 2 is not designed to calculate every conceivable property you might wish from
a simulation. Apart from some obvious thermodynamic quantities and radial distribution
functions, it does not calculate anything beyond the atomic trajectories on-line. You must
therefore be prepared to post-process the HISTORY le if you want other information.
There are some utilities in the DL POLY 2 package to help with this, but the list is far
from exhaustive. In time, we hope to have many more. Our users are invited to submit
code to the DL POLY 2 public library to help with this.
The utilities available are described in the DL POLY 2 Reference Manual 6. Users
should also be aware that many of these utilities are incorporated into the DL POLY 2
Graphical User Interface [20].
3.3.5 Choosing Ewald Sum Variables
This section outlines how to optimise the accuracy of the Ewald sum parameters for a
given simulation. In what follows the directive spme may be used anywhere in place of the
c CCLRC
94
directive ewald if the user wishes to use the Smooth Particle Mesh Ewald method.
As a guide to beginners DL POLY 2 will calculate reasonable parameters if the ewald
precision directive is used in the CONTROL le (see section 4.1.1). A relative error (see
below) of 10 is normally suÆcient so the directive
6
ewald precision 1d-6
will cause DL POLY 2 to evaluate its best guess at the Ewald parameters , kmax1, kmax2
and kmax3. (The user should note that this represents an estimate, and there are sometimes circumstances where the estimate can be improved upon. This is especially the case
when the system contains a strong directional anisotropy, such as a surface.) These four
parameters may also be set explicitly by the ewald sum directive in the CONTROL le.
For example the directive
ewald sum 0.35 6 6 8
would set = 0:35 A , kmax1 = 6, kmax2 = 6 and kmax3 = 8. The quickest check on
the accuracy of the Ewald sum is to compare the Coulombic energy (U ) and the coulombic
virial (W ) in a short simulation. Adherence to the relationship U = W shows the extent
to which the Ewald sum is correctly converged. These variables can be found under the
columns headed eng cou and vir cou in the OUTPUT le (see section 4.2.2).
The remainder of this section explains the meanings of these parameters and how they
can be chosen. The Ewald sum can only be used in a three dimensional periodic system.
There are three variables that control the accuracy: , the Ewald convergence parameter;
r the real space forces cuto; and the kmax1,2,3 integers that eectively dene the
range of the reciprocal space sum (one integer for each of the three axis directions). These
variables are not independent, and it is usual to regard one of them as pre-determined and
adjust the other two accordingly. In this treatment we assume that r (dened by the
cuto directive in the CONTROL le) is xed for the given system.
The Ewald sum splits the (electrostatic) sum for the innite, periodic, system into
a damped real space sum and a reciprocal space sum. The rate of convergence of both
sums is governed by . Evaluation of the real space sum is truncated at r = r so it is
important that be chosen so that contributions to the real space sum are negligible for
terms with r > r . The relative error () in the real space sum truncated at r is given
approximately by
erfc(r )=r exp[ (:r ) ]=r
(3.1)
The recommended value for is 3.2/r or greater (too large a value will make the
reciprocal space sum very slowly convergent). This gives a relative error in the energy of no
greater than = 4 10 in the real space sum. When using the directive ewald precision
DL POLY 2 makes use of more sophisticated approximation:
erfc(x) 0:56exp( x )=x
(3.2)
1
1
cut
cut
cut
cut
cut
cut
cut
cut
2
cut
cut
5
2
1
Important note: For the SPME method the values of kmax1,2,3 should be double those obtained in
this prescription, since they specify a cubic lattice, not a radius of convergence.
c CCLRC
95
to solve recursively for , using equation 3.1 to give the rst guess.
The relative error in the reciprocal space term is approximately
exp( kmax =4 )=kmax
(3.3)
where
2 kmax
kmax =
(3.4)
L
is the largest k-vector considered in reciprocal space, L is the width of the cell in the
specied direction and kmax is an integer.
For a relative error of 4 10 this means using kmax 6:2. kmax is then
kmax > 3:2 L=r
(3.5)
In a cubic system, r = L=2 implies kmax = 7. In practice the above equation
slightly over estimates the value of kmax required, so optimal values need to be found
experimentally. In the above example kmax = 5 or 6 would be adequate.
If your simulation cell is a truncated octahedron or a rhombic dodecahedron then the
estimates for the kmax need to be multiplied by 2 = . This arises because twice the normal
number of k-vectors are required (half of which are redundant by symmetry) for these
boundary contributions [30].
If you wish to set the Ewald parameters manually (via the ewald sum or spme sum
directives) the recommended approach is as follows. Preselect the value of r , choose a
working a value of of about 3:2=r and a large value for the kmax (say 10 10 10 or more).
Then do a series of ten or so single step simulations with your initial conguration and with
ranging over the value you have chosen plus and minus 20%. Plot the Coulombic energy
(and W ) versus . If the Ewald sum is correctly converged you will see a plateau in the
plot. Divergence from the plateau at small is due to non-convergence in the real space
sum. Divergence form the plateau at large is due to non-convergence of the reciprocal
space sum. Redo the series of calculations using smaller kmax values. The optimum values
for kmax are the smallest values that reproduce the correct Coulombic energy (the plateau
value) and virial at the value of to be used in the simulation.
Note that one needs to specify the three integers (kmax1, kmax2, kmax3) referring to
the three spatial directions, to ensure the reciprocal space sum is equally accurate in all
directions. The values of kmax1, kmax2 and kmax3 must be commensurate with the cell
geometry to ensure the same minimum wavelength is used in all directions. For a cubic cell
set kmax1 = kmax2 = kmax3. However, for example, in a cell with dimensions 2A = 2B = C
(ie. a tetragonal cell, longer in the c direction than the a and b directions) use 2kmax1 =
2kmax2 = (kmax3).
If the values for the kmax used are too small, the Ewald sum will produce spurious
results. If values that are too large are used, the results will be correct but the calculation
will consume unnecessary amounts of cpu time. The amount of cpu time increases with
kmax1 kmax2 kmax3.
2
2
2
5
cut
cut
1 3
cut
cut
c CCLRC
96
3.4 DL POLY 2 Error Processing
3.4.1 The DL POLY 2 Internal Error Facility
DL POLY 2 contains a number of in-built error checks scattered throughout the package
which detect a wide range of possible errors. In all cases, when an error is detected the
subroutine error is called, resulting in an appropriate message and termination of the
program execution (either immediately, or after additional processing.).
Users intending to insert new error checks should ensure that all error checks are performed concurrently on all nodes, and that in circumstances where a dierent result may
obtain on dierent nodes, a call to the global status routine gstate is made to set the
appropriate global error ag on all nodes. Only after this is done, a call to subroutine
error may be made. An example of such a procedure might be:
logical safe
safe=(test condition)
call gstate(safe)
if(.not.safe) call error(node id,message number)
In this example it is assumed that the logical operation test condition will result in the
answer .true. if it is safe for the program to proceed, and .false. otherwise. The call to
error requires the user to state the identity of the calling node (node id), so that only
the nominated node in error (i.e. node 0) will print the error message. The variable
message number is an integer used to identify the appropriate message to be printed.
In all cases, if error is called with a non-negative message number, the program run
terminates. If the message number is negative, execution continues, but even in this case
DL POLY 2 will terminate the job at a more appropriate place. This feature is used in
processing the CONTROL and FIELD le directives. A possible modication users may
consider is to dump additional data before the call to error is made.
A description of the error subroutine is found in chapter 7 the DL POLY 2 Reference
Manual.
A full list of the DL POLY 2 error messages and the appropriate user action can be
found in Appendix C of this document.
Chapter 4
DL POLY 2 Data Files
97
c CCLRC
98
Scope of Chapter
This chapter describes all the input and output les for DL POLY 2 , examples of which
are to be found in the data sub-directory.
c CCLRC
99
4.1 The INPUT les
REVCON
CONFIG
OUTPUT
CONTROL
HISTORY *
FIELD
STATIS *
TABLE *
RDFDAT *
REVOLD *
ZDNDAT *
REVIVE
Figure 4.1: DL POLY 2 input (left) and output (right) les. Note: les marked with an
asterisk are non-mandatory.
DL POLY 2 requires ve input les named CONTROL, CONFIG, FIELD, TABLE and
REVOLD. The rst three les are mandatory, while TABLE is used only to input certain
kinds of pair potential, and is not always required. REVOLD is required only if the job
represents a continuation of a previous job. In the following sections we describe the form
and content of these les.
4.1.1 The CONTROL File
The CONTROL le is read by the subroutine simdef and denes the control variables for
running a DL POLY 2 job. It makes extensive use of directives and keywords. Directives
are character strings that appear as the rst entry on a data record (or line) and which
invoke a particular operation or provide numerical parameters. Also associated with each
directive may be one or more keywords, which may qualify a particular directive by, for
example, adding extra options. Directives can appear in any order in the CONTROL le,
except for the nish directive which marks the end of the le. Some of the directives
c CCLRC
100
are mandatory (for example the timestep directive that denes the timestep), others are
optional.
This way of constructing the le is very convenient, but it has inherent dangers. It is, for
example, quite easy to specify the same directive more than once, or specify contradictory
directives, or invoke algorithms that do not work together. By and large DL POLY 2 tries
to sort out these diÆculties and print helpful error messages, but it does not claim to be
foolproof. Fortunately in most cases the CONTROL le will be small and easy to check
visually. It is important to think carefully about a simulation beforehand and ensure that
DL POLY 2 is being asked to do something that is physically reasonable. It should also be
remembered that the present capabilites the package may not allow the simulation required
and it may be necessary for you yourself to add new features.
An example CONTROL le appears below. The directives and keywords appearing are
described in the following section.
Title Record: Example CONTROL file for DL_POLY
# define the state point
temperature
300.0
# simulation length and equilibration
steps
2000
equilibration steps
1000
scale every
5 steps
timestep
0.0005 ps
multiple timestep
1 steps
# specify cutoffs
cutoff
delr
7.6 angstrom
0.5 angstrom
# print controller
print every
100 steps
# rdf options
rdf sampling every
print rdf
10 steps
# job time and permitted wind-up time
job time
21000 seconds
close time
200 seconds
# forces options
ewald sum
0.48 6 6 6
cap forces in equilibration mode 2000 kT/A
c CCLRC
101
# ensemble options
ensemble nve (default option)
# statistics controls
stats every
stack
2000 steps
100 deep
# trajectory dumping controls
trajectory nstraj 1 istraj 50 keytrj 0
finish
4.1.1.1 The CONTROL le format
The le is free-formatted, integers, reals and additional keywords are entered following the
directive on each record. Real and integer numbers must be separated by a non-numeric
character (preferably a space or comma) to be correctly interpreted. No logical variables
appear in the control le. Comment records (beginning with a #) and blank lines may
be added to aid legibility (see example above). Additional annotation may be added onto
the directive line, provided it does not contain numerical characters, or appear where a
directive or keyword is expected. The CONTROL le is not case sensitive.
The rst record in the CONTROL le is a header 80 characters long, to aid identication of the le.
The last record is a nish directive, which marks the end of the input data.
Between the header and the nish directive, a wide choice of control directives may be
inserted. These are described below.
4.1.1.2 The CONTROL File Directives
The directives available are as follows.
directive:
meaning:
all pairs
cap f
use all pairs for electrostatic calculations
cap forces during equilibration period
f is maximum cap in units of kT/
A
(default f=1000)
set job closure time to f seconds
include equilibration data in overall statistics
calculate coulombic forces
set required forces cuto to f (A)
close time f
collect
coul
cut f
c CCLRC
102
calculate coulombic forces using distance dependent dielectric
set Verlet neighbour list shell width to f (A)
select NVE ensemble (default)
select NVT ensemble with Berendsen thermostat
with relaxation constant f (ps)
ensemble nvt evans
select NVT ensemble with Evans thermostat
ensemble nvt hoover f
select NVT ensemble with Hoover-Nose thermostat
with relaxation constant f (ps)
ensemble npt ber f f
select Berendsen NPT ensemble with f ; f
as the thermostat and barostat relaxation times (ps)
ensemble npt hoover f f
select Hoover NPT ensemble with f ; f
as the thermostat and barostat relaxation times (ps)
ensemble nst ber f f
select Berendsen NT ensemble, with f ; f
as the thermostat and barostat relaxation times (ps)
ensemble nst hoover f f
select Hoover NT ensemble with f ; f
as the thermostat and barostat relaxation times (ps)
ensemble pmf
select (NVE) potential of mean force ensemble
eps f
set relative dielectric constant to f (default 1.0)
equil n
equilibrate simulation for rst n timesteps
ewald precision f select Ewald sum for electrostatics, with
automatic parameter optimisation (0 < f < :5)
ewald sum k1 k2 k3
select Ewald sum for electrostatics, with:
= Ewald convergence parameter (
A )
k1 = maximum k-vector index in x-direction
k2 = maximum k-vector index in y-direction
k3 = maximum k-vector index in z-direction
nish
close the CONTROL le (last data record)
job time f
set job time to f seconds
mult n
set multiple timestep (multi-step)interval (activated when n>2)
no elec
ignore coulombic interactions
no vdw
ignore short range (non-bonded) interactions
pres f
set required system pressure to f k.bars
(target pressure for constant pressure ensembles)
prim f
set primary cuto to f (A)
(for multiple timestep algorithm only)
distan
delr f
ensemble nve
ensemble nvt ber f
1
2
1
1
2
1
1
2
2
2
1
1
2
1
2
1
2
c CCLRC
103
print system data every n timesteps
print radial distribution functions
set quaternion tolerance to f (default 10 )
calculate radial distribution functions at intervals
of f timesteps
reaction
select reaction eld electrostatics
restart
restart job from end point of previous run
(i.e. continue current simulation)
restart scale
restart job from previous run with temperature scaling
(i.e. begin a new simulation from older run)
scale n
rescale atomic velocities every n steps (during equilibration)
shake f
set shake tolerance to f (default 10 )
shift
calculate electrostatic forces using shifted coulombic potential
spme precision f select Ewald sum for electrostatics, with
automatic parameter optimisation (0 < f < :5)
spme sum k1 k2 k3
select Ewald sum for electrostatics, with:
= Ewald convergence parameter (
A )
k1 = maximum k-vector index in x-direction
k2 = maximum k-vector index in y-direction
k3 = maximum k-vector index in z-direction
stack n
set rolling average stack to n timesteps
stats n
accumulate statistics data every n timesteps
steps n
run simulation for n timesteps
temp f
set required simulation temperature to f K
traj i j k
write HISTORY le with controls:
i = start timestep for dumping congurations
j = timestep interval between congurations
k = data level (i.e. variable keytrj see table 4.3)
timestep f
set timestep to f ps
zden
calculate the z-density prole
zero
perform zero temperature MD run
print n
print rdf
quaternion f
rdf f
8
8
1
4.1.1.3 Further Comments on the CONTROL File
1. A number of the directives (or their mutually exclusive alternatives) are mandatory:
(a) timestep: specifying the simulation timestep;
(b) temp or zero : specifying the system temperature (not mutually exclusive);
(c) ewald sum or ewald precision or coul or shift or distan or reaction or no
elec: specifying the required coulombic forces option;
(d) cut and delr: specifying the short range forces cuto and Verlet strip;
c CCLRC
2.
3.
4.
5.
6.
7.
104
(e) prim: specifying primary forces cuto (if mult>2 only).
The job time and close time directives are required to ensure a controlled close
down procedure when a job runs out of time. The time specied by the job time
directive indicates the total time allowed for the job. (This must obviously be set
equal to the time specied to the operating system when the job is submitted.) The
close time directive represents the time DL POLY 2 will require to write and close
all the data les at the end of processing. This means the eective processing time
limit is equal to the job time minus the close time. Thus when DL POLY 2 reaches
the eective job time limit it begins the close down procedure with enough time in
hand to ensure the les are correctly written. In this way you may be sure the restart
les etc. are complete when the job terminates. Note that setting the close time too
small will mean the job will crash before the les have been nished. If it is set too
large DL POLY 2 will begin closing down too early. How large the close time needs
to be to ensure safe close down is system dependent and a matter of experience. It
generally increases with the job size.
The starting options for a simulation are governed by the keyword restart. If this
is not specied in the CONTROL le, the simulation will start as new. If specifed,
it will either continue a previous simulation (restart) or start a new simulation with
initial temperature scaling of the previous conguration (restart scale). Internally
these options are handled by the integer variable keyres, which is explained in table
4.1.
The various ensemble options (i.e. nve, nvt ber, nvt evans, nvt hoover, npt
ber, npt hoover, nst ber, nst hoover) are mutually exclusive, though none is
mandatory (the default is the NVE ensemble). These options are handled internally
by the integer variable keyens. The meaning of this variable is explained in table 4.2.
The force selection directives ewald sum, ewald precision, reaction, coul, shift,
dist, no elec and no vdw are handled internally by the integer variable keyfce. See
table 4.4 for an explanation of this variable. Note that these options are mutually
exclusive.
The choice of reaction eld electrostatics (directive reaction) requires also the specication of the relative dielectric constant external to the cavity. This is specied in
the eps directive.
DL POLY 2 uses as many as three dierent potential cutos. These are as follows:
(a) rcut - this is the universal cuto. It applies to the real space part of the electrostatics calculations and to the van der Waals potentials if no other cuto is
applied;
(b) rvdw - this is the user-specied cuto for the van der Waals potentials. If not
specied its value defaults to rcut;
c CCLRC
(c)
105
- this is used in the multiple timestep algorithm to specify the primary
atom region (see section 2.5.7). It has no meaning if the multiple timestep option
is not used.
8. Some directives are optional. If not specied DL POLY 2 will take default values if
necessary. The defaults appear in the above table.
9. The zero directive, enables a zero temperature simulation. This is intended as a
crude energy minimizer to help relax a system before a simulation begins. It should
not be thought of as a true energy minimization method.
10. The DL POLY 2 multiple timestep option is invoked if the number appearing with
the mult directive is greater than 2. This number (stored in the variable multt)
species the number of timesteps (the multi-step) that elapse between partitions of
the full Verlet neighbour list into primary and secondary atoms.
11. If a multiple time-step is used, (i.e. multt>2), then statistics for radial distribution
functions are collected only at updates of the secondary neighbour list. The number specied on the rdf directive (the variable nstbgr) means that RDF data are
accumulated at intervals of nstbgrmultt timesteps.
12. As a default, DL POLY 2 does not store statistical data during the equilibration
period. If the directive collect is used, equilibration data will be incorporated into
the overall statistics.
13. The directive delr species the width of the border to be used in the Verlet neighbour
list construction. The width is stored in the variable delr. The list is updated
whenever two or more atoms have moved a distance of more then delr/2 from their
positions at the last update of the Verlet list.
Users are advised to study the example CONTROL les appearing in the data subdirectory to see how dierent les are constructed.
rprim
c CCLRC
106
Table 4.1: Internal Restart Key
keyres
meaning
0 start new simulation from CONFIG le,
and assign velocities from Gaussian distribution.
1 continue current simulation
2 start new simulation from CONFIG le,
and rescale velocities to desired temperature
Table 4.2: Internal Ensemble Key
keyens
meaning
0 Microcanonical ensemble (NVE)
1 Evans NVT ensemble
2 Berendsen NVT ensemble
3 Nose-Hoover NVT ensemble
4 Berendsen NPT ensemble
5 Nose-Hoover NPT ensemble
6 Berendsen NT ensemble
7 Nose-Hoover NT ensemble
8 Potential of mean force (NVE) ensemble
Table 4.3: Internal Trajectory File Key
keytrj
meaning
0 coordinates only in le
1 coordinates and velocities in le
2 coordinates, velocities and forces in le
Table 4.4: Non-bonded force key
keyfce
meaning
odd evaluate short-range potentials and electrostatics
even evaluate Electrostatic potential only
Electrostatics are evaluated as follows:
0y, 1z Ignore Electrostatic interactions
2, 3 Ewald summation
4, 5 distance dependent dielectric constant
6, 7 standard truncated Coulombic potential
8, 9 truncated and shifted Coulombic potential
10,11 Reaction Field electrostatics
y keyfce = 0 means no non-bonded terms are evaluated.
z keyfce = 1 means only short-range potentials are evaluated.
c CCLRC
107
4.1.2 The CONFIG File
The CONFIG le contains the dimensions of the unit cell, the key for periodic boundary
conditions and the atomic labels, coordinates, velocities and forces. This le is read by
the subroutine sysgen. (It is also read by the subroutine simdef if the ewald precision
directive is used.) The rst few records of a typical CONFIG le are shown below:
IceI structure 6x6x6 unit cells with proton disorder
2
3
26.988000000000000 0.000000000000000 0.000000000000000
-13.494000000000000 23.372293600000000 0.000000000000000
0.000000000000000 0.000000000000000 44.028000000000000
OW
1
-2.505228382
-1.484234330
-7.274585343
0.5446573999
-1.872177437
-0.7702718106
3515.939287
13070.74357
4432.030587
HW
2
-1.622622646
-1.972916834
-7.340573742
1.507099154
-1.577400769
4.328786484
7455.527553
-4806.880540
-1255.814536
HW
3
-3.258494716
-2.125627191
-7.491549620
2.413871957
-4.336956694
2.951142896
-7896.278327
-8318.045939
-2379.766752
OW
4
0.9720599243E-01
-2.503798635
-3.732081894
1.787340483
-1.021777575
0.5473436377
9226.455153
9445.662860
5365.202509
etc.
4.1.2.1 Format
The le is xed-formatted: integers as \i10", reals as \f20.0". The header record is formatted as 80 alphanumeric characters.
4.1.2.2 Denitions of Variables
record 1
header
record 2
levcfg
imcon
record 3
cell(1)
a80
title line
integer
CONFIG le key. See table 4.5 for permitted values
integer
Periodic boundary key. See table 4.6 for permitted values
omitted if imcon = 0
real
x component of a cell vector
c CCLRC
cell(2)
cell(3)
record 4
cell(4)
cell(5)
cell(6)
record 5
cell(7)
cell(8)
cell(9)
108
real
y component of a cell vector
real
z component of a cell vector
omitted if imcon = 0
real
x component of b cell vector
real
y component of b cell vector
real
z component of b cell vector
omitted if imcon = 0
real
x component of c cell vector
real
y component of c cell vector
real
z component of c cell vector
Subsequent records consists of blocks of between 2 and 4 records depending on the
value of the levcfg variable. Each block refers to one atom. The atoms must be listed
sequentially in order of increasing index. Within each block the data are as follows:
record i
atmnam
index
atmnum
record ii
xxx
yyy
zzz
record iii
vxx
vyy
vzz
record iv
fxx
fyy
fzz
a8
atom name.
integer atom index
integer atomic number
real
x coordinate
real
y coordinate
real
z coordinate
included only if levcfg > 0
real
x component of velocity
real
y component of velocity
real
x component of velocity
included only if levcfg > 1
real
x component of force
real
y component of force
real
z component of force
Note that on record i only the atom name is mandatory, any other items are not read
by DL POLY 2 but may be added to aid alternative uses of the le, for example the
DL POLY 2 Graphical User Interface[20].
4.1.2.3 Further Comments
The CONFIG le has the same format as the output le REVCON (section 4.2.3). When
restarting from a previous run of DL POLY 2 (i.e. using the restart or restart scale directives in the CONTROL le - above), the CONFIG le must be replaced by the REVCON
le, which is renamed as the CONFIG le. The copy macro in the execute sub-directory of
DL POLY 2 does this for you.
c CCLRC
109
Table 4.5: CONFIG le key (record 2)
levcfg
meaning
0 Coordinates included in le
1 Coordinates and velocities included in le
2 Coordinates, velocities and forces included in le
Table 4.6: Periodic boundary key (record 2)
imcon
meaning
0 no periodic boundaries
1 cubic boundary conditions
2 orthorhombic boundary conditions
3 parallelepiped boundary conditions
4 truncated octahedral boundary conditions
5 rhombic dodecahedral boundary conditions
6 x-y parallelogram boundary conditions with
no periodicity in the z direction
7 hexagonal prism boundary conditions
c CCLRC
4.1.3 The FIELD File
110
The FIELD le contains the force eld information dening the nature of the molecular
forces. It is read by the subroutine sysdef. Excerpts from a force eld le are shown
below. The example is the antibiotic Valinomycin in a cluster of 146 water molecules.
Valinomycin Molecule with 146 SPC Waters
UNITS kcal
MOLECULES
2
Valinomycin
NUMMOLS 1
ATOMS 168
O
16.0000
-0.4160
1
OS
16.0000
-0.4550
1
"
"
"
"
"
"
"
"
HC
1.0080
0.0580
1
C
12.0100
0.4770
1
BONDS 78
harm 31 19 674.000
1.44900
harm 33 31 620.000
1.52600
"
"
"
"
"
"
"
"
"
"
harm 168 19 980.000
1.33500
harm 168 162 634.000
1.52200
CONSTRAINTS 90
20 19
1.000017
22 21
1.000032
"
"
"
"
"
"
166 164
1.000087
167 164
0.999968
ANGLES 312
harm 43
2 44 200.00
116.40
harm 69
5 70 200.00
116.40
"
"
"
"
"
"
"
"
"
"
"
"
harm 18 168 162 160.00
120.40
harm 19 168 162 140.00
116.60
DIHEDRALS 371
harm
1 43
2 44 2.3000
180.00
harm 31 43
2 44 2.3000
180.00
"
"
"
"
"
"
"
"
"
"
"
"
"
"
c CCLRC
cos 149
cos 162
FINISH
SPC Water
NUMMOLS 146
ATOMS 3
OW
HW
HW
CONSTRAINTS
1
2
1
3
2
3
FINISH
VDW 45
C
C
C
CT
"
"
"
"
"
"
OW
OS
OS
OS
CLOSE
111
17 161
19 168
16.0000
1.0080
1.0080
3
1.0000
1.0000
1.63299
lj
lj
"
"
"
lj
lj
16 10.500
18 10.500
180.00
180.00
-0.8200
0.4100
0.4100
0.12000
0.08485
"
"
"
0.15100
0.15000
3.2963
3.2518
"
"
"
3.0451
2.9400
4.1.3.1 Format
The FIELD le is xed-formatted. Integers are formatted as \i5", reals as \f12.0" and
characters as \a4", \a8", \a40" or \a80", depending on context. The contents of the le
are variable and are dened by the use of directives. Additional information is associated
with the directives, and is free formatted as in the CONTROL le above. The le is not
case sensitive.
4.1.3.2 Denitions of Variables
The le divides into three sections: general information, molecular descriptions, and nonbonded interaction descriptions, appearing in that order in the le.
4.1.3.2.1 General information
The rst record in the FIELD le is the title. It must be followed by the units directive.
Both of these are mandatory. These records may optionally be followed by the neut
directive.
record 1
header
a80
eld le header
c CCLRC
112
record 2
units
a40
record 3 (optional)
neut
a40
Unit of energy used for input and output
activate the neutral/charge groups option for
the electrostatic calculations
The energy units on the units directive are described by additional keywords:
a eV, for electron-volts
b kcal, for k-calories mol
c kJ, for k-Joules mol
d internal, for DL POLY 2 internal units (10 J mol ).
If no units keyword is entered, DL POLY 2 units are assumed for both input and output.
The units keyword may appear anywhere on the data record provided it does not exceed
column 40. The units directive only aects the input and output interfaces, all internal
calculations are handled using DL POLY 2 units.
1
1
1
4.1.3.2.2 Molecular details
It is important for the user to understand that there is an organisational correspondence
between the FIELD le and the CONFIG le described above. It is required that the order
of specication of molecular types and their atomic constituents in the FIELD le follows
the order in which they appear in the CONFIG le. Failure to adhere to this common
sequence will be detected by DL POLY 2 and result in premature termination of the job.
It is therefore essential to work from the CONFIG le when constructing the FIELD le.
It is not as diÆcult as it sounds!
The entry of the molecular details begins with the mandatory directive:
molecules n
where n is an integer specifying the number of dierent types of molecule appearing in
the FIELD le. Once this directive has been encountered, DL POLY 2 enters the molecular
description environment in which only molecular decription keywords and data are valid.
Immediately following the molecules directive, are the records dening individual
molecules:
1. name-of-molecule
which can be any character string up to 80 characters in length. (Note: this is not a
directive, just a simple character string.)
c CCLRC
113
2. nummols n
where n is the number of times a molecule of this type appears in the simulated
system. The molecular data then follow in subsequent records:
3. atoms n
where n indicates the number of atoms in this type of molecule. A number of records
follow, each giving details of the atoms in the molecule i.e. site names, masses and
charges. Each record carries the entries:
sitnam
a8
atomic site name
weight
real
atomic site mass
chge
real
atomic site charge
nrept
integer
repeat counter
ifrz
integer
`frozen' atom (if ifrz> 0)
igrp
integer
neutral/charge group number
The integer nrept need not be specied (in which case a value of 1 is assumed.) A
number greater than 1 specied here indicates that the next (nrept - 1) entries in
the CONFIG le are ascribed the atomic characteristics given in the current record.
The sum of the repeat numbers for all atoms in a molecule should equal the number
specied by the atoms directive.
4. shell n
where n is the number of core-shell units. Each of the subsequent n records contains:
index 1
integer
site index of core
index 2
integer
site index of shell
spring
real
force constant of core-shell spring
The spring force constant is entered in units of engunit A , where engunit is the
energy unit specied in the units directive.
Note that the atomic site indices referred to in this table are indices arising from
numbering each atom in the molecule from 1 to the number specied in the atoms
directive for this molecule. This same numbering scheme should be used for all descriptions of this molecule, including the bonds, constraints, angles, and dihedrals entries described below. DL POLY 2 will itself construct the global indices for
all atoms in the systems.
This directive (and associated data records) need not be specied if the molecule
contains no core-shell units.
2
5. bonds n
where n is the number of exible chemical bonds in the molecule. Each of the subsequent n records contains:
c CCLRC
bond key
index 1
index 2
variable 1
variable 2
variable 3
variable 4
114
a4
integer
integer
real
real
real
real
see table 4.7
rst atomic site in bond
second atomic site in bond
potential parameter see table 4.7
potential parameter see table 4.7
potential parameter see table 4.7
potential parameter see table 4.7
The meaning of these variables is given in table 4.7. This directive (and associated
data records) need not be specied if the molecule contains no exible chemical bonds.
See the note on the atomic indices appearing under the shell directive above.
key
Table 4.7: Chemical bond potentials
potential type Variables (1-4)
functional form
harm
-hrm
Harmonic
k
U (r) = 21 k(r r0 )2
mors
-mrs
Morse
E0 r0
12-6
-126
12-6
A
B
rhrm
Restraint
k
r0 rc
r0
-rhm
k
U (r) = E0 [f1
exp( k(r
U (r ) =
A
r12
r0 ))g2
B
r6
1]
U (r) = 12 k(r r0 )2
jr r0j rc
U (r) = 21 krc2 + krc (jr r0 j rc ) jr r0 j > rc
0
00
Quartic
k r k0 k00 U (r) = k (r r ) + k (r r ) + k (r r )
bond potentials with a dash (-) as the rst character of the keyword, do not contribute to the excluded atoms list (see section 2.1). In this case DL POLY 2 will also
calculate the nonbonded pair potentials between the described atoms, unless these are
deactivated by another potential specication.
quar
-qur
Note:
0
2
0
2
3
0
3
4
0
6. constraints n
where n is the number of constraint bonds in the molecule. Each of the following n
records contains:
index 1
integer
rst atomic index
index 2
integer
second atomic index
bondlength
real
constraint bond length
4
c CCLRC
115
This directive (and associated data records) need not be specied if the molecule
contains no constraint bonds. See the note on the atomic indices appearing under the
shell directive above.
7. pmf b
where b is the potential of mean force bondlength (A). There follows the denitions
of two PMF units:
(a) pmf unit n
where n is the number of sites in the rst unit. The subsequent n records
provide the site indices and weighting. Each record contains:
index
integer
atomic site index
weight
real
site weighting
1
1
1
(b) pmf unit n
where n is the number of sites in the second unit. The subsequent n records
provide the site indices and weighting. Each record contains:
index
integer
atomic site index
weight
real
site weighting
2
2
2
This directive (and associated data records) need not be specied if no PMF constraints are present. See the note on the atomic indices appearing under the shell
directive above. The pmf bondlength applies to the distance between the centres of
the two pmf units. The centre, R, of each unit is given by
R=
P
w r w
P
where r is a site position and w the site weighting. Note that the pmf constraint is
intramolecular. To dene a constraint between two molecules, the molecules must be
described as part of the same DL POLY \molecule". This is illustrated in test case
6, where a pmf constraint is imposed between a potassium ion and the centre of mass
of a water molecule. DL POLY 2 allows only one type of pmf constraint per system.
The value of nummols for this molecule determines the number of pmf constraint in
the system.
8. angles n
where n is the number of valence angle bonds in the molecule. Each of the n records
following contains:
angle key
a4
potential key. See table 4.8
index 1
integer
rst atomic index
c CCLRC
index 2
index 3
variable 1
variable 2
116
integer
integer
real
real
second atomic index (central site)
third atomic index
potential parameter see table 4.8
potential parameter see table 4.8
The meaning of these variables is given in table 4.8. See the note on the atomic
indices appearing under the shell directive above. This directive (and associated
data records) need not be specied if the molecule contains no angular terms.
key
Table 4.8: Valence Angle potentials
potential type
Variables (1-4)
functional formy
harm
-hrm
Harmonic
k 0
U ( ) =
quar
-qur
Quartic
k 0 k0 k00 U () =
thrm
-thm
Truncated harmonic
k 0
shrm
-shm
Screened harmonic
k 0 1 2
U () = k2 ( 0 )2 exp[ (rij =1 + rik =2 )]
bvs1
-bv1
Screened Vessal[24]
k 0 1 2
U () =
bvs2
-bv2
Truncated Vessal[25]
k 0
hcos
-hcs
Harmonic Cosine
k 0
cos
-cos
Cosine
A
2
0 )2
00
0 )2 + k3 ( 0 )3 + k4 ( 0 )4
n
k
0
0 )2
rij =1
(
8(
)2 ( )2
+ rik =2)]
0
2
0
k
2
2
3
(cos()
0
2
8
8
2
cos(0 ))2
U () = A[1 + cos(m Æ)]
y is the a-b-c angle.
valence angle potentials with a dash (-) as the rst character of the keyword, do
not contribute to the excluded atoms list (see section 2.1). In this case DL POLY 2 will
calculate the nonbonded pair potentials between the described atoms.
Note:
2 o
exp[ (
U () = k[a ( ) ( + 2) a a
( ) ( ) ] exp[ (rij + rik )= ]
U ( ) =
m
(
0
(
0
Æ
2
U () = k2 ( 0 )2 exp[ (rij8 + rik8 )=8 ]
a
k
k
8
1
c CCLRC
117
9. dihedrals n
where n is the number of dihedral interactions present in the molecule. Each of the
following n records contains:
dihedral key
a4
potential key. See table 4.9
index 1
integer
rst atomic index
index 2
integer
second atomic index
index 3
integer
third atomic index
index 4
integer
fourth atomic index
variable 1
real
potential parameter see table 4.9
variable 2
real
potential parameter see table 4.9
variable 3
real
potential parameter see table 4.9
variable 4
real
1-4 electrostatic interaction scale factor.
variable 5
real
1-4 Van der Waals interaction scale factor.
The meaning of the variables 1-3 is given in table 4.9. The variables 4 and 5 specify
the scaling factor for the 1-4 electrostatic and Van der Waals nonbonded interactions
respectively. This directive (and associated data records) need not be specied if
the molecule contains no dihedral angle terms. See the note on the atomic indices
appearing under the shell directive above.
key
Table 4.9: Dihedral Angle Potentials
potential type Variables (1-3)
functional formz
Cosine
harm Harmonic
A
Æ
k
0
Harmonic cosine
cos3 Triple cosine
k
0
cos
hcos
A1 A2
m
U () = A [1 + cos(m Æ)]
U () = 12 k( 0 )2
U () =
A3
(cos() cos( ))
U () = A (1 + cos()) + A (1 cos(2))
+ A (1 + cos(3))
1
2
1
1
2
k
0
2
1
2
2
2
3
z is the a-b-c-d dihedral angle.
10. inversions n
where n is the number of inversion interactions present in the molecule. Each of the
following n records contains:
inversion key
a4
potential key. See table 4.10
index 1
integer
rst atomic index
c CCLRC
118
index 2
index 3
index 4
variable 1
variable 2
integer
integer
integer
real
real
second atomic index
third atomic index
fourth atomic index
potential parameter see table 4.10
potential parameter see table 4.10
The meaning of the variables 1-2 is given in table 4.10. This directive (and associated
data records) need not be specied if the molecule contains no inversion angle terms.
See the note on the atomic indices appearing under the shell directive above.
key
Table 4.10: Inversion Angle Potentials
potential type Variables (1-2)
functional formz
Harmonic
hcos Harmonic cosine
plan Planar
harm
k
0
k
0
A
U () = 21 k( 0 )2
U () =
(cos() cos( ))
U () = A [1 cos()]
k
2
0
2
z is the inversion angle.
11. rigid n
where n is the number of rigid units in the molecule. It is followed by at least n
records, each specifying the sites in a rigid unit:
m
integer
number of sites in rigid unit
site 1
integer
rst site atomic index
site 2
integer
second site atomic index
site 3
integer
third site atomic index
..
..
etc.
site m
integer
m'th site atomic index
Up to 15 sites can be specied on the rst record. Additional records are used if
necessary. Up to 16 sites are specied per record thereafter.
This directive (and associated data records) need not be specied if the molecule
contains no rigid units. See the note on the atomic indices appearing under the shell
directive above.
12. teth n
where n is the number of tethered atoms in the molecule. It is followed by n records
specifying the tethered sites in the molecule:
c CCLRC
119
tether key
index
variable 1
variable 2
variable 3
variable 4
a4
integer
real
real
real
real
tethering potential key see table 4.11
atomic index
potential parameter see table 4.11
potential parameter see table 4.11
potential parameter see table 4.11
potential parameter see table 4.11
This directive (and associated data records) need not be specied if the molecule
contains no tethered atoms. See the note on the atomic indices appearing under the
shell directive above.
key
Table 4.11: Tethering potentials
potential type Variables (1-3)
functional form
Harmonic
rhrm Restraint
harm
quar
Quartic
U (r) = 21 kr2
k
k rc
k k0
U
k00
=
U (r) = 12 kr2
r rc
krc2 + krc (r rc )
r > rc
1
2
0
00
U (r) = k2 r2 + k3 r3 + k4 r4
13. nish
This directive is entered to signal to DL POLY 2 that the entry of the details of a
molecule has been completed.
The entries for a second molecule may now be entered, beginning with the name-ofmolecule record and ending with the nish directive.
The cycle is repeated until all the types of molecules indicated by the molecules
directive have been entered.
The user is recommended to look at the example FIELD les in the data directory to
see how typical FIELD les are constructed.
4.1.3.3 Non-bonded Interactions
Non-bonded interactions are identied by atom types as opposed to specic atomic indices.
The rst type of non-bonded potentials are the pair potentials. The input of pair potential
data is signalled by the directive:
vdw n
c CCLRC
120
where n is the number of pair potentials to be entered. There follows n records, each
specifying a particular pair potential in the following manner:
atmnam 1
a8
rst atom type
atmnam 2
a8
second atom type
key
a4,1X
potential key. See table 4.12
variable 1
real
potential parameter see table 4.12
variable 2
real
potential parameter see table 4.12
variable 3
real
potential parameter see table 4.12
variable 4
real
potential parameter see table 4.12
variable 5
real
potential parameter see table 4.12
The variables pertaining to each potential are described in table 4.12.Note that there is an
empty column after the potential key. This means that the potential paramaters are enterd
in columns 22 to 81. Note that any pair potential not specied in the FIELD le, will be
assumed to be zero. Note also that the Sutton-Chen potential for metals is classied as a
pair potential for input purposes.
The specication of three body potentials is initiated by the directive:
tbp n
where n is the number of three-body potentials to be entered. There follows n records,
each specifying a particular three body potential in the following manner:
atmnam 1
a8
rst atom type
atmnam 2
a8
second atom type (central site)
atmnam 3
a8
third atom type
key
a4
potential key. See table 4.13
variable 1
real
potential parameter see table 4.13
variable 2
real
potential parameter see table 4.13
variable 3
real
potential parameter see table 4.13
variable 4
real
potential parameter see table 4.13
variable 5
real
cuto range for this potential (A)
The variables pertaining to each potential are described in table 4.13. Note that the fth
variable is the range at which the three body potential is truncated. The distance is in A,
measured from the central atom.
The specication of four body potentials is initiated by the directive:
fbp n
c CCLRC
121
where n is the number of four-body potentials to be entered. There follows n records,
each specifying a particular four-body potential in the following manner:
atmnam 1
a8
rst atom type (central site)
atmnam 2
a8
second atom type
atmnam 3
a8
third atom type
atmnam 4
a8
fourth atom type
key
a4
potential key. See table 4.14
variable 1
real
potential parameter see table 4.14
variable 2
real
potential parameter see table 4.14
variable 3
real
cuto range for this potential (A)
The variables pertaining to each potential are described in table 4.14. Note that the third
variable is the range at which the four-body potential is truncated. The distance is in A,
measured from the central atom.
4.1.3.4 External Field
The presence of an external eld is agged by the extern directive. The next line in the
FIELD le should have another directive indicating what type of eld is to be applied. On
the following lines comes the mxfld parameters, ve per line, that describe the eld. In the
include les supplied with DL POLY 2 mxfld is set to 10.
The variables pertaining to each potential are described in table 4.15.
4.1.3.5 Closing the FIELD File
The FIELD le must be closed with the directive:
close
which signals the end of the force eld data. Without this directive DL POLY 2 will
abort.
4.1.4 The REVOLD File
This le contains statistics arrays from a previous job. It is not required if the current job
is not a continuation of a previous run (ie. if the restart directive is not present in the
CONTROL le - see above). The le is unformatted and therefore not readable by normal
people. DL POLY 2 normally produces the le REVIVE (see section 4.2.4) at the end of
a job which contains the statistics data. REVIVE should be copied to REVOLD before a
continuation run commences. This may be done by the copy macro supplied in the execute
sub-directory of DL POLY 2 .
c CCLRC
4.1.4.1 Format
122
The REVOLD le is unformatted. All variables appearing are written in native real*8
representation. Nominally integer quantities (e.g. the timestep number nstep) are represented by the the nearest real number. The contents are as follows (the dimensions of array
variables are given in brackets, in terms of parameters from the dl params.inc le - see
section 7.1.1).
record 1:
nstep
timestep of nal conguration
numacc
number of congurations used in averages
numrdf
number of congurations used in rdf averages
chit
relaxation time of thermostat
chip
relaxation time of barostat
conint
conserved quantity for selected ensemble
nzden
number of congurations used in z density
record 2:
eta
scaling factors for simulation cell matrix elements (9)
record 3:
stpval
instantaneous values of thermodynamic variables (mxnstk)
record 4:
sumval
average values of thermodynamic variables (mxnstk)
record 5:
ssqval
uctuation (squared) of thermodynamic variables (mxnstk)
record 6:
zumval
running totals of thermodynamic variables (mxnstk)
record 7:
ravval
rolling averages of thermodynamic variables (mxnstk)
record 8:
stkval
stacked values of thermodynamic variables (mxstakmxnstk)
record 9:
xx0
atomic x-coordinates at MSD time origin (mxatms)
yy0
atomic y-coordinates at MSD time origin (mxatms)
zz0
atomic z-coordinates at MSD time origin (mxatms)
record 10:
xxs
instantaneous atomic x-coordinates for MSD (mxatms)
yys
instantaneous atomic y-coordinates for MSD (mxatms)
zzs
instantaneous atomic z-coordinates for MSD (mxatms)
record 11:
rdf
(Optional) RDF array (mxrdfmxvdw)
record 12:
zdens
(Optional) z-density array (mxrdfmxsvdw)
c CCLRC
123
4.1.4.2 Further Comments
Note that recompiling DL POLY 2 with a dierent dl params.inc le, may render any
existing REVOLD le unreadable by the code.
4.1.5 The TABLE File
The TABLE le provides an alternative way of reading in the short range potentials - in
tabular form. This is particularly useful if an analytical form of the potential does not exist
or is too complicated to specify in the forgen subroutine. The table le is read by the
subroutine fortab (see chapter 7).
The option of using tabulated potentials is specied in the FIELD le (see above). The
specic potentials that are to be tabulated are indicated by the use of the tab keyword
on the record dening the short range potential (see table 4.12). The directive vdwtable
may be used in place of vdw to indicate that one or more of the short ranged potentials is
specied in the form of a table.
4.1.5.1 Format
The le is xed-formatted with integers as \i10", reals as \e15.8". Character variables are
read as \a8". The header record is formatted as 80 alphanumeric characters.
4.1.5.2 Denitions of Variables
record 1
header
record 2
delpot
cutpot
ngrid
a80
real
real
integer
le header
mesh resolution in A
cuto used to dene tables A
number of grid points in tables
The subsequent records dene each tabulated potential in turn, in the order indicated by
the specication in the FIELD le. Each potential is dened by a header record and a set
of data records with the potential and force tables.
header record:
a8
rst atom type
a8
second atom type
potential data records: (number of data records = Int((ngrid+3)/4))
data 1
real
data item 1
data 2
real
data item 2
data 3
real
data item 3
data 4
real
data item 4
force data records: (number of data records = Int((ngrid+3)/4))
data 1
real
data item 1
atom 1
atom 2
c CCLRC
data 2
data 3
data 4
124
real
real
real
data item 2
data item 3
data item 4
4.1.5.3 Further Comments
It should be noted that the number of grid points in the TABLE le should not be less than
the number of grid points DL POLY 2 is expecting. (This number is given by the parameter
mxgrid in the dl params.inc le - see section 7.1.1.) DL POLY 2 will re-interpolate the
tables if ngridmxgrid, but will abort if ngrid<mxgrid.
The potential and force tables are used to ll the internal arrays vvv and ggg respectively
(see section 2.3.1). The contents of force arrays are derived from the potential via the
formula:
@
G(r) = r U (r):
@r
Note this is not the same as the true force.
c CCLRC
125
4.2 The OUTPUT Files
DL POLY 2 produces up to seven output les: HISTORY, OUTPUT, REVCON, REVIVE,
RDFDAT, ZDNDAT and STATIS. These respectively contain: a dump le of atomic coordinates, velocities and forces; a summary of the simulation; the restart conguration;
statistics accumulators; radial distribution data, Z-density data and a statistical history.
4.2.1 The HISTORY File
The HISTORY le is the dump le of atomic coordinates, velocities and forces. Its principal
use is for o-line analysis. The le is written by the subroutines traject or traject u.
The control variables for this le are ltraj, nstraj, istraj and keytrj which are created internally, based on information read from the traj directive in the CONTROL le
(see above). The HISTORY le will be created only if the directive traj appears in the
CONTROL le. Note that the HISTORY le can be written in either a formatted or
unformatted version. We describe each of these separately below.
The HISTORY le can become very large, especially if it is formatted. For serious
simulation work it is recommended that the le be written to a scratch disk capable of
accommodating a large data le. Alternatively the le may be written as unformatted
(below), which has the additional advantage of speed. However, writing an unformatted
le has the disadvantage that the le may not be readily readable except by the machine
on which it was created. This is particularly important if graphical processing of the data
is required.
4.2.1.1 The Formatted HISTORY File
The formatted HISTORY le is written by the subroutine traject and has the following
structure.
record 1 (a80)
header
a80
le header
record 2 (2i10)
keytrj
integer
trajectory key (see table 4.3)
imcon
integer
periodic boundary key (see table 4.6)
natms
integer
number of atoms in simulation cell
For timesteps greater than nstraj the HISTORY le is appended at intervals specied by the traj directive in the CONTROL le, with the following information for each
conguration:
record i (a8,4i10,f12.6)
timestep
a8
the character string \timestep"
nstep
integer
the current time-step
natms
integer
number of atoms in conguration
keytrj
integer
trajectory key (again)
c CCLRC
integer
real
record ii (3g12.4) for imcon > 0
cell(1)
real
cell(2)
real
cell(3)
real
record iii (3g12.4) for imcon > 0
cell(4)
real
cell(5)
real
cell(6)
real
record iv (3g12.4) for imcon > 0
cell(7)
real
cell(8)
real
cell(9)
real
imcon
tstep
126
periodic boundary key (again)
integration timestep
x component of a cell vector
y component of a cell vector
z component of a cell vector
x component of b cell vector
y component of b cell vector
z component of b cell vector
x component of c cell vector
y component of c cell vector
z component of c cell vector
This is followed by the conguration for the currect timestep. i.e. for each atom in the
system the following data are included:
record a (a8,i10,2f12.6)
atmnam
a8
atomic label
iatm
i10
atom index
weight
f12.6
atomic mass (a.m.u.)
charge
f12.6
atomic charge (e)
record b (3e12.4)
xxx
real
x coordinate
yyy
real
y coordinate
zzz
real
z coordinate
record c (3e12.4) only for keytrj > 0
vxx
real
x component of velocity
vyy
real
y component of velocity
vzz
real
z component of velocity
record d (3e12.4) only for keytrj > 1
fxx
real
x component of force
fyy
real
y component of force
fzz
real
z component of force
Thus the data for each atom is a minimum of two records and a maximum of 4.
4.2.1.2 The Unformatted HISTORY File
The unformatted HISTORY le is written by the subroutine traject u and has the following structure:
c CCLRC
record 1
header
record 2
natms
record 3
atname(1,...,natms)
record 4
weight(1,...,natms)
record 5
charge(1,...,natms)
127
conguration name (character*80)
number of atoms in the conguration (real*8)
atom names or symbols (character*8)
atomic masses (real*8)
atomic charges (real*8)
For time-steps greater than nstraj, the HISTORY le is appended, at intervals specied
by the traj directive in the CONTROL le, with the following information:
record i
the current time-step (real*8)
number of atoms in conguration (real*8)
trajectory key (real*8)
image convention key (real*8)
integration timestep (real*8)
record ii for imcon > 0
cell(1,...,9)
a; b and c cell vectors (real*8)
record iii
xxx(1,...,natms)
atomic x-coordinates (real*8)
record iv
yyy(1,...,natms)
atomic y-coordinates (real*8)
record v
zzz(1,...,natms)
atomic z-coordinates (real*8)
record vi only for keytrj> 0
vxx(1,...,natms)
atomic velocities x-component (real*8)
record vii only for keytrj> 0
vyy(1,...,natms)
atomic velocities y-component (real*8)
record viii only for keytrj> 0
vzz(1,...,natms)
atomic velocities z-component (real*8)
record ix only for keytrj> 1
fxx(1,...,natms)
atomic forces x-component (real*8)
record x only for keytrj> 1
fyy(1,...,natms)
atomic forces y-component (real*8)
record xi only for keytrj> 1
fzz(1,...,natms)
atomic forces z-component (real*8)
nstep
natms
keytrj
imcon
tstep
Note the implied conversion of integer variables to real on record i.
c CCLRC
128
4.2.2 The OUTPUT File
The job output consists of 7 sections: Header; Simulation control specications; Force
eld specication; Summary of the initial conguration; Simulation progress; Summary
of statistical data; Sample of the nal conguration; and Radial distribution functions.
These sections are written by dierent subroutines at various stages of a job. Creation of
the OUTPUT le always results from running DL POLY 2 . It is meant to be a human
readable le, destined for hardcopy output.
4.2.2.1 Header
Gives the DL POLY 2 version number, the number of processors used and a title for the
job as given in the header line of the input le CONTROL. This part of the le is written
from the subroutines dlpoly and simdef
4.2.2.2 Simulation Control Specications
Echoes the input from the CONTROL le. Some variables may be reset if illegal values
were specied in the CONTROL le. This part of the le is written from the subroutine
simdef.
4.2.2.3 Force Field Specication
Echoes the FIELD le. A warning line will be printed if the system is not electrically
neutral. This warning will appear immediately before the non-bonded short-range potential
specications. This part of the le is written from the subroutine sysdef.
4.2.2.4 Summary of the Initial Conguration
This part of the le is written from the subroutine sysgen. It states the periodic boundary
specication, the cell vectors and volume (if appropriate) and the initial conguration of
(a maximum of) 20 atoms in the system. The conguration information given is based on
the value of levcfg in the CONFIG le. If levcfg is 0 (or 1) positions (and velocities) of
the 20 atoms are listed. If levcfg is 2 forces are also written out.
For periodic systems this is followed by the long range corrections to the energy and
pressure.
4.2.2.5 Simulation Progress
This part of the le is written by the DL POLY 2 root segment dlpoly. The header line
is printed at the top of each page as:
-------------------------------------------------------------------------------------------------step
time(ps)
cpu (s)
eng_tot
eng_pv
volume
temp_tot
temp_rot
temp_shl
eng_cfg
vir_cfg
eng_shl
eng_vdw
vir_vdw
vir_shl
eng_cou
vir_cou
alpha
eng_bnd
vir_bnd
beta
eng_ang
eng_dih
vir_ang
vir_con
gamma
vir_pmf
eng_tet
vir_tet
press
c CCLRC
129
--------------------------------------------------------------------------------------------------
The labels refer to :
line 1
step
eng tot
temp tot
eng cfg
eng vdw
eng cou
eng bnd
eng ang
eng dih
eng tet
line 2
time(ps)
eng pv
temp rot
vir cfg
vir vdw
vir cou
vir bnd
vir ang
vir con
vir tet
line 3
cpu (s)
volume
temp shl
eng shl
vir shl
alpha
beta
gamma
vir pmf
press
MD step number
total internal energy of the system
system temperature
congurational energy of the system
congurational energy due to short-range potentials
congurational energy due to electrostatic potential
congurational energy due to chemical bond potentials
congurational energy due to valence angle and three-body potentials
congurational energy due to dihedral inversion and four-body potentials
congurational energy due to tethering potentials
elapsed simulation time (ps) since the beginning of the job
enthalpy of system
rotational temperature
total congurational contribution to the virial
short range potential contribution to the virial
electrostatic potential contribution to the virial
chemical bond contribution to the virial
angular and three body potentials contribution to the virial
constraint bond contribution to the virial
tethering potential contribution to the virial
elapsed cpu time since the beginning of the job
system volume
core-shell temperature
congurational energy due to core-shell potentials
core-shell potential contribution to the virial
angle between b and c cell vectors
angle between c and a cell vectors
angle between a and b cell vectors
Potential of mean force constraint contribution to the virial
pressure
Note: The total internal energy of the system (variable tot energy) includes all contributions to the energy (including system extensions due to thermostats etc.) It is nominally
the conserved variable of the system, and is not to be confused with conventional system
energy, which is a sum of the kinetic and conguration energies.
The interval for printing out these data is determined by the directive print in the
CONTROL le. At each time-step that printout is requested the instantaneous values of
c CCLRC
130
the above statistical variables are given in the appropriate columns. Immediately below
these three lines of output the rolling averages of the same variables are also given. The
maximum number of time-steps used to calculate the rolling averages is determined by the
parameter mxstak in the dl params.inc le (see section 7.1.1). The working number of
time-steps for rolling averages is controlled by the directive stack in le CONTROL (see
above). The default value is mxstak.
Energy Units: The energy unit for the data appearing in the OUTPUT is dened by
the units directive appearing in the CONTROL le.
Pressure units:
The unit of pressure is k bar, irrespective of what energy unit is chosen.
4.2.2.6 Summary of Statistical Data
This portion of the OUTPUT le is written from the subroutine result. The number of
time-steps used in the collection of statistics is given. Then the averages over the production
portion of the run are given for the variables described in the previous section. The root
mean square variation in these variables follow on the next two lines. The energy and
pressure units are as for the preceeding section.
Also provided in this section is an estimate of the diusion coeÆcient for the dierent
species in the simulation, which is determined from a single time origin and is therefore
very approximate. Accurate determinations of the diusion coeÆcients can be obtained
using the msd utility program, which processes the HISTORY le (see chapter 6).
If an NPT or NT simulation is performed the OUTPUT le also provides the mean
stress (pressure) tensor and mean simulation cell vectors.
4.2.2.7 Sample of Final Conguration
The positions, velocities and forces of the 20 atoms used for the sample of the initial
conguration (see above) are given. This is written by the subroutine result.
4.2.2.8 Radial Distribution Functions
If both calculation and printing of radial distribution functions have been requested (by
selecting directives rdf and print rdf in the CONTROL le) radial distribution functions
are printed out. This is written from the subroutine rdf1. First the number of time-steps
used for the collection of the histograms is stated. Then each function is given in turn. For
each function a header line states the atom types (`a' and `b') represented by the function.
Then r; g(r) and n(r) are given in tabular form. Output is given from 2 entries before the
rst non-zero entry in the g(r) histogram. n(r) is the average number of atoms of type `b'
within a sphere of radius r around an atom of type `a'. Note that a readable version of
these data is provided by the RDFDAT le (below).
c CCLRC
4.2.2.9
131
Z Density Prole
If both calculation and printing of Z density proles has been requested (by selecting directives zden and print rdf in the CONTROL le Z density proles are printed out as the
last part of the OUTPUT le. This is written by the subroutine zden1. First the number
of time-steps used for the collection of the histograms is stated. Then each function is given
in turn. For each function a header line states the atom type represented by the function.
Then z; (z) and n(z) are given in tabular form. Output is given from Z = [ L=2; L=2]
where L is the length of the MD cell in the Z direction and (z) is the mean number density.
n(z ) is the running integral from L=2 to z of (xy cell area)(s)ds. Note that a readable
version of these data is provided by the ZDNDAT le (below).
4.2.3 The REVCON File
This le is formatted and written by the subroutine revive. REVCON is the restart
conguration le. The le is written every ndump time steps in case of a system crash
during execution and at the termination of the job. A successful run of DL POLY 2 will
always produce a REVCON le, but a failed job may not produce the le if an insuÆcient
number of timesteps have elapsed. ndump is a parameter dened in the dl params.inc le
found in the source directory of DL POLY 2 (section 7.1.1). Changing ndump necessitates
recompiling DL POLY 2 . REVCON is identical in format to the CONFIG input le (see
section 4.1.2). REVCON should be renamed CONFIG to continue a simulation from one
job to the next. This is done for you by the copy macro supplied in the execute directory
of DL POLY 2 .
4.2.4 The REVIVE File
This le is unformatted and written by the subroutine revive. It contains the accumulated
statistical data. It is updated whenever the le REVCON is updated (see previous section).
REVIVE should be renamed REVOLD to continue a simulation from one job to the next.
This is done by the copy macro supplied in the execute directory of DL POLY 2 . In
addition, to continue a simulation from a previous job the restart keyword must be included
in the CONTROL le.
The format of the REVIVE le is identical to the REVOLD le described in section
4.1.4.
4.2.5 The RDFDAT File
This is a formatted le containing em Radial Distribution Function (RDF) data. Its contents are as follows:
record 1
cfgname
record 2
ntpvdw
character (A80)
integer (i10)
conguration name
number of RDFs in le
c CCLRC
mxrdf
132
integer (i10)
number of data points in each RDF
There follow the data for each individual RDF i.e.
are as follows:
ntpvdw
times. The data supplied
rst record
character (A8)
rst atom name
character (A8)
second atom name
following records (mxrdf records)
radius
real (e14)
interatomic distance (A)
g(r)
real (e14)
RDF at given radius.
atname 1
atname 2
Note the RDFDAT le is optional and appears when the print rdf option is specied in
the CONTROL le.
4.2.6 The ZDNDAT File
This is a formatted le containing the Z-density data. Its contents are as follows:
record 1
character (A80) conguration name
mxrdf
integer (i10)
number of data points in the Z-density function
following records (mxrdf records)
z
real (e14)
distance in z direction (A)
(z )
real (e14)
Z-density at given height z
cfgname
record 2
Note the ZDNDAT le is optional and appears when the print rdf option is specied
in the CONTROL le.
4.2.7 The STATIS File
The le is formatted, with integers as \i10" and reals as \e14.6". It is written by the
subroutine static. It consists of two header records followed by many data records of
statistical data.
record 1
cfgname
record 2
string
character
character
conguration name
energy units
c CCLRC
133
Data records
Subsequent lines contain the instantaneous values of statistical variables dumped from
the array stpval. A specied number of entries of stpval are written in the format
\(1p,5e14.6)". The number of array elements required (determined by the parameter
mxnstk in the dl params.inc le) is
mxnstk 27 + ntpatm(number of unique atomic sites)
+9(if stress tensor calculated)
+9(if constant pressure simulation requested)
The STATIS le is appended at intervals determined by the stats directive in the CONTROL le. The energy unit is as specied in the CONTROL le with the the units
directive, and are compatible with the data appearing in the OUTPUT le. The contents
of the appended information is:
record i
integer
real
integer
record ii stpval(1) { stpval(5)
engcns
real
temp
real
engcfg
real
engsrp
real
engcpe
real
record iii stpval(6) { stpval(10)
engbnd
real
engang
real
engdih
real
engtet
real
enthal
real
record iv stpval(11) { stpval(15)
tmprot
real
vir
real
virsrp
real
vircpe
real
virbnd
real
record v stpval(16) -stpval(20)
virang
real
vircon
real
virtet
real
volume
real
tmpshl
real
nstep
time
nument
current MD time-step
elapsed simulation time = nstept
number of array elements to follow
total extended system energy
(i.e. the conserved quantity)
system temperature
congurational energy
short range potential energy
electrostatic energy
chemical bond energy
valence angle and 3-body potential energy
dihedral interaction energy
tethering energy
enthalpy (total energy + PV)
rotational temperature
total virial
short-range virial
electrostatic virial
bond virial
valence angle and 3-body virial
constraint virial
tethering virial
volume
core-shell temperature
c CCLRC
134
record vi stpval(21) -stpval(25)
real
core-shell potential energy
real
core-shell virial
real
MD cell angle real
MD cell angle real
MD cell angle record vii stpval(26) -stpval(27)
virpmf
real
Potential of Mean Force virial
press
real
pressure
the next ntpatm entries
amsd(1)
real
mean squared displacement of rst atom types
amsd(2)
real
mean squared displacement of second atom types
...
...
...
amsd(ntpatm)
real
mean squared displacement of last atom types
the next 9 entries - if the stress tensor is calculated
stress(1)
real
xx component of stress tensor
stress(2)
real
xy component of stress tensor
stress(3)
real
xz component of stress tensor
stress(4)
real
yx component of stress tensor
...
real
...
stress(9)
real
zz component of stress tensor
the next 9 entries - if a NPT simulation is undertaken
cell(1)
real
x component of a cell vector
cell(2)
real
y component of a cell vector
cell(3)
real
z component of a cell vector
cell(4)
real
x component of b cell vector
...
real
...
cell(9)
real
z component of c cell vector
engshl
virshl
alpha
beta
gamma
Note. The stress tensor is calculated only if the code is compiled with the \-STRESS"
option (see section 3.2.1). Cell shape varying constant pressure simulations (keyword ensemble nst ... in the CONTROL le) are only possible if the stress tensor is calculated.
If isotropic constant pressure simulations are required, where the cell volume but not the
shape may vary, (keyword ensemble npt ...) the stress tensor need not be calculated.
c CCLRC
135
key
Table 4.12: Denition of pair potential functions and variables
potential type
Variables (1-5)
functional form
12-6
12-6
A
B
U (r ) =
lj
Lennard-Jones
U (r) = 4
nm
n-m
Eo n m r0
buck
Buckingham
A
C
bhm
Born-Huggins
-Meyer
A
B
hbnd
12-10 H-bond
A
B
snm
Shifted forcey
U (r) = nEm n-m [27]
Eo n m r0 rc z
o
(
U (r) =
stch
Sutton-Chen
tab
Tabulation
h
m n
a
n m
C
n
B
r6
12
r
exp
r
r)]
A
r12
6
r
i
n
ro m r
exp[B (
U (r) =
)
Eo ro n
n m) m r
U (r) = A
D
h
A
r12
(
U (r ) = A
C
B
r10
C
r6
C
r6
n o
n
m oi
ro n
1
1
m ro m
n
r
n n r m o nmEo r ro
ro
(n m)
+
h
Ui (r) = ar n
m
P
i = j raij
C p
2
i
i
tabulated potential
Note: in this formula the terms , and are compound expressions involving the
variables Eo; n; m; r and rc. See section 2.3.1 for further details.
z Note: rc defaults to the general van der Waals cuto (rvdw or rcut) if it is set to zero or
not specied or not specied in the FIELD le.
y
0
D
r8
c CCLRC
136
Table 4.13: Three-body potentials
Variables (1-4)
key
potential type
functional formy
thrm
Truncated harmonic
k
0
shrm
Screened harmonic
k
0
1 2
U ( ) =
bvs1
Screened Vessal[24]
k
0
1 2
U () = 8( k0 )2
bvs2
Truncated Vessal[25]
k
0
a
U () =
k
2
2
(
(
exp[
U () = k[a (
( ) (
0
hbnd H-bond [7]
y is the a-b-c angle.
k
2
8
0 )2 exp[ (rij8 + rik
)=8 ]
0 )2 exp[ (rij =1 + rik =2 )]
n
(
)2 ( )2
0
(rij =1 + rik =2 )]
0 )2 ( + 0 2)2 a2 a
8
0 )3 ] exp[ (rij8 + rik
)=8 ]
U () = Dhb cos4 ()[5(Rhb =rjk )12
Dhb Rhb
key
Table 4.14: Four-body Potentials
potential type Variables (1-2)
functional formz
harm
Harmonic
Harmonic cosine
plan Planar
hcos
z is the inversion angle.
k
0
k
0
A
U () = 21 k( 0 )2
U () =
(cos() cos( ))
U () = A [1 cos()]
k
2
2 o
0
2
1
6(Rhb=rjk ) ]
10
c CCLRC
key
potential type
elec
Electric eld
Oscillating Shear
Continuous Shear
Gravitational Field
Magnetic Field
Containing Sphere
oshm
shrx
grav
magn
sphr
137
Table 4.15: External elds
Variables (1-4) functional formy
Ex Ey Ez
A
n
A
z0
0
Gx Gy Gz
Hx Hy Hz
A
R0
= q:E
F x = Acos(2n:z=Lz )
j z j> z : vx = (1=2)A(j z j =z)
F = m:G
F = q(v H )
r > R : F = A(R r) n
F
n
Rcut
cut
0
Chapter 5
DL POLY 2 Examples
138
c CCLRC
139
Scope of Chapter
This chapter describes the standard test cases for DL POLY 2 , the input and output les
for which are in the data sub-directory.
c CCLRC
140
5.1 DL POLY Examples
5.1.1 Test Cases
The following example data sets (both input and output) are stored in the subdirectory
data. These are provided so that you may check that your version of DL POLY is working
correctly. All the jobs are short and should require no more than a few minutes execution
time, even on a single processor computer. The output les are stored in compressed format.
The test cases can be run by typing
select n
from the execute directory, where n is the number of the test case. The select macro will
copy the appropriate CONTROL, CONFIG, and FIELD les to the execute directory ready
for execution. The output les OUTPUT, REVCON and STATIS may be compared with
the les supplied in the data directory.
The example output les provided in the data directory were obtained on 4 processors
of an IBM SP/2 parallel system (120 MHz P2SC `thin' nodes). The program was compiled
with the three point interpolation option.
It should be noted that the potentials and the simulation conditions used in the following
test cases are chosen to demonstrate functionality only. They are not necessarily appropriate for serious simulation of the test systems. Note also that the DL POLY 2
Graphical User Interface [20] provides a convenient means for running and viewing these
test cases.
5.1.1.1 Test Case 1: KNaSi2 O5
Potassium Sodium disilicate glass (NaKSi O ) using two and three body potentials. Some
of the two body potentials are read from the TABLE le. Electrostatics are handled by a
multiple timestep Ewald sum method. Cubic periodic boundaries are in use.
2
5
5.1.1.2 Test Case 2: Metal simulation with Sutton Chen potentials
FCC Aluminium using Sutton-Chen potentials. Temperature is controlled by the method
of Gaussian constraints.
5.1.1.3 Test Case 3: An antibiotic in water
Valinomycin in 1223 spc water molecules. The temperature is controlled by a Nose-Hoover
thermostat while electrostatics are handled by a shifted Coulombic potential. The water
is dened as a rigid body while bond constraints are applied to all chemical bonds in the
valinomycin. Truncated octahedral boundary conditions are used.
5.1.1.4 Test Case 4: Shell model of water
256 molecules of water with a polarizable oxygen atom. Temperature is controlled by the
Berendsen thermostat while electrostatics are handled by the reaction eld method with
c CCLRC
141
a \charge group" cuto scheme. \Slab" period boundary conditions are used. The water
molecule (apart from the shell) is treated as a rigid body.
5.1.1.5 Test Case 5: Shell model of MgCl2 at constant pressure
Dynamical Shell model simulation of MgCl . Temperature and pressure are controlled by a
Berendsen thermostat and barostat. An Ewald sum is used with cubic periodic boundary
conditions.
2
5.1.1.6 Test Case 6: PMF calculation
Potential of mean force calculation of a potassium ion in SPC water. Electrostatics are
handled by the Ewald sum. The water is treated as a constrained triangle.
5.1.1.7 Test Case 7: Linked rigid bodies at constant pressure
8 biphenyl molecules in cubic boundary conditions. Temperature and pressure are controlled by a Hoover type thermostat and barostat. Each phenyl ring is treated as a rigid
body, with a constraint bond to the other ring of the molecule. In the centre of each ring
are three massless charge sites which imparts a quadrupole moment to the ring.
5.1.1.8 Test Case 8: An osmosis experiment with a semi permeable membrane
The membrane is a collection of tethered sites interconnected by harmonic springs. There
are no electrostatic forces in the system. The simulation is run with the Hoover anisotropic
constant presure algorithm.
5.1.1.9 Test Case 9: A surfactant at the air-water interface
The system is comprised of 32 surfactant molecules (trimethylaminododecane bromide or
TAB-C12) arranged either side of a slab of 342 water molecules approximately 30 A thick.
The surfactant chains are treated with rigid bonds and the water molecules are treated as
rigid bodies. The TAB headgroup has fractional charges summing to +1 (the bromide ion
has charge -1). The Ewald sum handles the electrostatic calculations. The short range
forces are taken from the Dreiding force eld.
5.1.1.10 Test Case 10: DNA strand in water
This system consists of a strand of DNA 1260 atoms in length in a solution of 706 (SPC)
water molecules. The DNA is aligned in the Z-direction and hexagonal prism periodic
boundary conditions applied. The electrostatic interactions are calculated using the Smooth
Particle Mesh Ewald method. Note that the system has a strong overall negative charge
which is strongly anisotropic in distribution. The short range forces are taken from the
Dreiding force eld, and constraints are used for all covalent bonds. For simplicity H-bonds
are treated as harmonic bonds with an equilibrium bondlength of 1.724 A.
c CCLRC
142
5.1.2 Benchmark Cases
These represent rather larger test cases for DL POLY 2 that are also suitable for benchmarking the code on large scale computers. They have been selected to show fairly the the
capabilities and limitations of the code.
5.1.2.1 Benchmark 1
Simulation of metallic aluminium at 300K using a Sutton-Chen density dependent potential.
The system is comprised of 19652 identical atoms. The simulation runs on 16 to 512
processors only.
5.1.2.2 Benchmark 2
Simulation of a 15-peptide in 1247 water molecules. This was designed as an AMBER
comparison. The system consists of 3993 atoms in all and runs on 8-512 processors. It
uses neutral group electrostatics and rigid bond constraints and is one of the smallest
benchmarks in the set.
5.1.2.3 Benchmark 3
Simulation of the enzyme transferrin in 8102 water molecules. The simulation makes use
of neutral group electrostatics and rigid bond constraints. The system is 27539 atoms and
runs on 8-512 processors.
5.1.2.4 Benchmark 4
Simulation of a sodium chloride melt with Ewald sum electrostatics and a multiple timestep
algorithm to enhance performance. The system is comprised of 27000 atoms and runs on
8-512 processors.
5.1.2.5 Benchmark 5
Simulation of a sodium-potassium disilicate glass. Uses Ewald sum electrostatics, a multiple timestep algorithm and a three-body valence angle potentials to support the silicate
structure. It also using tabluated two-body potentials stored in the le TABLE. The system
is comprised of 8640 atoms and runs on 16-512 processors.
5.1.2.6 Benchmark 6
Simulation of a potassium-valinomycin complex in 1223 water molecules using an adapted
AMBER forceeld and truncated octahedral periodic boundary conditions. The system
size is 3838 atoms and runs on 16-512 processors.
c CCLRC
143
5.1.2.7 Benchmark 7
Simulation of gramicidin A molecule in 4012 water molecules using neutral group electrostatics. The system is comprised of 12390 atoms and runs on 8-512 processors. This
example was provided by Lewis Whitehead at the University of Southampton.
5.1.2.8 Benchmark 8
Simulation of an isolated magnesium oxide microcrystal comprised of 5416 atoms originally
in the shape of a truncated octahedron. Uses full coulombic potential. Runs on 16-512
processors.
5.1.2.9 Benchmark 9
Simulation of a model membrane with 196 41-unit membrane chains, 8 valinomycin molecules
and 3144 water molecules using an adapted AMBER potential, multiple timestep algorithm
and Ewald sum electrostatics. The system is comprised of 18866 atoms and runs on 8-512
processors.
Chapter 6
DL POLY 2 Utilities
144
c CCLRC
145
Scope of Chapter
This chapter describes the more important utility programs and subroutines of DL POLY 2
, found in the sub-directory utility. A more complete description of the sub-directory
contents is to be found in the DL POLY 2 Reference Manual.
6.1 Miscellaneous Utilities
6.1.1 parset
6.1.1.1 Header records
program parset
c
c***********************************************************************
c
c
dl_poly utility program to prepare the dl_params.inc file
c
for specific dl_poly applications
c
c
author - w.smith, t.forester jan 1995
c
copyright daresbury laboratory 1995
c
c***********************************************************************
c
6.1.1.2 Function
is designed to provide estimates of the FORTRAN parameters (e.g. array dimensions) required by versions of DL POLY 2 prior to 2.11 to simulate a given system i.e. those
required for the dl params.inc le. By scanning the CONTROL, FIELD and CONFIG les
of the intended simulation parset is able to calculate estimates of minimum parameters
needed. The calculated parameters are written into a le: new params.inc, which is FORTRAN compatible. Once this has been renamed dl params.inc, it can be used directly
when DL POLY 2 is compiled. Use of parset is strongly recommended as a means of
reducing the eort needed to create a working DL POLY 2 executable.
Note. parset is required only for versions of DL POLY 2 prior to version 2.11.
parset
6.1.1.3 Dependencies
None (parset is self contained.)
6.1.1.4 Parameters
None (There are no internal arrays.)
c CCLRC
146
6.1.1.5 Input
Interactive:
record 1:
min nodes
record 2:
max nodes
integer
integer
minimum number of processing nodes
maximum number of processing nodes
Data Files:
input.data:
CONTROL
CONFIG
FIELD
TABLE
Standard DL POLY 2 CONTROL input le
Standard DL POLY 2 CONFIG input le
Standard DL POLY 2 FIELD input le
Standard DL POLY 2 TABLE input le (optional)
output.data:
new params.inc
6.1.1.6 Comments
New parameters include le
does not undertake any error checking of the CONTROL, FIELD and CONFIG
les. Any errors in these les will result in an incorrect parameters le. It must also
be recognised that for some of the parameters, there is no straightforward formula for
calculating suitable values from the input les. In these cases the parameters produced
represent a reasonable estimate only. Fortunately, these cases are few in number and as
a rule parset will signicantly reduce the time needed to prepare a working version of
DL POLY 2 .
It is useful to prepare the input les assuming the largest simulation you are likely to
attempt on a given system. This will generate the largest executable necessary to prevent
you having to recompile the code in the course of your study.
parset
c CCLRC
147
6.1.2 Useful Macros
6.1.2.1 Macros
Macros are simple executable les containing standard unix commands. A number of the
are supplied with DL POLY and are found in the execute sub-directory. The available
macros are as follows.
cleanup
copy
gopoly
select
store
The function of each of these is described below. It is worth noting that most of these
functions can be perfomed by the DL POLY 2 GUI [20].
6.1.2.2 cleanup
cleanup removes several standard data les from the execute sub-directory. It contains the
unix commands:
rm OUTPUT REVCON REVOLD STATIS REVIVE gopoly.*
and removes the les OUTPUT, REVCON, REVOLD, STATIS, REVIVE and gopoly.* (all
variants). It is useful for cleaning the sub-directory up after a run. (Useful data should be
stored elsewhere however!)
6.1.2.3 copy
copy invokes the unix commands:
mv CONFIG CONFIG.OLD
mv REVCON CONFIG
mv REVIVE REVOLD
which collectively prepare the DL POLY les in the execute sub-directory for the continuation of a simulation. It is always a good idea to store these les elsewhere in addition to
using this macro.
c CCLRC
148
6.1.2.4 gopoly
gopoly is used to submit a DL POLY job to the Daresbury IBM SP/2, which operates a
LOADLEVELLER job queuing system. It invokes the following script.
#@
#@
#@
#@
#@
#@
#@
#@
#@
#@
#@
min_processors = 4
max_processors = 4
job_type = parallel
requirements = (Adapter == "hps_ip") && ( Pool == 2)
executable = /usr/bin/poe
cpu_limit = 00:10:00
arguments = ~/dl_poly_2.10/execute/DLPOLY.X -euilib ip
output = gopoly.o
error = gopoly.e
class = dev
queue
Using LOADLEVELLER, the job is submitted by the unix command:
llsubmit gopoly
where llsubmit is a local command for submission to the SP/2. The number of required
nodes and the job time are indicated in the above script.
6.1.2.5 select
select is a macro enabling easy selection of one of the test cases. It invokes the unix
commands:
cp ../data/TEST$1/CONTROL CONTROL
cp ../data/TEST$1/FIELD FIELD
cp ../data/TEST$1/CONFIG CONFIG
select requires one argument (an integer) to be specied:
select n
where n is test case number, which ranges from 1 to 10.
This macro sets up the required input les in the execute sub-directory to run the n-th
test case.
6.1.2.6 store
The store macro provides a convenient way of moving data back from the execute subdirectory to the data sub-directory. It invokes the unix commands:
c CCLRC
149
mkdir ../data/TEST$1
mv OUTPUT ../data/TEST$1/OUTPUT
mv REVCON ../data/TEST$1/REVCON
mv STATIS ../data/TEST$1/STATIS
mv REVIVE ../data/TEST$1/REVIVE
mv RDFDAT ../data/TEST$1/RDFDAT
mv ZDNDAT ../data/TEST$1/ZDNDAT
chmod 400 ../data/TEST$1/*
which rst creates a new DL POLY data/TEST.. sub-directory and then moves the standard DL POLY output data les into it.
store requires one argument:
store n
where n is a unique string or number to label the output data in the data/TESTn subdirectory.
Note that store sets the le access to read-only. This is to prevent the store macro
overwriting existing data without your knowledge.
Chapter 7
DL POLY 2 Subroutines and
Functions
150
c CCLRC
151
Scope of Chapter
This chapter describes all the subroutines of DL POLY 2 to be found in the source subdirectory. A fuller description of the contents of the source sub-directory is available in the
DL POLY 2 Reference Manual.
c CCLRC
152
7.1 Subroutine and Function Specications
7.1.1 dl params.inc: The DL POLY Parameters (Include) File
7.1.1.1 Header
c*********************************************************************
c
c
dl_poly insert file specifying array sizes for the
c
entire package
c
c
copyright - daresbury laboratory 1994
c
authors - w. smith & t. forester november 1994.
c
c
c
note the following internal units apply everywhere
c
c
unit of time
(to)
=
1 x 10**(-12) seconds
c
unit of length
(lo)
=
1 x 10**(-10) metres
c
unit of mass
(mo)
= 1.6605402 x 10**(-27) kilograms
c
unit of charge
(qo)
= 1.60217733 x 10**(-19) coulombs
c
unit of energy
(Eo)
= 1.6605402 x 10**(-23) joules
c
unit of pressure (Po)
= 1.6605402 x 10**( 7) pascals
c
= 163.842151
atmospheres
c
c*********************************************************************
c
7.1.1.2 Function
The DL POLY 2 parameters le for version 2.10 (and earlier) contains all the parameters
dening the arrays dimensions of DL POLY 2 plus the fundamental constants and conversion factors. In the include le for version 2.11 (and after) the bulk of these parameters
take the form of FORTRAN integer variables, which are stored in the COMMON block
/params/. Apart from this dierence, the meaning and function of the parameters is the
same. The dl params.inc le is included in all relevant subroutines at compile time.
7.1.1.3 The Parameters and their Function
In the following table the values of parameters that are dependent on the simulated system
are given as variable. Some parameter values may be derived from others, and a simple
formula is given. An example of a working parameters le can be found in the source
subdirectory.
parameter value
function
c CCLRC
boltz
kmaxb
kmaxc
minnode
msatms
msbad
msgrp
mslst
mspmf
msteth
mx2tbp
mx3fbp
mxangl
mxatms
mxbond
mxbuff
mxcell
mxcons
mxdihd
mxewld
mxexcl
mxfbd
mxfld
mxgatm
mxgrid
mxgrp
mxinv
mxlist
mxlshp
mxmols
mxneut
mxngp
mxnstk
mxpang
mxpbnd
mxpdih
mxpfbp
153
0.831451115
variable
variable
variable
1
mxatms/minnode+1
max(mxbond,mxangl,
mxdihd,mxteth,mxinv,
mxshl)
mxgrp/minnode+1
mxatms/minnode+1
variable
variable
variable le mxvdw
variable
variable
variable
variable
max(6*mxatms,
8*(mxcons+1),
8*(mxgrp+1),
mxnstk*mxstak,
mxebuf, mxgrid)
variable
variable
variable
msatms or mxatms
variable
variable
10
variable
variable
variable
variable
variable
2*mxcons
mxatms
variable
variable
variable 3
mxsvdw+45
4
4
5
3
boltzmann constant in internal units
max reciprocal space vector index (b direction)
max reciprocal space vector index (c direction)
min number of nodes for code execution
max number of atoms in working arrays
max size of working arrays for bond, angle,
dihedral, tether,inversion and shell
routines
max number of rigid groups per node
max number of atoms in Verlet test arrays
max number of potential of mean force
constraints per node
max number of tethered atoms per node
array dimension of 3-body potential parameters
array dimension of 4-body potential parameters
max number of bond angles on a node
max number of atoms in system
max number of chemical bonds on a node
max dimension of atomic transfer buer
max number of link cells in system
max number of constraint bonds on a node
max number of torsion angles on a node
max of array elements in ewald1(a) work arrays
max number of excluded interactions per atom
max number of dened 4-body force potentials
max number of external eld parameters
max number of sites in rigid units
max number of grid points in potential arrays
max number of rigid body units in system
max number of inversion potentials per node
max number of atoms in verlet list
max dimension of shape routine transfer array
max number of molecules
max number of neutral groups + 1
max number of sites in a rigid unit
max number of stacked variables
max number of angle potential parameters
max number of bond potential parameters
max number of dihedral potential parameters
max number of 4-body potential parameters
c CCLRC
mxpinv
mxpmf
mxproc
mxptbp
mxpvdw
mxquat
mxrdf
154
2
variable mxatms
variable
mxpang+1
5
variable
variable
mxshak
mxshl
mxsite
mxspmf
mxstak
mxsvdw
variable
vaiable
variable
variable
variable
variable
mxtang
mxtbnd
mxtbp
mxtcon
mxtdih
mxteth
mxtinv
mxtmls
mxtshl
mxungp
mxvdw
variable
variable
mxxdf
nconf
ndump
nfield
nhist
nrdfdt
nread
nrest
nrite
nstats
ntable
nzdfdt
pi
mxvdw*mxsvdw
variable
variable
variable
variable
variable
variable
variable
((mxsvdw+1)*
mxsvdw)/2
max(mxlist,msatms,
mxcons,mxn1*mxn1*
(mxneut+1)/2)
8
variable
7
21
24
5
22
6
20
23
25
3.141592653589793
max number of inversion potential parameters
number of atoms in potential of mean
force constraints
max number of nodes (used in parallel
constraint algorithm)
max number of 3-body potential parameters
max number of van der Waals potential parameters
max iterations in quaternion integration
number of tabulation points for radial distribution
functions
max number of iterations in shake algorithm
max number of core-shell units
max number of molecular sites
max number sites to dene pmf units
dimension of stack arrays for rolling averages
max number of dierent types of sites for pair
potentials
max number of dierent bond angle potentials
max number of chemical bond potentials
max number of 3-body potentials
max number of specied bondlength constraints
max number of dierent dihedral potentials
max number of tethered atom potentials
max number of inversion potentials
max number of molecule types
max number of core-shell unit types
max number unique rigid body units
max number of dierent pair potentials
(2 if Sutton-Chen potentials used)
max number of atoms in xdf,ydf and zdf arrays
(mxn1 is number of sites in largest
neutral group)
conguration le input channel
data dumping interval in event of system crash
force eld input channel
trajectory history le channel
output channel for RDF data
main input channel
output channel accumulators restart dump le
main output channel
statistical data le output channel
tabulated potentials le input channel
output channel for Z-density data le
c CCLRC
155
prsunt
r4pie0
1.63842151d-1
138935.4835
sqrpi
1.7724538509055159
pressure conversion factor
electrostatic conversion factor i.e.
(unit(charge)**2/(4 pi eps0 unit(length))/
unit(energy)
square root of 7.1.1.4 Comments
1. A working version of the parameters le (for DL POLY 2 versions prior to 2.11), for
any given application, can be constructed with the aid of the utility program parset
see section 6.1.1 of the DL POLY 2 Reference Manual.
2. Many of the above parameters refer to array dimensions. If the application does not
use the associated functionality, these parameters may be set to 1. e.g. mxtang and
mxangl may both be set to 1 if the simulation does not require bond angles.
3. Any changes made to the parameters le requires the entire program to be recompiled.
(The build directory contains example makeles which do this automatically.)
4. The parameters to found in the /params/ COMMON block (versions 2.11 and above)
may be determined from the following FORTRAN extract, taken from the dl params.inc
le. The variables appearing have the same meaning as the parameters described
above.
c
array allocation parameters (set by subroutine parset)
common/params/kmaxa,kmaxb,kmaxc,minnode,msatms,msbad,msgrp,
x
mspmf,msteth,mxangl,mxatms,mxbond,mxbuff,mxcell,
x
mxcons,mxdihd,mxewld,mxexcl,mxfbp,mxfld,mxgatm,mxgrid,
x
mxgrp,mxinv,mxlist,mxlshp,mxneut,mxngp,mxnstk,mxpang,
x
mxpbnd,mxpdih,mxpfbp,mxpinv,mxpmf,mxproc,mxptbp,mxpvdw,
x
mxrdf,mxshl,mxsite,mxspmf,mxstak,mxsvdw,mxtang,mxtbnd,
x
mxtbp,mxtcon,mxtdih,mxteth,mxtinv,mxtmls,mxtshl,mxungp,
x
mxvdw,mxxdf,mx2tbp,mx3fbp,mxebuf,mxquat,mxshak
Bibliography
[1] Smith, W., and Forester, T., 1996, J. Molec. Graphics, 14, 136.
[2] Smith, W., 1987, Molecular Graphics, 5, 71.
[3] van Gunsteren, W. F., and Berendsen, H. J. C. 1987, Groningen Molecular Simulation (GROMOS) Library Manual. BIOMOS, Nijenborgh, 9747 Ag Groningen, The
Netherlands. Standard GROMOS reference.
[4] Weiner, S. J., Kollman, P. A., Nguyen, D. T., and Case, D. A., 1986, J. Comp. Chem.,
7, 230.
[5] Brunger, A. T. 1992, X-PLOR: A System for X-Ray Crystallography and NMR. New
Haven and London: Yale University Press.
[6] Sutton, A. P., and Chen, J., 1990, Philos. Mag. Lett., 61, 139.
[7] Mayo, S., Olafson, B., and Goddard, W., 1990, J. Phys. Chem., 94, 8897.
[8] Smith, W., and Forester, T. R., 1994, Comput. Phys. Commun., 79, 52.
[9] Smith, W., and Forester, T. R., 1994, Comput. Phys. Commun., 79, 63.
[10] Allen, M. P., and Tildesley, D. J. 1989, Computer Simulation of Liquids. Oxford:
Clarendon Press.
[11] Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C., 1977, J. Comput. Phys., 23,
327.
[12] Fincham, D., 1992, Molecular Simulation, 8, 165.
[13] Forester, T., and Smith, W., 1995, In preparation.
[14] Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W., DiNola, A., and Haak,
J. R., 1984, J. Chem. Phys., 81, 3684.
[15] Evans, D. J., and Morriss, G. P., 1984, Computer Physics Reports, 1, 297.
[16] Hoover, W. G., 1985, Phys. Rev., A31, 1695.
[17] Tuckerman, M., Berne, B., and Rossi, A., 1990, J. Chem. Phys., 94, 1465.
156
c CCLRC
[18]
[19]
[20]
[21]
[22]
[23]
[24]
[25]
[26]
[27]
[28]
[29]
[30]
[31]
[32]
[33]
[34]
[35]
[36]
[37]
[38]
[39]
[40]
157
Stuart, S., Zhou, R., and Berne, B., 1996, J. Chem. Phys., 105, 1426.
Procacci, P., and Marchi, M., 1996, J. Chem. Phys., 104, 3003.
Smith, W., 1998, Daresbury Laboratory.
Melchionna, S., and Cozzini, S., 1998, University of Rome.
Brode, S., and Ahlrichs, R., 1986, Comput. Phys. Commun., 42, 41.
Hockney, R. W., and Eastwood, J. W. 1981, Computer Simulation Using Particles.
McGraw-Hill International.
Vessal, B., 1994, J. Non-Cryst. Solids, 177, 103.
Smith, W., Greaves, G. N., and Gillan, M. J., 1995, J. Chem. Phys., 103, 3091.
Smith, W., 1993, CCP5 Information Quarterly, 39, 14.
Clarke, J. H. R., Smith, W., and Woodcock, L. V., 1986, J. Chem. Phys., 84, 2290.
Finnis, M. W., and Sinclair, J. E., 1984, Philos. Mag. A, 50, 45.
Eastwood, J. W., Hockney, R. W., and Lawrence, D. N., 1980, Comput. Phys. Commun., 19, 215.
Smith, W., and Fincham, D., 1993, Molecular Simulation, 10, 67.
Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G.,
1995, J. Chem. Phys., 103, 8577.
Neumann, M., 1985, J. Chem. Phys., 82, 5663.
Fincham, D., and Mitchell, P. J., 1993, J. Phys. Condens. Matter, 5, 1031.
Lindan, P. J. D., and Gillan, M. J., 1993, J. Phys. Condens. Matter, 5, 1019.
McCammon, J. A., and Harvey, S. C. 1987, Dynamics of Proteins and Nucleic Acids.
Cambridge: University Press.
Brown, D., and Clarke, J. H. R., 1984, Molec. Phys., 51, 1243.
Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, Molec. Phys., 78, 533.
Tildesley, D. J., Streett, W. B., and Saville, G., l978, Molec. Phys, 35, 639.
Tildesley, D. J., and Streett, W. B. Multiple time step methods and an improved
potential function for molecular dynamics simulations of molecular liquids. In Lykos,
P., editor, Computer Modelling of Matter. ACS Symposium Series No. 86, 1978.
Forester, T., and Smith, W., 1994, Molecular Simulation, 13, 195.
c CCLRC
[41]
[42]
[43]
[44]
158
Smith, W., 1991, Comput. Phys. Commun., 62, 229.
Smith, W., 1993, Theoretica. Chim. Acta., 84, 385.
Smith, W., 1992, Comput. Phys. Commun., 67, 392.
Vessal, B., Amini, M., Leslie, M., and Catlow, C. R. A., 1990, Molecular Simulation,
5, 1.
Appendix A
The DL POLY 2 Makele
#
#
#
#
#
#
#
#
#
Master makefile for DL_POLY_2.0
Author: W. Smith November 1999
With DPP tool by J. Geronowicz
Original by T. Forester 1995
$Author: wl $
$Date: 1998/10/12 16:26:10 $
$Revision: 1.10 $
$State: Exp $
# Define default settings
#=======================================================================
FFTW_LIBRARY = ""
BINROOT = ../execute
CC = cc
DPP = ./dpp
EX = DLPOLY.X
EXE = $(BINROOT)/$(EX)
FC=undefined
PVM_EX=\'$(EX)\'
SHELL=/bin/sh
STRESS=STRESS
TYPE=3pt
# Define object files
#=====================================================================
159
c CCLRC
160
OBJ_ALL = angfrc.o bndfrc.o cfgscan.o corshl.o coul0.o coul4.o \
coul2.o coul3.o conscan.o dblstr.o dcell.o diffsn0.o \
diffsn1.o dlpoly.o duni.o error.o ewald1.o ewald3.o \
exclude.o exclude_atom.o fldscan.o exclude_link.o \
exitcomms.o extnfld.o fbpfrc.o fcap.o forces.o freeze.o gauss.o \
gdsum.o getrec.o gimax.o gisum.o gstate.o images.o initcomms.o \
intlist.o intstr.o invert.o invfrc.o jacobi.o lowcase.o lrcmetal.o \
lrcorrect.o machine.o merge.o merge1.o merge4.o multiple.o \
multiple_nsq.o npt_b1.o npt_b3.o parset.o npt_h1.o npt_h3.o nve_1.o \
nvt_b1.o nvt_e1.o nvt_h1.o parlst_nsq.o parlink.o parlst.o passcon.o \
passpmf.o pmf_1.o pmf_shake.o primlst.o quench.o rdf0.o rdf1.o \
rdshake_1.o result.o revive.o scdens.o shellsort.o shlfrc.o \
shlmerge.o shlqnch.o shmove.o simdef.o splice.o static.o strip.o \
strucopt.o sysdef.o sysgen.o systemp.o sysbook.o sysinit.o \
tethfrc.o thbfrc.o timchk.o traject.o vertest.o vscaleg.o \
warning.o xscale.o zden0.o zden1.o
OBJ_SPME = bspcoe.o bspgen.o cpy_rtc.o ele_prd.o ewald_spme.o \
scl_csum.o set_block.o spl_cexp.o spme_for.o
OBJ_NEU = coul0neu.o coul2neu.o coul3neu.o excludeneu.o forcesneu.o \
multipleneu.o neutlst.o parneulst.o prneulst.o \
parlinkneu.o rdf0neu.o
OBJ_RIG = nptq_b1.o nptq_b2.o nptq_b3.o nptq_b4.o nptq_h1.o nptq_h2.o \
nptq_h3.o nptq_h4.o nveq_1.o nveq_2.o nvtq_b1.o nvtq_b2.o \
nvtq_h1.o nvtq_h2.o passquat.o qshake.o quatbook.o quatqnch.o
OBJ_RRR = denloc.o dihfrc.o erfcgen.o ewald2.o ewald4.o forgen.o \
fortab.o metgen.o srfrce.o srfrceneu.o suttchen.o
OBJ_4PT = denloc_4pt.o dihfrc_4pt.o erfcgen.o ewald2_4pt.o ewald4_4pt.o \
forgen.o fortab.o metgen.o srfrce_4pt.o srfrceneu_4pt.o \
suttchen_4pt.o
OBJ_RSQ = denloc_rsq.o dihfrc_rsq.o erfcgen_rsq.o ewald2_rsq.o ewald4_rsq.o \
forgen_rsq.o fortab_rsq.o metgen_rsq.o srfrce_rsq.o srfrceneu_rsq.o\
suttchen_rsq.o
OBJ_EXT = crecv.o csend.o gsync.o mynode.o nodedim.o numnodes.o
TIMER = etime.o
# Define targets
c CCLRC
161
#=====================================================================
all:
@echo "Error - please specify a target machine!"
@echo "Permissible targets for this Makefile are:"
@echo "
"
@echo "alpha-linux"
@echo "alpha-linux-fftw"
@echo "beowulf-absoft"
@echo "cray-t3e"
@echo "cray-t3e-serial"
@echo "cray-t3e-totalview"
@echo "dec-alpha"
@echo "dec-alpha-ev6"
@echo "exemplar"
@echo "hitachi-sr2201"
@echo "hp"
@echo "hp-c240"
@echo "intel"
@echo "linux"
@echo "pentium-absoft"
@echo "pentium-portland"
@echo "rs6k"
@echo "rs6k-pwr3"
@echo "sg10k"
@echo "sg10k-fftw"
@echo "sg2-r5k"
@echo "sg2k"
@echo "sg2k-i6.5"
@echo "sg2k-shmem"
@echo "sg8k-mpi"
@echo "sg8k-mpi-f"
@echo "sp2-mpi"
@echo "sp2-mpi-debug"
@echo "sp2-mpi-fftw"
@echo "sun"
@echo "sun-ultra"
@echo "
"
@echo "Please examine Makefile for details"
# system specific targets follow :
#================== IBM SP2 version =======================================
sp2-mpi: dpp
c CCLRC
162
cp /usr/lpp/ppe.poe/include/mpif.h mpif.h
$(MAKE) FC=mpxlf FFLAGS="-c -NS2048 -qarch=pwr2 -qnosave" \
CPFLAGS="-D$(STRESS) -DMPI -DESSL -D'POINTER=integer'" intlist.o
$(MAKE) LD="mpxlf -o" LDFLAGS="-lesslp2" FC=mpxlf \
FFLAGS="-c -O3 -NS2048 -qarch=pwr2 -qnosave" \
CPFLAGS="-D$(STRESS) -DMPI -DESSL -D'POINTER=integer'" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#================== IBM SP2 debug version ==============================
sp2-mpi-debug: dpp
cp /usr/lpp/ppe.poe/include/mpif.h mpif.h
$(MAKE) LD="mpxlf -o" LDFLAGS="-lesslp2" FC=mpxlf \
FFLAGS="-g -c -C -NS2048 -qarch=pwr2 -qnosave" \
CPFLAGS="-D$(STRESS) -DMPI -DESSL -D'POINTER=integer'" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#================== IBM SP2 FFTW version ===============================
sp2-mpi-fftw: dpp
cp /usr/lpp/ppe.poe/include/mpif.h mpif.h
$(MAKE) FC=mpxlf FFLAGS="-c -NS2048 -qarch=pwr2 -qnosave" \
CPFLAGS="-D$(STRESS) -DMPI -D'POINTER=integer' -DFFTW
$(MAKE) LD="mpxlf -o" LDFLAGS="-lesslp2 -lfftw -lrfftw -L$(FFTW_LIBRARY)" \
FC=mpxlf FFLAGS="-c -O3 -NS2048 -qarch=pwr2 -qnosave" \
CPFLAGS="-D$(STRESS) -DMPI -D'POINTER=integer' -DFFTW -DESSL" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#===== Cray t3e (Manchester) ===========================================
cray-t3e: dpp
cp /opt/ctl/mpt/mpt/include/mpif.h mpif.h
$(MAKE) FC="f90" FFLAGS="-c -dp -lmpi" \
CPFLAGS="-Wp'-DCRAY -DCRAY_T3D -D'POINTER=integer' -DSHMEM -D$(STRESS) -P'" \
lowcase.o
$(MAKE) LD="f90 -o" FC="f90" FFLAGS="-c -dp -lmpi" LDFLAGS="-lmpi" \
CPFLAGS="-Wp'-DCRAY -DCRAY_T3D -D'POINTER=integer' \
-DSHMEM -D$(STRESS) -P'" TIMER="" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#===== Cray t3e (Manchester) with totalview flags ======================
cray-t3e-totalview: dpp
cp /opt/ctl/mpt/mpt/include/mpif.h mpif.h
$(MAKE) FC="f90" FFLAGS="-c -dp -lmpi -g -X8" \
CPFLAGS="-Wp'-DCRAY -DCRAY_T3D -D'POINTER=integer' -DSHMEM -D$(STRESS) -P'" \
lowcase.o
$(MAKE) LD="f90 -o" FC="f90" FFLAGS="-c -dp -lmpi -g -X8" \
LDFLAGS="-lmpi -g -X8" \
c CCLRC
163
CPFLAGS="-Wp'-DCRAY -DCRAY_T3D -D'POINTER=integer' \
-DSHMEM -D$(STRESS) -P'" TIMER="" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========== Cray t3e (serial) ===========================================
cray-t3e-serial: dpp
$(MAKE) LD="f90 -o" LDFLAGS="" FC=f90 \
FFLAGS="-c -dp -O3,aggress,unroll2,nojump" TIMER="" \
CPFLAGS="-D$(STRESS) -DSERIAL -P -D'POINTER=intger'" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========= Linux (no SPME) ==============================================
linux: dpp
$(MAKE) FC=f77 FFLAGS="-c" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer'" qshake.o
$(MAKE) LD="f77 -o" LDFLAGS="" FC=f77 FFLAGS="-c -g" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer'" \
OBJ_SPME="" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========== DEC Alpha (no SPME) =========================================
dec-alpha: dpp
$(MAKE) LD="f90 -o" FC=f90 FFLAGS="-c -fast" \
LDFLAGS="-math_library fast -assume noaccuracy_sensitive" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer*8'" \
TIMER="" OBJ_SPME="" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========== DEC Alpha ev6 (no SPME) =====================================
dec-alpha-ev6: dpp
$(MAKE) LD="f90 -o" FC=f90 FFLAGS="-c -arch ev6 -fast" \
LDFLAGS="-arch ev6 -math_library fast -assume noaccuracy_sensitive" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer*8'" \
TIMER="" OBJ_SPME="" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#======== Alpha Linux (no SPME) =========================================
alpha-linux: dpp
$(MAKE) FC=fort FFLAGS="-c -O -fast" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer*8'" qshake.o
$(MAKE) FC=fort LD="fort -o" FFLAGS="-c -O -fast" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer*8' \
LDFLAGS="" OBJ_SPME="" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#======== Alpha Linux (plus SPME via FFTW) ==============================
alpha-linux-fftw: dpp
$(MAKE) FC=fort FFLAGS="-c -O -fast" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer*8'" qshake.o
c CCLRC
164
$(MAKE) FC=fort LD="fort -o" FFLAGS="-c -O -fast" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer*8' -DFFTW" \
LDFLAGS="-lfftw -lrfftw -L$(FFTW_LIBRARY)" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#================== HP Workstation version (no SPME) ===================
hp: dpp
$(MAKE) FC=f77 FFLAGS="-c" CPFLAGS="-D$(STRESS) -DSERIAL
-D'POINTER=integer'" qshake.o
$(MAKE) LD="f77 -o" LDFLAGS="" FC=f77 FFLAGS="-c -O" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer'" \
OBJ_SPME="" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========= Convex/HP exemplar (serial) (no SPME) =======================
exemplar: dpp
$(MAKE) LD="f90 -o" LDFLAGS="" FC=f90 FFLAGS=" -c +ppu +O2 +DA2.0" \
CPFLAGS="-D$(STRESS) -DSERIAL" -D'POINTER-integer' \
OBJ_SPME="" TIMER="" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========= HP PA 9000 / C240 (serial) (no SPME) ========================
hp-c240: dpp
$(MAKE) LD="f90 -o" LDFLAGS= FC=f90 FFLAGS=" -c +ppu +O2 +DA2.0" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer'" \
OBJ_SPME="" TIMER="" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#============= IBM (AIX) Workstation version (no SPME) ===================
aix: dpp
$(MAKE) FC=mpxlf FFLAGS="-c -NS2048 -qarch=pwr2 -qnosave" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer'" intlist.o
$(MAKE) LD="xlf -o" LDFLAGS="" FC=xlf FFLAGS="-c -O3 -NS2048 -qarch=pwr2 -qnosave"\
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer'" \
OBJ_SPME="" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========= RS/6000 P2SC (serial) (no SPME) ===============================
rs6k: dpp
$(MAKE) LD="xlf -o" LDFLAGS= FC=xlf \
FFLAGS="-c -O -qarch=pwr2 -qtune=pwr2" TIMER="" OBJ_SPME=""\
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer'" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========= RS/6000 Power3 (serial) =======================================
rs6k-pwr3: dpp
$(MAKE) LD="xlf -o" LDFLAGS="-L/usr/local/lib -lmass -lessl" \
FC=xlf FFLAGS="-c -O -qnosave -qarch=pwr3" TIMER="" \
CPFLAGS="-D$(STRESS) -DSERIAL" -DESSL -D'POINTER=integer' \
c CCLRC
165
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========== PentiumII (absoft) (serial) (no SPME) ========================
pentium-absoft: dpp
$(MAKE) LD="/usr/bin/f90 -o" LDFLAGS="-lfio" TIMER="" OBJ_SPME="" \
FC=/usr/bin/f90 FFLAGS="-c -YEXT_NAMES=LCS -B108 -B100 -O" \
CPFLAGS="-D$(STRESS) -DSERIAL -P -D'POINTER=integer' " \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========== PentiumII (portland) (serial) (no SPME) ======================
pentium-portland: dpp
$(MAKE) LD="/usr/local/pgi/linux86/bin/pgf90 -o" LDFLAGS="" \
FC=/usr/local/pgi/linux86/bin/pgf90 FFLAGS="-c -O -Mdalign" \
CPFLAGS="-D$(STRESS) -DSERIAL -P -D'POINTER=integer'" \
TIMER="" OBJ_SPME="" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#======== Hitachi SR2201 Multiprocessor (no SPME) ========================
hitachi-sr2201: dpp
cp /usr/include/mpif.h mpif.h
$(MAKE) FC=xf90 \
FFLAGS="-c -W0,'form(fixed),opt(o(3)),langlvl(save(0))' -s,TRACE" \
CPFLAGS="-D$(STRESS) -DMPI -D'POINTER=integer'" intlist.o
$(MAKE) LDFLAGS="" LDLIBS="-lfmpi -lmpi" LD="xf90 -o" FC=xf90 \
FFLAGS="-c -W0, 'form(fixed),opt(o(3)),langlvl(save(0))' -s,TRACE" \
CC=xcc TIMER="" CPFLAGS="-D$(STRESS) -DMPI
-D'POINTER=integer'" OBJ_SPME="" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#======== Intel (no SPME) ================================================
intel: dpp
$(MAKE) FC=if77 LD="if77 -o" LDFLAGS="-node -glob -Knoieee" \
FFLAGS="-c -O2" CPFLAGS="-D$(STRESS) -DINTEL \
-D'POINTER=integer'" OBJ_SPME="" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#======== Silicon Graphics 10000 Worskstation ============================
sg10k: dpp
$(MAKE) LD="f90 -o" LDFLAGS="-lscs" \
FC=f90 FFLAGS="-c -O2 -OPT:Olimit=0 -lscs" TIMER="" \
CPFLAGS="-DCRAY -D$(STRESS) -DSERIAL -D'POINTER=integer'" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#======== Silicon Graphics 10000 Worskstation (SPME via FFTW) ============
sg10k-fftw: dpp
$(MAKE) LD="f90 -o" LDFLAGS="-lscs -lfftw -lrfftw -L$(FFTW_LIBRARY)" \
FC=f90 FFLAGS="-c -O2 -OPT:Olimit=0 -lscs" TIMER="" \
c CCLRC
CPFLAGS="-DCRAY -D$(STRESS) -DSERIAL -D'POINTER=integer' -DFFTW" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========= Silicon Graphics 8000 (parallel) ==========================
sg8k-mpi: dpp
cp /usr/include/mpif.h mpif.h
$(MAKE) LD="f90 -O3 -64 -o" FC=f90 LDFLAGS="-lmpi" TIMER="" \
FFLAGS="-c -O3 -64 " CPFLAGS="-D$(STRESS) -DMPI \
-DCRAY -D'POINTER=integer'" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========= Silicon Graphics 8000 (parallel) ==========================
sg8k-mpi-f: dpp
cp /usr/include/mpif.h mpif.h
$(MAKE) LD="f90 -Ofast -64 -o" FC=f90 LDFLAGS="-lmpi" TIMER=""\
FFLAGS="-c -Ofast -64" CPFLAGS="-D$(STRESS) -DMPI \
-DCRAY -D'POINTER=integer'" EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#======= Silicon Graphics Origin 2000 (parallel/SHMEM) ===============
sg2k-shmem: dpp
cp /usr/include/mpif.h mpif.h
$(MAKE) LD="f90 -o" FC=f90 \
FFLAGS="-c -64 -mips4 -Ofast=ip27 -IPA -OPT:Olimit=0 " \
LDFLAGS="-64 -mips4 -Ofast=ip27 -IPA -OPT:Olimit=0 -lsma -lmpi -lblas" \
OBJ_EXT="gsync.o mynode.o nodedim.o numnodes.o" TIMER="" \
CPFLAGS="-DMPI -D$(STRESS) -DSHMEM_O2K -DCRAY -D'POINTER=integer'" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========= Silicon Graphics Origin 2000 (serial) (no SPME) ===========
sg2k: dpp
$(MAKE) LD="f90 -o" LDFLAGS="-n32 -mips4" FC=f90 \
FFLAGS="-c -O3 -G 0 -mips4 -r10000 -c -r8 -n32" \
TIMER="" OBJ_SPME="" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer'" \
CFLAGS="-c -O3 -n32 -mips4 -r10000" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#=== Silicon Graphics Origin 2000 (serial, Irix 6.5) (no SPME) =======
sg2k-i6.5: dpp
$(MAKE) LD="f90 -o" LDFLAGS="-n32 -mips4 -IPA" \
FC=f90 FFLAGS="-c -n32 -mips4 -Ofast=ip27 -LNO:fusion=2" \
TIMER="" OBJ_SPME="" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer'" \
CFLAGS="-c -O3 -n32 -mips4 -r10000" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
166
c CCLRC
167
#=== Silicon Graphics O2 R5k (serial) (no SPME) ======================
sg2-r5k: dpp
$(MAKE) LD="f90 -o" LDFLAGS="-n32 -mips4" \
FC=f90 FFLAGS="-c -O3 -G 0 -mips4 -r5000 -c -r8 -n32" \
TIMER="" OBJ_SPME="" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer'" \
CFLAGS="-c -O3 -n32 -mips4 -r5000" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========= SUN Workstation version (no SPME) =========================
sun: dpp
$(MAKE) LD="f77 -o" LDFLAGS="" FC=f77 FFLAGS="-c -O2" \
TIMER="" OBJ_SPME="" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer'" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#======== Sun Ultra-2 (serial) (no SPME) =============================
sun-ultra: dpp
$(MAKE) LD="/opt/SUNWspro/bin/f90 -o" LDFLAGS= \
FC=/opt/SUNWspro/bin/f90 \
FFLAGS="-c -fnonstd -xarch=v8plusa -xchip=ultra -O2 -libmil -dalign" \
TIMER="" OBJ_SPME="" \
CPFLAGS="-D$(STRESS) -DSERIAL -D'POINTER=integer'" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#========= Daresbury Beowulf (Absoft compiler) (no SPME)==============
beowulf-absoft: dpp
cp /usr/local/lam-6.2/h/mpif.h mpif.h
$(MAKE) LD="/usr/bin/f90 -o" \
LDFLAGS="-L/home/kcm/mpich-absoft/mpich/lib/LINUX/ch_p4/ -lmpich" \
FC=/usr/bin/f90 FFLAGS="-c -O -B100" TIMER="" OBJ_SPME="" \
CPFLAGS="-D$(STRESS) -DMPI -P -D'POINTER=integer' \
-I/home/kcm/mpich-absoft/mpich/include" \
EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
#=====================================================================
# Interpolation tables options
# Default code. Force tables interpolation in r-space 3pt interpolation
3pt: check $(OBJ_ALL) $(OBJ_RRR) $(OBJ_NEU) $(OBJ_RIG) $(OBJ_EXT) $(TIMER) $(OBJ_SPME)
$(LD) $(EXE) $(OBJ_ALL) $(OBJ_RRR) $(OBJ_NEU) $(OBJ_RIG) $(OBJ_EXT) $(TIMER) \
$(LDFLAGS) $(LDLIBS) $(OBJ_SPME)
c CCLRC
168
# Force tables interpolation in r-space, 4pt interpolation
4pt: check $(OBJ_ALL) $(OBJ_4PT) $(OBJ_NEU) $(OBJ_RIG) $(OBJ_EXT) $(TIMER) $(OBJ_SPME)
$(LD) $(EXE) $(OBJ_ALL) $(OBJ_4PT) $(OBJ_NEU) $(OBJ_RIG) $(OBJ_EXT) $(TIMER) \
$(LDFLAGS) $(LDLIBS) $(OBJ_SPME)
# Force tables interpolation in r-squared
rsq: check $(OBJ_ALL) $(OBJ_RSQ) $(OBJ_NEU) $(OBJ_RIG) $(OBJ_EXT) $(TIMER) $(OBJ_SPME)
$(LD) $(EXE) $(OBJ_ALL) $(OBJ_RSQ) $(OBJ_NEU) $(OBJ_RIG) $(OBJ_EXT) $(TIMER) \
$(LDFLAGS) $(LDLIBS) $(OBJ_SPME)
#=====================================================================
# Check that a machine has been specified
check:
@if test $(FC) = "undefined";\
then echo "You must specify a target machine!"; \
exit 99;\
fi
#=====================================================================
# Clean up the source directory
clean:
rm -f $(OBJ_ALL) $(OBJ_RRR) $(OBJ_EXT) $(OBJ_NEU) \
$(OBJ_RIG) $(TIMER) $(OBJ_SPME) $(OBJ_4PT) $(OBJ_RSQ) \
*.tmp.f mpif.h
#=====================================================================
# Compile preprocessor code
dpp: dpp.c
$(CC) dpp.c -o dpp
#=====================================================================
# Declare dependencies : c preprocess all .f files
.f.o:
$(DPP) $(CPFLAGS) $*.f > $*.tmp.f
$(FC) $(FFLAGS) $*.tmp.f
mv $*.tmp.o $*.o
.c.o:
$(CC) -c $*.c
#=====================================================================
# Declare dependency on parameters file
$(OBJ_ALL): dl_params.inc
c CCLRC
$(OBJ_RRR): dl_params.inc
$(OBJ_4PT): dl_params.inc
$(OBJ_RSQ): dl_params.inc
$(OBJ_NEU): dl_params.inc
$(OBJ_RIG): dl_params.inc
$(OBJ_EXT): dl_params.inc
$(OBJ_SPME): dl_params.inc
169
Appendix B
Periodic Boundary Conditions in
DL POLY
Introduction
DL POLY 2 is designed to accommodate a number of dierent periodic boundary conditions, which are dened by the shape and size of the simulation cell. Briey, these are
as follows (which also indicates the IMCON ag dening the simulation cell type in the
CONFIG File - see 4.1.2):
1. None e.g. isolated polymer in space. (IMCON=0).
2. Cubic periodic boundaries.(IMCON=1).
3. Orthorhombic periodic boundaries.(IMCON=2).
4. Parallelepiped periodic boundaries.(IMCON=3).
5. Truncated octahedral periodic boundaries. (IMCON=4).
6. Rhombic dodecahedral periodic boundaries. (IMCON=5).
7. Slab (X,Y periodic, Z nonperiodic). (IMCON=6).
8. Hexagonal prism periodic boundaries. (IMCON=7).
We shall now look at each of these in more detail. Note that in all cases the cell vectors
and the positions of the atoms in the cell are to be specied in Angstroms (A).
No periodic boundary (IMCON=0)
Simulations requiring no periodic boundaries are best suited to in vacuuo simulations, such
as the conformational study of an isolated polymer molecule. This boundary condition is
not recommended for studies in a solvent, since evaporation is likely to be a problem.
Note this boundary condition cannot be used with the Ewald summation method.
170
c CCLRC
171
Cubic periodic boundaries (IMCON=1)
The cubic MD cell.
The cubic MD cell is perhaps the most commonly used in simulation and has the
advantage of great simplicity. In DL POLY 2 the cell is dened with the principle axes
passing through the centres of the faces. Thus for a cube with sidelength D, the cell vectors
appearing in the CONFIG le should be: (D,0,0); (0,D,0); (0,0,D). Note the origin of the
atomic coordinates is the centre of the cell.
The cubic boundary condition can be used with the Ewald summation method.
Orthorhombic periodic boundaries (IMCON=2)
The orthorhombic cell is also a common periodic boundary, which closely resembles the
cubic cell in use. In DL POLY 2 the cell is dened with principle axes passing through the
centres of the faces. For an orthorhombic cell with sidelengths D (in X-direction), E (in
Y-direction) and F (in Z-direction), the cell vectors appearing in the CONFIG le should
be: (D,0,0); (0,E,0); (0,0,F). Note the origin of the atomic coordinates is the centre of the
cell.
The orthorhombic boundary condition can be used with the Ewald summation method.
c CCLRC
172
The orthorhomic MD cell.
Parallelepiped periodic boundaries (IMCON=3)
The parallelepiped MD cell.
The parallelepiped (e.g. monoclinic or triclinic) cell is generally used in simulations of
crystalline materials, where its shape and dimension is commensurate with the unit cell of
the crystal. Thus for a unit cell specied by three principal vectors a, b, c, the MD cell
is dened in the DL POLY 2 CONFIG le by the vectors (La ,La ,La ), (Mb ,Mb ,Mb ),
(Nc ,Mc ,Nc ), in which L,M,N are integers, reecting the multiplication of the unit cell
in each principal direction. Note that the atomic coordinate origin is the centre of the MD
cell.
The parallelepiped boundary condition can be used with the Ewald summation method.
1
1
2
3
Truncated octahedral boundaries (IMCON=4)
2
3
1
2
3
c CCLRC
173
The truncated octahedral MD cell.
This is one of the more unusual MD cells available in DL POLY, but it has the advantage
of being more nearly spherical than most other MD cells. This means it can accommodate
a larger spherical cuto for a given number of atoms, which leads to greater eÆciency. This
can be very useful when simulating (for example) a large molecule in solution, where fewer
solvent molecules are required for a given simulation cell width.
The principal axes of the truncated octahedron (see gure) pass through the centres
of the square faces, and the width of the cell, measured from square face to square face
along a principal axis denes the width D of the cell. From this, the cell vectors required
in the DL POLY 2 CONFIG le are simply: (D,0,0), (0,D,0), (0,0,D). These are also the
cell vectors dening the enscribing cube, which posseses twice the volume of the truncated
octahedral cell. Once again, the atomic positions are dened with respect to the cell centre.
The truncated octahedron can be used with the Ewald summation method.
Rhombic dodecahedral boundaries (IMCON=5)
This is another unusual MD cell (see gure), but which possesses similar advantages to the
truncated octahedron, but with a slightly greater eÆciency in its use of the cell volume (the
ratio is about 74% to 68%).
The principal axis in the X-direction of the rhombic dodecahedron passes through the
centre of the cell and the centre of a rhombic face. The Y-axis does likewise, but is set at 90
degrees to the X-axis. The Z-axis completes the orthonormal set and passes through a vertex
where four faces meet. If the width D of the cell is dened as the perpendicular distance
between two opposite faces, the cell vectors required for the DL POLY 2 CONFIG le are:
(D,0,0), (0,D,0), (0,0,p2D).These also dene the enscribing orthorhombic cell, which has
twice the MD cell volume. In DL POLY 2 the centre of the cell is also the origin of the
atomic coordinates.
The rhombic dodecahedron can be used with the Ewald summation method.
c CCLRC
174
The rhombic dodecahedral MD cell.
Slab boundary conditions (IMCON=6)
Slab boundaries are periodic in the X- and Y-directions, but not in the Z-direction. They
are particularly useful for simulating surfaces. The periodic cell in the XY plane can be any
parallelogram. The origin of the X,Y atomic coordinates lies on an axis perpendicular to
the centre of the parallelogram. The origin of the Z coordinate is where the user species
it, but at or near the surface is recommended.
If the XY parallelogram is dened by vectors A and B, the vectors required in the
CONFIG le are: (A ,A ,0), (B ,B ,0), (0,0,D), where D is any real number (including
zero). If D is nonzero, it will be used by DL POLY to help determine a `working volume'
for the system. This is needed to help calculate RDFs etc. (The working value of D is in
fact taken as one of: 3cuto; or 2max abs(Z coordinate)+cuto; or the user specied
D, whichever is the larger.)
Note that the Ewald sum cannot be used with this boundary condition.The surface in a
system with charges can be modelled with DL POLY 2 however, if periodicity is allowed in
the Z-direction. In this case `slabs' of ions well-separated by vacuum zones in the Z-direction
can be handled with IMCON=2 or 3.
1
2
1
2
Hexagonal prism boundaries (IMCON=7)
In this case the Z-axis lies along a line joining the centres of the hexagonal faces. The Yaxis is perpendicular to this and passes through the centre of one of the faces. The X-axis
completes the orthonormal set and passes through the centre of an edge that is parallel to
the Z-axis. (Note: It is important to get this convention right!) The origin of the atomic
coordinates is the centre of the cell. If the length of one pof the hexagon edges is D, the
cell vectors required in the CONFIG le are: (3D,0,0), (0, 3D,0), (0,0,H), where H is the
prism height (the distance between hexagonal faces). The orthorhombic cell also dened by
these vectors enscribes the hexagonal prism and possesses twice the volume, but the height
and the centre are the same.
The Ewald summation method may be used with this periodic boundary condition.
c CCLRC
175
The hexagonal MD cell.
This MD cell is particularly suitable for simulating strands or bres (i.e. systems with
a pronounced anisotropy in the Z-direction), such as DNA strands in solution, or stretched
polymer chains.
Appendix C
DL POLY Error Messages and
User Action
Introduction
In this appendix we document the error messages encoded in DL POLY 2 and the recommended user action. The user response to these messages is dierent according to
which version of the code is being run. Versions preceding DL POLY 2 version 2.11 are
signicantly dierent from those appearing after. This is primariliy because version 2.11
intriduced FORTRAN 90 dynamic array allocation, which greatly simplies the use of the
code, but requires a dierent form of user intervention when array boundaries are violated. The correct response is described as the standard user response in the approriate
sections below, to which the user should refer before acting on the error encountered.
The reader should also be aware that some of the error messages listed below may
be either disabled in, or absent from, the installed version of DL POLY 2 . Disabled
messages generally apply to older releases of the code, while missing messages apply to
newer versions of the code and will not usually apply to previous releases. They are all
included for completeness. Note that the wording of some of the messages may also have
changed over time, usually to provide more specic information. The most recent wording
appears below.
DL POLY 2 Versions 2.10 and Earlier
Many of the DL POLY 2 error messages refer to array bound checks and the user is advised
to consider what other arrays may need to be altered when making the appropriate change.
(If you are not familiar with DL POLY 2 , the error messages will advise you as each array
bound is violated, but you will not be told of all errors in one pass.) Users are warned that
reckless increases in the array dimensions are likely to result in the code being too large for
any given memory. A way to avoid many of these diÆculties is to make use of the utility
program parset (see 6.1.1), which can greatly reduce the work required.
The standard user response when an array dimension error occurs is to locate the
relevant parameter in the DL POLY 2 dl params.inc le and increase the default number.
176
c CCLRC
177
It should be remembered that any change in a parameter specied in dl params.inc
requires the whole program to be recompiled. However the standard makele provided in
the build directory does this automatically.
DL POLY 2 Versions 2.11 and Later
Version 2.11 of DL POLY 2 diers from previous versions in that it incorporates the functionality of the utility code parset within the code itself and uses FORTRAN 90 dynamic
array allocation to set the array sizes at run time. This is a considerable advance on previous practice and means that a single executable may be compiled to over all the likely uses
of the code. It is not foolproof however. Sometimes an estimate of the required array sizes
is diÆcult to obtain and the calculated value may be too small. For this reason DL POLY 2
retains all the old array dimension checks and will terminate as before when an array bound
error occurs.
When a dimension error occurs, the standard user response is to edit the DL POLY 2
subroutine parset.f. Locate where the variable dening the array dimension is xed and
increase accordingly. To do this you should make use of the dimension information that
DL POLY 2 prints in the OUTPUT le prior to termination. If no information is supplied,
simply doubling the size of the variable will usually do the trick. If the variable concerned
is dened in one of the support subroutines cfgscan.f, fldscan.f, conscan.f you will
need to insert a new line in parset.f to redene it - after the relevant subroutine has been
called! Finally the code must be recompiled, but in this case it will be necessary only to
recompile parset.f and not the whole code.
The DL POLY 2 Error Messages
Message 1: error - PVM NODES unset
The code was C-preprocessed with the ag -DPVM set but the number of PVM nodes was
not stated.
Action:
Delete the module initcomms.o from the source directory and re-make the executable,this
time including the directive PVM NODES=n (where n is the number of nodes you require)
with the make command.
Message 2: error - machine not a hypercube
The number of nodes on the parallel machine is not a power of 2.
Action:
Specify an appropriate number of processors for job execution. If you are using PVM see
Action: for error message 1.
c CCLRC
178
Message 3: error - unknown directive found in CONTROL le
This error most likely arises when a directive is misspelt.
Action:
Locate incorrect directive in CONTROL le and replace.
Message 4: error - unknown directive found in FIELD le
This error most likely arises when a directive is misspelt or is encountered in an incorrect location in the FIELD le, which can happen if too few or too many data records are included.
Action:
Locate the erroneous directive in the FIELD le and correct error.
Message 5: error - unknown energy unit requested
The DL POLY 2 FIELD le permits a choice of units for input of energy parameters. These
may be: electron volts (ev); kilocalories (kcal); kilojoules (kj); or the DL POLY 2 internal
units (10 J mol ) (internal). There is no default value. Failure to specify any of these
correctly, or reference to other energy units, will result in this error message. See documentation of the FIELD le.
1
Action:
Correct energy keyword on units directive in FIELD le and resubmit.
Message 6: error - energy unit not specied
A units directive is mandatory in the FIELD le. This error indicates that DL POLY 2
has failed to nd the required record.
Action:
Add units directive to FIELD le and resubmit.
Message 7: error - energy unit respecied
DL POLY 2 expects only one units directive in
the FIELD le. This error results if it
encounters another - implying an ambiguity in units.
Action:
Locate extra units directive in FIELD le and remove.
Message 8: error - time step not specied
DL POLY 2 requires a timestep directive in the CONTROL le.
is encountered.
This error results if none
c CCLRC
179
Action:
Inserttimestep directive in CONTROL le with an appropriate numerical value.
Message 10: error - too many molecule types specied
DL POLY 2 has a set limit on the number of kinds of molecules it will handle in any simulation (this is not the same as the number of molecules). If this permitted maximum is
exceeded, the program terminates. The error arises when the molecules directive in the
FIELD le specifes too large a number.
Action:
Standard user response. Fix parameter mxtmls.
Message 11: error - duplicate molecule directive in FIELD le
The number of dierent types of molecules in a simulation should only be specied once.
If DL POLY 2 encounters more than one molecules directive, it will terminate execution.
Action:
Locate the extra molecule directive in the FIELD le and remove.
Message 12: error - unknown molecule directive in FIELD le
Once DL POLY 2 encounters the molecules directive in the FIELD le,
it assumes the
following records will supply data describing the intramolecular force eld. It does not then
expect to encounter directives not related to these data. This error message results if it
encounters a unrelated directive. The most probable cause is incomplete specication of
the data (e.g. when the nish directive has been omitted.)
Action:
Check the molecular data entries in the FIELD le and correct.
Message 13: error - molecule species not specied
This error arises when DL POLY 2 encounters non-bonded force data in the FIELD le,
the molecular species have been specied. Under these circumstances it cannot assign the data correctly, and therefore terminates.
before
Action:
Make sure the molecular data appears before the non-bonded forces data in the FIELD le
and resubmit.
c CCLRC
180
Message 14: error - too many unique atom types specied
This error arises when DL POLY 2 scans the FIELD le and discovers that there are too
many dierent types of atoms in the system (i.e. the number of unique atom types exceeds
the mxsvdw parameter.
Action:
Standard user response. Fix parameter mxsvdw.
Message 15: error - duplicate pair potential specied
In processing the FIELD le, DL POLY 2 keeps a record of the specied short range pair
potentials as they are read in. If it detects that a given pair potential has been specied
before, no attempt at a resolution of the ambiguity is made and this error message results.
See specication of FIELD le.
Action:
Locate the duplication in the FIELD le and rectify.
Message 16: error - strange exit from FIELD le processing
This should never happen! However one remote possibility is that there are more than
10,000 directives in the FIELD le! It simply means that DL POLY 2 has ceased processing the FIELD data, but has not reached the end of the le or encountered a close
directive. Probable cause: corruption of the DL POLY 2 executable or of the FIELD le.
We would be interested to hear of other reasons!
Action:
Recompile the program or recreate the FIELD le. If neither of these works, send the
problem to us.
Message 17: error - strange exit from CONTROL le processing
See notes on message 16 above.
Message 18: error - duplicate 3-body potential specied
DL POLY 2 has encountered a repeat specication of a 3-body potential in the FIELD le.
Action:
Locate the duplicate entry, remove and resubmit job.
Message 19: error - duplicate 4-body potential specied
A 4-body potential has been duplicated in the FIELD le.
c CCLRC
181
Action:
Locate the duplicated 4-body potential and remove. Resubmit job.
Message 20: error - too many molecule sites specied
DL POLY 2 has a xed limit on the number of unique molecular sites in any given simulation. If this limit is exceeded, the program terminates.
Action:
Standard user response. Fix parameter mxsite.
Message 22: error - unsuitable radial increment in TABLE le
This arises when the tabulated potentials presented in the TABLE le have an increment
that is greater than that used to dene the other potentials in the simulation. Ideally the
increment should be rcut=(mxgrid 4), where rcut is the potential cuto for the short range
potentials and mxgrid is the parameter dening the length of the interpolation arrays. An
increment less than this is permissible however.
Action:
The tables must be recalculated with an appropriate increment.
Message 23: error - incompatible FIELD and TABLE le potentials
This error arises when the specication of the short range potentials is dierent in the
FIELD and TABLE les. This usually means that the order of specication of the potentials is dierent. When DL POLY 2 nds a change in the order of specication, it assumes
that the user has forgotten to enter one.
Action:
Check the FIELD and TABLE les. Make sure that you correctly specify the pair potentials
in the FIELD le, indicating which ones are to be presented in the TABLE le. Then check
the TABLE le to make sure all the tabulated potentials are present in the order the FIELD
le indicates.
Message 24: error - end of le encountered in TABLE le
This means the TABLE le is incomplete in some way: either by having too few potentials
included, or the number of data points is incorrect.
Action:
Examine the TABLE le contents and regenerate it if it appears to be incomplete. If it look
intact, check that the number of data points specied is what DL POLY 2 is expecting.
c CCLRC
182
Message 25: error - wrong atom type found in CONFIG le
On reading the input le CONFIG, DL POLY 2 performs a check to ensure that the atoms
specied in the conguration provided are compatible with the corresponding FIELD le.
This message results if they are not.
Action:
The possibility exists that one or both of the CONFIG or FIELD les has incorrectly
specied the atoms in the system. The user must locate the ambiguity, using the data
printed in the OUTPUT le as a guide, and make the appropriate alteration.
Message 30: error - too many chemical bonds specied
DL POLY 2 sets a limit on the number of chemical bond potentials that can be specied
in the FIELD le. Termination results if this number is exceeded. See FIELD le documentation. Do not confuse this error with that described by message 31 (below).
Action:
Standard user response. Fix parameter mxtbnd.
Message 31: error - too many chemical bonds in system
DL POLY 2 sets a limit on the number of chemical bond potentials in the simulated system
as a whole. (This number is a combination of the number of molecules and the number
of bonds per molecule, divided by the number of processing nodes.) Termination results
if this number is exceeded. Do not confuse this error with that described by message 30
(above).
Action:
Standard user response. Fix the parameter mxbond.
Message 32: error - integer array memory allocation failure
DL POLY 2 has failed to allocate suÆcient memory to accommodate one or more of the
integer arrays in the code.
Action:
This may simply mean that your simulation is too large for the machine you are running
on. Consider this before wasting time trying a x. Try using more processing nodes if they
are available. If this is not an option investigate the possibility of increasing the heap size
for your application. Talk to your systems support people for advice on how to do this.
Message 33: error - real array memory allocation failure
DL POLY 2 has failed to allocate suÆcient memory to accommodate one or more of the
real arrays in the code.
c CCLRC
183
Action:
This may simply mean that your simulation is too large for the machine you are running
on. Consider this before wasting time trying a x. Try using more processing nodes if they
are available. If this is not an option investigate the possibility of increasing the heap size
for your application. Talk to your systems support people for advice on how to do this.
Message 34: error - character array memory allocation failure
DL POLY 2 has failed to allocate suÆcient memory to accommodate one or more of the
character arrays in the code.
Action:
This may simply mean that your simulation is too large for the machine you are running
on. Consider this before wasting time trying a x. Try using more processing nodes if they
are available. If this is not an option investigate the possibility of increasing the heap size
for your application. Talk to your systems support people for advice on how to do this.
Message 35: error - logical array memory allocation failure
DL POLY 2 has failed to allocate suÆcient memory to accommodate one or more of the
logical arrays in the code.
Action:
This may simply mean that your simulation is too large for the machine you are running
on. Consider this before wasting time trying a x. Try using more processing nodes if they
are available. If this is not an option investigate the possibility of increasing the heap size
for your application. Talk to your systems support people for advice on how to do this.
Message 40: error - too many bond constraints specied
DL POLY 2 sets a limit on the number of bond constraints that can be specied in the
FIELD le. Termination results if this number is exceeded. See FIELD le documentation.
Do not confuse this error with that described by message 41 (below).
Action:
Standard user response. Fix the parameter mxtcon.
Message 41: error - too many bond constraints in system
DL POLY 2 sets a limit on the number of bond constraints in the simulated system as a
whole. (This number is a combination of the number of molecules and the number of per
molecule, divided by the number of processing nodes.) Termination results if this number
is exceeded. Do not confuse this error with that described by message 40 (above).
c CCLRC
184
Action:
Standard user response. Fix the parameter mxcons.
Message 42: error - transfer buer too small in merge1
The buer used to transfer data between nodes in the merge1 subroutines has been dimensioned too small.
Action:
Standard user response. Fix the parameter mxbuff.
Message 45: error - too many atoms in CONFIG le
DL POLY 2 limits the number of atoms in the system to be simulated and checks for the
violation of this condition when it reads the CONFIG le. Termination will result if the
condition is violated.
Action:
Standard user response. Fix the parameter mxatms. Consider the possibility that the wrong
CONFIG le is being used (e.g similar system, but larger size.)
Message 46: ewlbuf array too small in ewald1
The ewlbuf array used to store structure factor data in subroutine ewald1 has been dimensioned too small.
Action:
Standard user response. Fix the parameter mxebuf.
Message 47: error - transfer buer too small in merge
The buer used to transfer data between nodes in the merge subroutines has been dimensioned too small.
Action:
Standard user response. Fix the parameter mxbuff.
Message 48: error - transfer buer too small in fortab
The buer used to transfer data between nodes in the fortab subroutines has been dimensioned too small.
Action:
Standard user response. Fix the parameter mxbuff.
c CCLRC
185
Message 49: error - frozen core-shell unit specied
The DL POLY 2 option to freeze the location of an atom (i.e. hold it permanently in one
position) is not permitted for core-shell units. This includes freezing the core or the shell
independently.
Action:
Remove the frozen atom option from the FIELD le. Consider using a non-polarisable
atom instead.
Message 50: error - too many bond angles specied
DL POLY 2 limits the number of valence angle potentials that can be specied in the
FIELD le and checks for the violation of this. Termination will result if the condition is
violated. Do not confuse this error with that described by message 51 (below).
Action:
Standard user response. Fix the parameter mxtang.
Message 51: error - too many bond angles in system
DL POLY 2 limits the number of valence angle potentials in the system to be simulated
(actually, the number to be processed by each node) and checks for the violation of this.
Termination will result if the condition is violated. Do not confuse this error with that
described by message 50 (above).
Action:
Standard user response. Fix the parameter mxangl. Consider the possibility that the wrong
CONFIG le is being used (e.g similar system, but larger size.)
Message 52: error - end of FIELD le encountered
This message results when DL POLY 2 reaches the end of the FIELD le, without having
read all the data it expects. Probable causes: missing data or incorrect specication of
integers on the various directives.
Action:
Check FIELD le for missing or incorrect data and correct.
Message 53: error - end of CONTROL le encountered
This message results when DL POLY 2 reaches the end of the CONTROL le, without
having read all the data it expects. Probable cause: missing nish directive.
Action:
Check CONTROL le and correct.
c CCLRC
186
Message 55: error - end of CONFIG le encountered
This error arises when DL POLY 2 attempts to read more data from the CONFIG le than
is actually present. The probable cause is an incorrect or absent CONFIG le, but it may
be due to the FIELD le being incompatible in some way with the CONFIG le.
Action:
Check contents of CONFIG le. If you are convinced it is correct, check the FIELD le for
inconsistencies.
Message 57: error - too many core-shell units specied
DL POLY 2 has a restriction of the number of types of core-shell unit in the FIELD le
and will terminate if too many are present. Do not confuse this error with that described
by message 59 (below).
Action:
Standard user response. Fix the parameter mxtshl.
Message 59: error - too many core-shell units in system
DL POLY 2 limits the number of core-shell units in the simulated system. Termination
results if too many are encountered. Do not confuse this error with that described by message 57 (above).
Action:
Standard user response. Fix the parameter mxshl.
Message 60: error - too many dihedral angles specied
DL POLY 2 will accept only a limited number of dihedral angles in the FIELD le and
will terminate if too many are present. Do not confuse this error with that described by
message 61 (below).
Action:
Standard user response. Fix the parameter mxtdih.
Message 61: error - too many dihedral angles in system
The number of dihedral angles in the whole simulated system is limited by DL POLY 2
. Termination results if too many are encountered. Do not confuse this error with that
described by message 60 (above).
Action:
Standard user response. Fix the parameter mxdihd.
c CCLRC
187
Message 62: error - too many tethered atoms specied
DL POLY 2 will accept only a limited number of tethered atoms in the FIELD le and
will terminate if too many are present. Do not confuse this error with that described by
message 63 (below).
Action:
Standard user response. Fix the parameter mxteth.
Message 63: error - too many tethered atoms in system
The number of tethered atoms in the simulated system is limited by DL POLY 2 . Termination results if too many are encountered. Do not confuse this error with that described
by message 62 (above).
Action:
Standard user response. Fix the parameter msteth.
Message 65: error - too many excluded pairs specied
This error can arise when DL POLY 2 is identifying the atom pairs that cannot have a pair
potential between them, by virtue of being chemically bonded for example (see subroutine
exclude). Some of the working arrays used in this operation may be exceeded, resulting
in termination of the program.
Action:
Standard user response. Fix the parameter mxexcl.
Message 67: error - incorrect boundary condition in thbfrc
Three body forces in DL POLY 2 are only permissible with cubic , orthorhombic and parallelepiped periodic boundaries. Use of other boundary conditions results in this error.
Action:
If nonperiodic boundaries are required, the only option is to use a very large simulation cell,
with the required system at the centre surrounded by a vacuum. This is not very eÆcient
however and use of a realistic periodic system is the best option.
Message 69: error - too many link cells required in thbfrc
The calculation of three body forces in DL POLY 2 is handled by the link cell algorithm.
This error arises if the required number of link cells exceeds the permitted array dimension
in the code.
Action:
Standard user response. Fix the parameter mxcell.
c CCLRC
188
Message 70: error - constraint bond quench failure
When a simulation with bond constraints is started, DL POLY 2 attempts to extract the
kinetic energy of the constrained atom-atom bonds arising from the assignment of initial
random velocities. If this procedure fails, the program will terminate. The likely cause is a
badly generated initial conguration.
Action:
Some help may be gained from increasing the cycle limit, by following the standard user
response to increase the control parameter mxshak. You may also consider reducing the
tolerance of the SHAKE iteration, the directive shake in the CONTROL le. However it
is probably better to take a good look at the starting conditions!
Message 71: error - too many metal potentials specied
The number of metal potentials that can be speced in the FIELD le is limited. This
error results if too many are used.
Action:
Standard user response. Fix the parameter mxvdw. Note that this parameter must be double
the number of required metal potentials. Recompile the program.
Message 73: error - too many inversion potentials specied
The number of inversion potentials specied in the FIELD le exceeds the permitted maximum.
Action:
Standard user response. Fix the parameter mxtinv.
Message 75: error - too many atoms in specied system
DL POLY 2 places a limit on the number of atoms that can be simulated. Termination
results if too many are specied.
Action:
Standard user response. Fix the parameter mxatms.
Message 77: error - too many inversion potentials in system
The simulation contains too many inversion potentials overall, causing termination of run.
Action:
Standard user response. Fix the parameter mxinv.
c CCLRC
189
Message 79: error - incorrect boundary condition in fbpfrc
The 4-body force routine assumes a cubic or parallelepiped periodic boundary condition is
in operation. The job will terminate if this is not adhered to.
Action:
You must recongure your simulation to an appropriate boundary condition.
Message 80: error - too many pair potentials specied
DL POLY 2 places a limit on the number of pair potentials that can be specied in the
FIELD le. Exceeding this number results in termination of the program execution.
Action:
Standard user response. Fix the parameters mxsvdw. and mxvdw.
Message 81: error - unidentied atom in pair potential list
DL POLY 2 checks all the pair potentials specied in the FIELD le and terminates the
program if it can't identify any one of them from the atom types specied earlier in the le.
Action:
Correct the erroneous entry in the FIELD le and resubmit.
Message 82: error - calculated pair potential index too large
In checking the pair potentials specied in the FIELD le DL POLY 2 calculates a unique
integer index that henceforth identies the potential within the program. If this index
becomes too large, termination of the program results.
Action:
Standard user response. Fix the parameters mxsvdw and mxvdw.
Message 83: error - too many three body potentials specied
DL POLY 2 has a limit on the number of three body potentials that can be dened in the
FIELD le. This error results if too many are included.
Action:
Standard user response. Fix the parameter mxtbp.
Message 84: error - unidentied atom in 3-body potential list
DL POLY 2 checks all the 3-body potentials specied in the FIELD le and terminates the
program if it can't identify any one of them from the atom types specied earlier in the le.
c CCLRC
190
Action:
Correct the erroneous entry in the FIELD le and resubmit.
Message 85: error - required velocities not in CONFIG le
If the user attempts to start up a DL POLY 2 simulation with the restart or restart scale
directives (see description of CONTROL le,) the program will expect the CONFIG le
to contain atomic velocities as well as positions. Termination results if these are not present.
Action:
Either replace the CONFIG le with one containing the velocities, or if not available, remove
the restart directive altogether and let DL POLY 2 create the velocities for itself.
Message 86: error - calculated 3-body potential index too large
DL POLY 2 has a permitted maximum for the calculated index for any three body potential in the system (i.e. as dened in the FIELD le). If there are m distinct types of atom
in the system, the index can possibly range from 1 to (m (m 1))=2. If the internally
calculated index exceeds this number, this error report results.
2
Action:
Standard user response. Fix the parameter mxtbp.
Message 87: error - too many link cells required in fbpfrc
The fbpfrc subroutine uses link cells to compute the four body forces. This message indicates that the link cell arrays have insuÆcient size to work properly.
Action:
Standard user response. Fix the parameter mxcell.
Message 89: error - too many four body potentials specied
Too many four body potential have been dened in the FIELD le. Certain arrays must
be increased in size to accommodate the data.
Action:
Standard user response. Fix the parameter mxfbp.
Message 90: error - system total electric charge nonzero
In DL POLY 2 a check on the total system charge will result in an error if the net charge of
the system is nonzero. (Note: In DL POLY 2 this message has been disabled. The program
merely prints a warning stating that the system is not electrically neutral but it does not
c CCLRC
191
terminate the program - watch out for this.)
Action:
Check the specied atomic charges and their populations. Make sure they add up to zero.
If the system is required to have a net zero charge, you can enable the call to this error
message in subroutine sysdef.
Message 91: error - unidentied atom in 4-body potential list
The specication of a four-body potential in the FIELD le has referenced an atom type
that is unknown.
Action:
Locate the errant atom type in the four body potential denition in the FIELD le and
correct. Make sure this atom type is specied by an atoms directive earlier in the le.
Message 93: error - cannot use shell model with rigid molecules
The dynamical shell model implemented in DL POLY 2 is not designed to work with rigid
molecules. This error results if these two options are simultaneously selected.
Action:
In some circumstances you may consider overriding this error message and continuing with
your simulation. For example if your simulation does not require the polarisability to be a
feature of the rigid species, but is conned to free atoms or exible molecules in the same
system. The appropriate error trap is found in subroutine sysdef.
Message 95: error - potential cuto exceeds half cell width
In order for the minimum image convention to work correctly within DL POLY 2 , it is
necessary to ensure that the cuto applied to the pair potentials does not exceed half
the perpendicular width of the simulation cell. (The perpendicular width is the shortest
distance between opposing cell faces.) Termination results if this is detected. In NVE
simulations this can only happen at the start of a simulation, but in NPT, it may occur at
any time.
Action:
Supply a cuto that is less than half the cell width. If running constant pressure calculations, use a cuto that will accommodate the uctuations in the simulation cell. Study the
uctuations in the OUTPUT le to help you with this.
Message 97: error - cannot use shell model with neutral groups
The dynamical shell model was not designed to work with neutral groups. This error results
if an attempt is made to combine both.
c CCLRC
192
Action:
There is no general remedy for this error if you wish to combine both these capabilities.
However if your simulation does not require the polarisability to be a feature of rigid species
(comprising the charged groups), but is conned to free atoms or exible molecules in the
same system, you may consider overriding this error message and continuing with your
simulation. The appropriate error trap is found in subroutine sysdef.
Message 99: error - cannot use shell model with constraints
The dynamical shell model was not designed to work in conjunction with constraint bonds.
This error results if both are used in the same simulation.
Action: There is no general remedy if you wish to combine both these capabilities. However
if your simulation does not require the polarisability to be a feature of the constrained
species, but is conned to free atoms or exible molecules, you may consider overriding
this error message and continuing with your simulation. The appropriate error trap is in
subroutine sysdef.
Message 100: error - forces working arrays too small
There are a number of arrays in DL POLY 2 that function as workspace for the forces calculations. Their dimension is equal to the number of atoms in the simulation cell divided by
the number of nodes. If these arrays are likely to be exceeded, DL POLY 2 will terminate
execution.
Action:
Standard user response. Fix the parameter msatms.
Message 101: error - calculated 4-body potential index too large
DL POLY 2 has a permitted maximum for the calculated index for any four body potential
in the system (i.e. as dened in the FIELD le). If there are m distinct types of atom
in the system, the index can possibly range from 1 to (m (m + 1) (m + 2))=6. If the
internally calculated index exceeds this number, this error report results.
2
Action:
Standard user response. Fix the parameter mxfbp.
Message 102: error - parameter mxproc exceeded in shake arrays
The RD-SHAKE algorithm distributes data over all nodes of a parallel computer. Certain
arrays in RD-SHAKE have a minimum dimension equal to the maximum number of nodes
DL POLY 2 is likely to encounter. If the actual number of nodes exceeds this, the program
c CCLRC
193
terminates.
Action:
Standard user response. Fix the parameter mxproc.
Message 103: error - parameter mxlshp exceeded in shake arrays
The RD-SHAKE algorithm requires that information about `shared' atoms be passed between nodes. If there are too many atoms, the arrays holding the information will be
exceeded and DL POLY 2 will terminate execution.
Action:
Standard user response. Fix the parameter mxlshp.
Message 105: error - shake algorithm failed to converge
The RD-SHAKE algorithm for bond constraints is iterative. If the maximum number of
permitted iterations is exceeded, the program terminates. Possible causes include: a bad
starting conguration; too large a time step used; incorrect force eld specication; too
high a temperature; inconsistent constraints involving shared atoms etc.
Action:
Corrective action depends on the cause. It is unlikely that simply increasing the iteration
number will cure the problem, but you can try: follow the standard user response to increase
the control parameter mxshak. But the trouble is much more likely to be cured by careful
consideration of the physical system being simulated. For example, is the system stressed
in some way? Too far from equilibrium?
Message 106: error - neighbour list array too small in parlink
Construction of the Verlet neighbour list in subroutine parlink nonbonded (pair) force has
exceeded the neighbour list array dimensions.
Action:
Standard user response. Fix the parameter mxlist.
Message 107: error - neighbour list array too small in parlinkneu
Construction of the Verlet neighbour list in subroutine parlinkneu nonbonded (pair) force
has exceeded the neighbour list array dimensions.
Action:
Standard user response. Fix the parameter mxlist.
c CCLRC
194
Message 108: error - neighbour list array too small in parneulst
Construction of the Verlet neighbour list in subroutine parneulst nonbonded (pair) force
has exceeded the neighbour list array dimensions.
Action:
Standard user response. Fix the parameter mxlist.
Message 109: error - neighbour list array too small in parlst nsq
Construction of the Verlet neighbour list in subroutine parlst nsq nonbonded (pair) force
has exceeded the neighbour list array dimensions.
Action:
Standard user response. Fix the parameter mxlist.
Message 110: error - neighbour list array too small in parlst
Construction of the Verlet neighbour list in subroutine parlst nonbonded (pair) force has
exceeded the neighbour list array dimensions.
Action:
Standard user response. Fix the parameter mxlist.
Message 112: error - vertest array too small
This error results when the dimension of the DL POLY 2 vertest arrays, which are used
in checking if the Verlet list needs updating, have been exceeded.
Action:
Standard user response. Fix the parameter mslst.
Message 120: error - invalid determinant in matrix inversion
DL POLY 2 occasionally needs to calculate matrix inverses (usually the inverse of the matrix of cell vectors, which is of size 3 3). For safety's sake a check on the determinant is
made, to prevent inadvertent use of a singular matrix.
Action:
Locate the incorrect matrix and x it - e.g. are cell vectors correct?
Message 130: error - incorrect octahedral boundary condition
When calculating minimum images DL POLY 2 checks that the periodic boundary of the
simulation cell is compatible with the specifed minimum image algorithm. Program termination results if an inconsistency is found. In this case the error refers to the truncated
c CCLRC
195
octahedral minimum image, which is inconsistent with the simulation cell. The most probable cause is the incorrect denition of the simulation cell vectors present in the input le
CONFIG, these must equal the vectors of the enscribing cubic cell.
Action:
Check the specied simulation cell vectors and correct accordingly.
Message 135: error - incorrect hexagonal prism boundary condition
When calculating minimum images DL POLY 2 checks that the periodic boundary of the
simulation cell is compatible with the specifed minimum image algorithm. Program termination results if an inconsistency is found. In this case the error refers to the hexagonal
prism minimum image, which is inconsistent with the simulation cell. The most probable
cause is the incorrect denition of the simulation cell vectors present in the input le CONFIG, these must equal the vectors of the enscribing orthorhombic cell.
Action:
Check the specied simulation cell vectors and correct accordingly.
Message 140: error - incorrect dodecahedral boundary condition
When calculating minimum images DL POLY 2 checks that the periodic boundary of the
simulation cell is compatible with the specifed minimum image algorithm. Program termination results if an inconsistency is found. In this case the error refers to the rhombic
dodecahedral minimum image, which is inconsistent with the simulation cell. The most
probable cause is the incorrect denition of the simulation cell vectors present in the input
le CONFIG, these must equal the vectors of the enscribing tetragonal simulation cell.
Action:
Check the specied simulation cell vectors and correct accordingly.
Message 145: error - no van der waals potentials dened
This error arises when there are no VDW potentials specied in the FIELD le but the
user has not specied no vdw in the CONTROL le. In other words DL POLY 2 expects
the FIELD le to contain VDW potential specications.
Action:
Edit the FIELD le to insert the required potentials or specify no vdw in the CONTROL
le.
Message 150: error - unknown van der waals potential selected
DL POLY 2 checks when constructing the interpolation tables for the short ranged potentials that the potential function requested is one which is of a form known to the program.
c CCLRC
196
If the requested potential form is unknown, termination of the program results. The most
probable cause of this is the incorrect choice of the potential keyword in the FIELD le or
one in the wrong columns (input is formatted).
Action:
Read the DL POLY 2 documentation and nd the potential keyword for the potential
desired. Insert the correct index in the FIELD le denition and ensure it occurs in the
correct columns (17-20). If the correct form is not available, look at the subroutine forgen
(or its variant) and dene the potential for yourself. It is easily done.
Message 151: error - unknown metal potential selected
The metal potentials available in DL POLY 2 are conned to density dependent forms of
the Sutton-Chen type. This error results if the user attempts to specify another.
Action:
Re-specify the potential as Sutton-Chen type if possible. Check the potential keyword
appears in columns 17-20 of the FIELD le.
Message 153: error - metals not permitted with multiple timestep
The multiple timestep algorithm cannot be used in conjunction with metal potentials in
DL POLY 2 .
Action:
The simulation must be run without the multiple timestep option.
Message 160: error - unaccounted for atoms in exclude list
This error message means that DL POLY 2 has been unable to nd all the atoms described
in the exclusion list within the simulation cell. This should never occur, if it does it means
a serious bookkeeping error has occured. The probable cause is corruption of the code
somehow.
Action:
If you feel you can tackle it - good luck! Otherwise we recommend you get in touch with
the program authors. Keep all relevant data les to help them nd the problem.
Message 170: error - too many variables for statistic array
This error means the statistics arrays appearing in subroutine static are too small. This
can happen if the number of unique atom types is too large.
c CCLRC
197
Action:
Standard user response. Fix the parameter mxnstk. mxnstk should be at least (45+number
of unique atom types).
Message 180: error - Ewald sum requested in non-periodic system
DL POLY 2 can use either the Ewald method or direct summation to calculate the electrostatic potentials and forces in periodic (or pseudo-periodic) systems. For non-periodic
systems only direct summation is possible. If the Ewald summation is requested (with
the ewald sum or ewald precision directives in the CONTROL le) without periodic
boundary conditions, termination of the program results.
Action:
Select periodic boundaries by setting the variable imcon>0 in the CONFIG le (if possible)
or use a dierent method to evaluate electrostatic interactions e.g. by usinf the coul
directive in the CONTROL le.
Message 185: error - too many reciprocal space vectors
DL POLY 2 places hard limit on the number of k vectors to be used in the Ewald sum and
terminates if more than this is requested.
Action:
Either consider using fewer k vectors in the Ewald sum (and a larger cuto in real space)
or follow standard user response to reset the parameters kmaxb, kmaxc.
Message 186: error - transfer buer array too small in sysgen
In the subroutine sysgen.f DL POLY 2 requires dimension of the array buffer (dened
by the parameter mxbuff) to be no less than the parameter mxatms or the product of parameters mxnstk*mxstak. If this is not the case it will be unable to restart the program
correctly to continue a run. (Applies to parallel implementations only.)
Action:
Standard user response. Fix the parameter mxbuff.
Message 190: error - buer array too small in splice
DL POLY 2 uses a workspace array named buffer in several routines. Its declared size
is a compromise of several r^oles and may sometimes be too small (though in the supplied
program, this should happen only very rarely). The point of failure is in the splice routine,
which is part of the RD-SHAKE algorithm.
Action:
Standard user response. Fix the parameter mxbuff.
c CCLRC
198
Message 200: error - rdf buer array too small in revive
This error indicates that the buer array used to globally sum the rdf arrays in subroutine
revive is too small.
Action:
Standard user response. Fix the parameter mxbuff. Alternatively mxrdf can be set smaller.
Message 220: error - too many neutral groups in system
DL POLY 2 has a xed limit on the number of charged groups in a simulation. This error
results if the number is exceeded.
Action:
Standard user response. Fix the parameter mxneut.
Message 230: error - neutral groups improperly arranged
In the DL POLY 2 FIELD le the charged groups must be dened in consecutive order.
This error results if this convention is not adhered to.
Action:
The arrangement of the data in the FIELD le must be sorted. All atoms in the same
group must be arranged consecutively. Note that reordering the le in this way implies a
rearrangement of the CONFIG le also.
Message 250: error - Ewald sum requested with neutral groups
DL POLY 2 will not permit the use of neutral groups with the Ewald sum. This error
results if the two are used together.
Action:
Either remove the neut directive from the FIELD le or use a dierent method to evaluate
the electrostatic interactions.
Message 260: error - parameter mxexcl exceeded in excludeneu routine
An error has been detected in the construction of the excluded atoms list for neutral groups.
This occurs when the parameter mxexcl is exceeded in the excludeneu routine.
Action:
Standard user response. Fix parameter mxexcl.
c CCLRC
199
Message 300: error - incorrect boundary condition in parlink
The use of link cells in DL POLY 2 implies the use of appropriate boundary conditions.
This error results if the user species octahedral, dodecahedral or slab boundary conditions.
Action:
The simulation must be run with cubic, orthorhombic or parallelepiped boundary conditions.
Message 301: error - too many rigid body types
The maximum number of rigid body types permitted by DL POLY 2 has been exceeded.
Action:
Standard user response. Fix the parameter mxungp.
Message 302: error - too many sites in rigid body
This error arises when DL POLY 2 nds that the number of sites in a rigid body exceeds
the dimensions of the approriate storage arrays.
Action:
Standard user response. Fix the parameter mxngp.
Message 303: error - too many rigid bodies specied
The maximum number of rigid bodies in a simulation has been reached. Do not confuse
this with message 304 below.
Action:
Standard user response. Fix the parameter mxgrp.
Message 304: error - too many rigid body sites in system
This error occurs when the total number of sites within all rigid bodies exceeds the permitted maximum. Do not confuse this with message 303 above.
Action:
Standard user response. Fix the parameter mxgatms.
Message 305: error - box size too small for link cells
The link cells algorithm in DL POLY 2 cannot work with less than 27 link cells. Depending
on the cell size and the chosen cut-o, DL POLY 2 may decide that this minimum cannot
be achieved and terminate.
c CCLRC
200
Action:
If a smaller cut-o is acceptable use it. Otherwise do not use link cells. Consider running
a larger system, where link cells will work.
Message 306: error - failed to nd principal axis system
This error indicates that the routine quatbook has failed to nd the principal axis for a
rigid unit.
Action:
This is an unlikely error. The code should correctly handle linear, planar and 3-dimensional
rigid units. Check the denition of the rigid unit in the CONFIG le, if sensible report the
error to the authors.
Message 310: error - quaternion setup failed
This error indicates that the routine quatbook has failed to reproduce all the atomic positions in rigid units from the centre of mass and quaternion vectors it has calculated.
Action:
Check the contents of the CONFIG le. DL POLY 2 builds its local body description of a
rigid unit type from the rst occurrence of such a unit in the CONFIG le. The error most
likely occurs because subsequent occurrences were not suÆciently similar to this reference
structure. If the problem persists increase the value of the variable tol in quatbook
and recompile. If problems still persist double the value of dettest in quatbook and
recompile. If you still encounter problems contact the authors.
Message 320: error - site in multiple rigid bodies
DL POLY 2 has detected that a site is shared by two or more rigid bodies. There is no
integration algorithm available in this version of the package to deal with this type of model.
Action:
The only course is to redene the molecular model (e.g. introducing exible bonds and
angles in suitable places) to allow DL POLY 2 to proceed.
Message 321: error - quaternion integrator failed
The quaternion algorithm has failed to converge. If the maximum number of permitted
iterations is exceeded, the program terminates. Possible causes include: a bad starting
conguration; too large a time step used; incorrect force eld specication; too high a temperature; inconsistent constraints involving shared atoms etc.
Action:
Corrective action depends on the cause. Try reducing the timestep or running a zero kelvin
c CCLRC
201
structure optimization for a hundred timesteps or so. It is unlikely that simply increasing
the iteration number will cure the problem, but you can try: follow the standard user
response to increase the parameter mxquat. But the trouble is much more likely to be
cured by careful consideration of the physical system being simulated. For example, is the
system stressed in some way? Too far from equilibrium?
Message 330: error - mxewld parameter incorrect
DL POLY 2 has two strategies for parallelization of the reciprocal space part of the Ewald
sum. If ewald1 is used the parameter mxewld should equal the parameter msatms. If
ewald1a is used this parameter should equal mxatms.
Action:
Standard user response. Set the parameter mxewld to the value appropriate for the version
of ewald1 you are using. Recompile the program.
Message 340: error - invalid integration option requested
DL POLY 2 has detected an incompatibility in the simulation instructions, namely that
the requested integration algorithm is not compatible with the physical model. It may be
possible to override this error trap, but it is up to the user to establish if this is sensible.
Action:
This is a non recoverable error, unless the user chooses to override the restriction.
Message 350: error - too few degrees of freedom
This error can arise if a small system is being simulated and the number of constraints
applied is too large.
Action:
Simulate a larger system or reduce the number of constraints.
Message 360: error - frozen atom found in rigid body
DL POLY 2 does not permit a site in a rigid body to be frozen i.e. xed in one location in
space.
Action:
Remove the `freeze' condition from the site concerned. Consider using a very high site mass
to achieve a similar eect.
Message 380: error - simulation temperature not specied
DL POLY 2 has failed to nd a temp directive in the CONTROL le.
c CCLRC
202
Action:
Place a temp directive in the CONTROL le, with the required temperature specied.
Message 381: error - simulation timestep not specied
DL POLY 2 has failed to nd a timestep directive in the CONTROL le.
Action:
Place a timestep directive in the CONTROL le, with the required timestep specied.
Message 382: error - simulation cuto not specied
DL POLY 2 has failed to nd a cuto directive in the CONTROL le.
Action:
Place a cuto directive in the CONTROL le, with the required forces cuto specied.
Message 383: error - simulation forces option not specied
DL POLY 2 has failed to nd any directive specifying the electrostatic interactions options
in the CONTROL le.
Action:
Ensure the CONTROL le contains at least one directive specifying the electrostatic potentials (e.g. ewald, coul, no electrostatics etc.)
Message 384: error - verlet strip width not specied
DL POLY 2 has failed to nd the delr directive in the CONTROL le.
Action:
Insert a delr directive in the CONTROL le, specifying the width of the verlet strip
augmenting the forces cuto.
Message 385: error - primary cuto not specied
DL POLY 2 has failed to nd the prim directive in the CONTROL le.
multiple timestep option required.
Action:
Necessary only if
Insert a prim directive in the CONTROL le, specifying the primary cuto radius in the
multiple timestep algorithm.
c CCLRC
203
Message 386: error - primary cuto larger than rcut
The primary cuto specied by the prim directive in the CONTROL le exceeds the value
specied for the forces cuto (directive cut). Applies only if the multiple timestep option
is required.
Action:
Locate the prim directive in the CONTROL le, and alter the chosen cuto. Alternatively,
increase the real space cuto specied with the cut directive. Take care to avoid error
number 398.
Message 387: error - system pressure not specied
The target system pressure has not been specied in the CONTROL le. Applies to NPT
simulations only.
Action:
Insert a press directive in the CONTROL le specifying the required system pressure.
Message 388: error - npt incompatible with multiple timestep
The use of NPT (constant pressure) and temperature is not compatible with the multiple
timestep option.
Action:
Simulation must be run at xed volume in this case. But note it may be possible to use
NPT without the multiple timestep, in ourder to estimate the required system volume, then
switch back to multiple timestep and NVT dynamics at the required volume.
Message 390: error - npt ensemble requested in non-periodic system
A non-periodic system has no dened volume, hence the NPT algorithm cannot be applied.
Action:
Either simulate the system with a periodic boundary, or use another ensemble.
Message 392: error - too many link cells requested
The number of link cells required for a given simulation exceeds the number allowed for by
the DL POLY 2 arrays.
Action:
Standard user response. Fix the parameter mxcell.
c CCLRC
204
Message 394: error - minimum image arrays exceeded
The work arrays used in images have been exceeded.
Action: Standard user response. Fix the parameter mxxdf.
Message 396: error - interpolation array exceeded
DL POLY 2 has sought to read past the end of an interpolation array. This should never
happen!
Action:
Contact the authors.
Message 398: error - cuto too small for rprim and delr
This error can arise when the multiple timestep option is used. It is essential that the
primary cuto (rprim) is less than the real space cuto (rcut) by at least the Verlet shell
width delr (preferably much larger!). DL POLY 2 terminates the run if this condition is
not satised.
Action:
Adjust rcut, rprim and delr to satisfy the DL POLY 2 requirement. These are dened
with the directives cut, prim and delr respectively.
Message 400: error - rvdw greater than cuto
DL POLY 2 requires the real space cuto (rcut) to be larger than, or equal to, the van
der Waals cuto (rvdw) and terminates the run if this condition is not satised.
Action:
Adjust rvdw and rcut to satisfy the DL POLY 2 requirement.
Message 402: error - van der waals cuto unset
The user has not set a cuto (rvdw) for the van der Waals potentials. The simulation
cannot proceed without this being specied.
Action:
Supply a cuto value for the van der Waals terms in the CONTROL le using the directive
rvdw, and resubmit job.
Message 410: error - cell not consistent with image convention
The simulation cell vectors appearing in the CONFIG le are not consistent with the specied image convention.
c CCLRC
205
Action:
Locate the variable imcon in the CONFIG le and correct to suit the cell vectors.
Message 412: error - mxxdf parameter too small for shake routine
In DL POLY 2 the parameter mxxdf must be greater than or equal to the parameter mxcons.
If it is not, this error is a possible result.
Action:
Standard user response. Fix the parameter mxxdf.
Message 414: error - conicting ensemble options in CONTROL le
DL POLY 2 has found more than one ensemble directive in the CONTROL le.
Action:
Locate extra ensemble directives in CONTROL le and remove.
Message 416: error - conicting force options in CONTROL le
DL POLY 2 has found incompatible directives in the CONTROL le specifying the electrostatic interactions options.
Action:
Locate the conicting directives in the CONTROL le and correct.
Message 418: error - bond vector work arrays too small in bndfrc
The work arrays in bndfrc have been exceeded.
Action:
Standard user response. Fix the parameter msbad.
Message 419: error - bond vector work arrays too small in angfrc
The work arrays in angfrc have been exceeded.
Action:
Standard user response. Fix the parameter msbad.
Message 420: error - bond vector work arrays too small in tethfrc
The work arrays in tethfrc have been exceeded.
Action:
Standard user response. Fix the parameter msbad.
c CCLRC
206
Message 421: error - bond vector work arrays too small in dihfrc
The work arrays in dihfrc have been exceeded.
Action:
Standard user response. Fix the parameter msbad.
Message 422: error - all-pairs must use multiple timestep
In DL POLY 2 the `all pairs' option must be used in conjunction with the multiple timestep.
Action:
Activate the multiple timestep option in the CONTROL le and resubmit.
Message 423: error - bond vector work arrays too small in shlfrc
The dimensions of the interatomic distance vectors have been exceeded in subroutine shlfrc.
Action:
Standard user response. Fix the parameter msbad. Set equal to the value of the parameter
mxshl.
Message 424: error - electrostatics incorrect for all-pairs
When using the all pairs option in conjunction with electrostatic forces, the electrostatics
must be handled with either the standard Coulomb sum, or with the distance dependent
dielectric.
Action:
Rerun the simulation with the appropriate electrostatic option.
Message 425: error - transfer buer array too small in shlmerge
The buer used to transfer data between nodes in the subroutine shlmerge has been dimensioned too small.
Action:
Standard user response. Fix the parameter mxbuff.
Message 426: error - neutral groups not permitted with all-pairs
DL POLY 2 will not permit simulations using both the neutral group and all pairs options
together.
c CCLRC
207
Action:
Switch o one of the conicting options and rerun.
Message 427: error - bond vector work arrays too small in invfrc
The work arrays in subroutine invfrc have been exceeded.
Action:
Standard user response. Fix the parameter msbad.
Message 430: error - integration routine not available
A request for a nonexistent ensemble has been made or a request with conicting options
that DL POLY 2 cannot deal with (e.g. a Evans thermostat with rigid body equations of
motion).
Action:
Examine the CONTROL and FIELD les and remove inappropriate specications.
Message 432: error - intlist failed to assign constraints
If the required simulation has constraint bonds DL POLY 2 attempts to apportion the
molecules to processors so that, if possible, there are no shared atoms between processors.
If this is not possible, one or more molecules may be split between processors. This message
indicates that the code has failed to carry out either of these successfully.
Action:
The error may arise from a compiler error. Try recompiling intlist without the optimization ag turned on. If the problem persists it should be reported to the authors, (after
checking the input data for inconsistencies).
Message 433: error - specify rcut before the Ewald sum precision
When specifying the desired precision for the Ewald sum in the CONTROL le, it is rst
necessary to specify the real space cuto rcut.
Action:
Place the cut directive before the ewald precision directive in the CONTROL le and
rerun.
Message 434: error - illegal entry into STRESS related routine
The calculation of the stress tensor in DL POLY 2 requires additional code that must be
included at compile time through the use of the STRESS keyword. If this is not done, and
c CCLRC
208
DL POLY 2 is later required to calculate the stress tensor, this error will result.
Action:
The program must be recompiled with the STRESS keyword activated. This will ensure
all the relevant code is in place. See section 3.2.1.
Message 436: error - unrecognised ensemble
An unknown ensemble option has been specied in the CONTROL le.
Action:
Locate ensemble directive in the CONTROL le and amend appropriately.
Message 438: error - PMF constraints failed to converge
The constraints in the potential of mean force algorithm have not converged in the permitted number of cycles. (The SHAKE algorithm for PMF constraints is iterative.) Possible
causes include: a bad starting conguration; too large a time step used; incorrect force eld
specication; too high a temperature; inconsistent constraints involving shared atoms etc.
Action:
Corrective action depends on the cause. It is unlikely that simply increasing the iteration
number will cure the problem, but you can try: follow standard user response to increase the
parameter mxshak. But the trouble is much more likely to be cured by careful consideration
of the physical system being simulated. For example, is the system stressed in some way?
Too far from equilibrium?
Message 440: error - undened angular potential
A form of angular potential has been requested which DL POLY 2 does not recognise.
Action:
Locate the oending potential in the FIELD le and remove. Replace with one acceptable
to DL POLY 2 if this is possible. Alternatively, you may consider dening the required
potential in the code yourself. Amendments to subroutines sysdef and angfrc will be
required.
Message 442: error - undened three body potential
A form of three body potential has been requested which DL POLY 2 does not recognise.
Action:
Locate the oending potential in the FIELD le and remove. Replace with one acceptable
to DL POLY 2 if this is reasonable. Alternatively, you may consider dening the required
c CCLRC
209
potential in the code yourself. Amendments to subroutines sysdef and thbfrc will be
required.
Message 443: error - undened four body potential
DL POLY 2 has been requested to process a four-body potential it does not recognise.
Action:
Check the FIELD le and make sure the keyword is correctly dened. Make sure that
subroutine fbpfrc contains the code necessary to deal with the requested potential. Add
the code required if necessary, by amending subroutines sysdef and fbpfrc.
Message 444: error - undened bond potential
DL POLY 2 has been requested to process a bond potential it does not recognise.
Action:
Check the FIELD le and make sure the keyword is correctly dened. Make sure that
subroutine bndfrc contains the code necessary to deal with the requested potential. Add
the code required if necessary, by amending subroutines sysdef and bndfrc.
Message 446: error - undened electrostatic key in dihfrc
The subroutine dihfrc has been requested to process a form of electrostatic potential it
does not recognise.
Action:
The error arises because the integer key keyfrc has an inappropriate value (which should
not happen in the standard version of DL POLY 2 ). Check that the FIELD le correctly
species the potential. Make sure the version of dihfrc does contain the potential you are
specifying. Report the error to the authors if these checks are correct.
Message 448: error - undened dihedral potential
A form of dihedral potential has been requested which DL POLY 2 does not recognise.
Action:
Locate the oending potential in the FIELD le and remove. Replace with one acceptable
to DL POLY 2 if this is reasonable. Alternatively, you may consider dening the required
potential in the code yourself. Amendments to subroutines sysdef and dihfrc (and its
variants) will be required.
Message 449: error - undened inversion potential
A form of inversion potential has been encountered which DL POLY 2 does not recognise.
c CCLRC
210
Action:
Locate the oending potential in the FIELD le and remove. Replace with one acceptable
to DL POLY 2 if this is reasonable. Alternatively, you may consider dening the required
potential in the code yourself. Amendments to subroutines sysdef and invfrc will be
required.
Message 450: error - undened tethering potential
A form of tethering potential has been requested which DL POLY 2 does not recognise.
Action:
Locate the oending potential in the FIELD le and remove. Replace with one acceptable
to DL POLY 2 if this is reasonable. Alternatively, you may consider dening the required
potential in the code yourself. Amendments to subroutines sysdef and tethfrc will be
required.
Message 451: error - three body potential cuto undened
The cuto radius for a three body potential has not been dened in the FIELD le.
Action:
Locate the oending three body force potential in the FIELD le and add the required
cuto. Resubmit the job.
Message 452: error - undened pair potential
A form of pair potential has been requested which DL POLY 2 does not recognise.
Action:
Locate the oending potential in the FIELD le and remove. Replace with one acceptable
to DL POLY 2 if this is reasonable. Alternatively, you may consider dening the required
potential in the code yourself. Amendments to subroutines sysdef and forgen will be
required.
Message 453: error - four body potential cuto undened
The cuto radius for a four-body potential has not been dened in the FIELD le.
Action:
Locate the oending four body force potential in the FIELD le and add the required cuto. Resubmit the job.
c CCLRC
211
Message 454: error - undened external eld
A form of external eld potential has been requested which DL POLY 2 does not recognise.
Action:
Locate the oending potential in the FIELD le and remove. Replace with one acceptable
to DL POLY 2 if this is reasonable. Alternatively, you may consider dening the required
potential in the code yourself. Amendments to subroutines sysdef and extnfld will be
required.
Message 456: error - core and shell in same rigid unit
It is not sensible to x both the core and the shell of a polarisable atom in the same molecular unit. Consequently DL POLY 2 will abandon the job if this is found to be the case.
Action:
Locate the oending core-shell unit (there may be more than one in your FIELD le) and
release the shell (preferably) from the rigid body specication.
Message 458: error - too many PMF constraints - param. mspmf too small
The number of constraints in the potential of mean force is too large. The dimensions of
the appropriate arrays in DL POLY 2 must be increased.
Action:
Standard user response. Fix the parameter mspmf.
Message 460: error - too many PMF sites - parameter mxspmf too small
The number of sites dened in the potential of mean force is too large. The dimensions of
the appropriate arrays in DL POLY 2 must be increased.
Action:
Standard user response. Fix the parameter mxspmf.
Message 462: error - PMF UNIT record expected
A pmf unit directive was expected as the next record in the FIELD le but was not found.
Action:
Locate the pmf directive in the FIELD le and examine the following entries. Insert the
missing pmf unit directive and resubmit.
c CCLRC
212
Message 464: error - thermostat time constant must be > 0.d0
A zero or negative value for the thermostat time constant has been encountered in the
CONTROL le.
Action:
Locate the ensemble directive in the CONTROL le and assign a positive value to the
time constant.
Message 466: error - barostat time constant must be > 0.d0
A zero or negative value for the barostat time constant has been encountered in the CONTROL le.
Action:
Locate the ensemble directive in the CONTROL le and assign a positive value to the
time constant.
Message 468: error - r0 too large for snm potential with current cuto
The specied location (r0) of the potential minimum for a shifted n-m potential exceeds
the specied potential cuto. A potential with the desired minimum cannot be created.
Action:
To obtain a potential with the desired minimum it is necessary to increase the van der
Waals cuto. Locate the rvdw directive in the CONTROL le and reset to a magnitude
greater than r0. Alternatively adjust the value of r0 in the FIELD le. Check that the
FIELD le is correctly formatted.
Message 470: error - n<m in denition of n-m potential
The specication of a n-m potential in the FIELD le implies that the exponent m is larger
than exponent n. (Not all versions of DL POLY 2 are aected by this.)
Action:
Locate the n-m potential in the FIELD le and reverse the order of the exponents. Resubmit
the job.
Message 474: error - mxxdf too small in parlst subroutine
The parameter mxxdf dening working arrays in subroutine parlst of DL POLY 2 has
been found to be too small.
Action:
Standard user response. Fix the parameter mxxdf.
c CCLRC
213
Message 475: error - mxxdf too small in parlst nsq subroutine
The parameter mxxdf dening working arrays in subroutine parlst nsq DL POLY 2 has
been found to be too small.
Action:
Standard user response. Fix the parameter mxxdf.
Message 476: error - mxxdf too small in parneulst subroutine
The parameter mxxdf dening working arrays in subroutine parneulst is too small.
Action:
Standard user response. Fix the parameter mxxdf.
Message 477: error - mxxdf too small in prneulst subroutine
The parameter mxxdf dening working arrays in subroutine prneulst is too small.
Action:
Standard user response. Fix the parameter mxxdf.
Message 478: error - mxxdf too small in forcesneu subroutine
The parameter mxxdf dening working arrays in subroutine forcesneu is too small.
Action:
Standard user response. Fix the parameter mxxdf.
Message 479: error - mxxdf too small in multipleneu subroutine
The parameter mxxdf dening working arrays in subroutine multipleneu is too small.
Action:
Standard user response. Fix the parameter mxxdf.
Message 484: error - only one potential of mean force permitted
It is not permitted to dene more than one potential of mean force in the FIELD le.
Action:
Check that the FIELD le contains only one PMF specication. If more than one is needed,
DL POLY 2 cannot handle it.
c CCLRC
214
Message 490: error - PMF parameter mxpmf too small in passpmf
The bookkeeping arrays have been exceeded in passpmf
Action:
Standard user response. Fix the parameter mxpmf. Set equal to mxatms.
Message 492: error - parameter mxcons < number of PMF constraints
The parameter mxcons is too small for the number of PMF constraints in the system.
Action:
Standard user response. Fix the value of mxcons.
Message 494: error in csend: pvmnitsend
The PVM routine pvmfinitsend has returned an error. It is invoked by the routine csend.
Action:
Check your system implementation of PVM.
Message 496: error in csend: pvmfpack
The PVM routine pvmfpack has returned an error. It is invoked by the routine csend.
Action:
Check your system implementation of PVM.
Message 498: error in csend: pvmfsend
The PVM routine pvmfsend has returned an error. It is invoked by the routine csend.
Action:
Check your system implementation of PVM.
Message 500: error in crecv: pvmfrecv
The PVM routine pvmfrecv has returned an error. It is invoked by the routine crecv.
Action:
Check your system implementation of PVM.
Message 502: error in crecv: pvmfunpack
The PVM routine pvmfunpack has returned an error. It is invoked by the routine crecv.
c CCLRC
215
Action:
Check your system implementation of PVM.
Message 504: error - cuto too large for TABLE le
The requested cuto exceeds the information in the TABLE le.
Action:
Reduce the value of the vdw cuto (rvdw) in the CONTROL le or reconstruct the TABLE
le.
Message 506: error - work arrays too small for quaternion integration
The working arrays associated with quaternions are too small for the size of system being
simulated. They must be redimensioned.
Action:
Standard user response. Fix the parameter msgrp.
Message 508: error - rigid bodies not permitted with RESPA algorithm
The RESPA algorithm implemented in DL POLY 2 is for atomic systems only. Rigid bodies or constraints cannot be treated.
Action:
There is no cure for this. The code simply does not have this capability. Consider writing
it for yourself!
Message 510: error - structure optimiser not permitted with RESPA
The RESPA algorithm in DL POLY 2 has not been implemented to work with the structure optimizer. You have asked for a forbidden operation.
Action:
There is no x for this. In any case it does not make sense to use the RESPA algorithm
for this purpose.
Message 513: error - SPME not available for given boundary conditions
The SPME algorithm in DL POLY 2 does not work for aperiodic (IMCON=0) or slab
(IMCON=6) boundary conditions.
Action:
If the system must have aperiodic or slab boundaries, nothing can be done. In the latter
case however, it may be acceptable to represent the same system with slabs replicated in
the z direction, thus permitting a periodic simulation.
c CCLRC
216
Message 514: error - SPME routines have not been compiled in
The inclusion of the SPME algorithm in DL POLY 2 is optional at the compile stage. If
the executable does not contain the SPME routines, but the method is requested by the
user, this error results.
Action:
DL POLY 2 must be recompiled with the SPME ags set. Beware that your system has
the necessary fast Fourier transform routines to permit this.
Index
PMF, 56, 112
CVS, 13, 14
direct Coulomb sum, 43, 44, 46
distance dependant dielectric, 46, 50, 99,
103, 200
distance restraints, 26
DLPROTEIN, 19, 89
ensemble, 11, 199, 201
Berendsen NT, 11, 54, 99, 101, 103
Berendsen NPT, 11, 54, 101, 103
Berendsen NVT, 11, 54, 99, 101, 103
canonical, 57
Evans NVT, 11, 54, 99, 101, 103
Hoover NT, 11, 12, 54, 101
Hoover NPT, 11, 54, 99, 101
Hoover NVT, 11, 54, 101
microcanonical, see ensemble,NVE
NVE, 57, 99, 101, 103
error messages, 93, 170{210
Ewald
optimisation, 91, 92
SPME, 13, 43, 49, 84, 91, 100, 138
summation, 43, 47{49, 67, 69, 72, 91,
92, 99{101, 137, 138, 191, 192,
195, 201
force eld, 9, 10, 22, 24, 31, 42, 43, 90,
173, 187
AMBER, 10, 22
DL POLY, 9, 22{52
DREIDING, 10, 22, 40, 41, 138
GROMOS, 10, 22
FORTRAN 77, 12{14, 78, 84, 142
FORTRAN 90, 12, 13
fortran 90, 12
algorithm, 10, 11, 53, 97
Brode-Ahlrichs, 23, 70, 71
FIQA, 11, 12, 54, 64
multiple timestep, 67, 68, 70, 79, 80,
99, 102, 127, 137, 190, 196{198,
200
QSHAKE, 11, 12, 54, 65, 67, 74
RD-SHAKE, 11, 12, 53, 54, 56, 73,
74, 186, 187, 191
SHAKE, 11, 69, 73, 151, 202
Verlet, 11, 23, 24, 38, 44, 53{57, 59,
60, 73
AMBER, 8, 10, 22, 89, 90
barostat, 11, 65, 99, 206
Berendsen, 62, 67, 138
Hoover, 59, 138
boundary conditions, 10, 43, 79, 89, 137,
138, 164, 181, 183
cubic, 106, 181, 183, 193
hexagonal prism, 106
parallelpiped, 181, 183, 193
rhombic dodecahedron, 106
slab, 193
truncated octahedron, 106
CCP5, 8, 17, 18
charge groups, 109, 138, 186, 192
COMMON blocks, 13, 14, 84
constrains
bond, 151
constraints
bond, 9, 11, 24, 54{56, 62, 63, 65, 73,
74, 79, 80, 111, 112, 126, 137, 138,
150, 177, 182, 186, 187, 201
Gaussian, 47, 57, 137
217
c CCLRC
FTP, 17{19
Graphical User Interface, 17, 88, 90, 105
GROMOS, 8, 10, 22
licence, 8
long range corrections
Sutton-Chen, 40
van der Waals, 38
parallelisation, 10, 69
Ewald summation, 72
intramolecular terms, 70
Replicated Data, 10
Verlet neighbour list, 71
polarisation, 51, 52, 138
dynamical shell model, 52, 185
potential
bond, 10, 23{26, 30, 32, 36, 41, 52, 70,
73, 89, 111, 126, 150, 151, 176,
203
Coulombic, see potential,electrostatic
dihedral, 10, 22, 23, 29, 30, 32, 33, 69,
70, 114, 126, 150, 151, 180, 203
electrostatic, 9, 15, 23, 26, 28, 43, 67,
68, 98{100, 103, 126, 137, 138,
196, 200, 203
four-body, 10, 22{24, 36, 41, 42, 117,
118, 126, 150, 175, 183{186, 203,
204
improper dihedral, 10, 32, 69
intramolecular, 36, 42, 79
inversion, 10, 22, 33{35, 41, 42, 115,
150, 151, 182, 203
metal, 10, 39, 182, 190
nonbonded, 9, 23, 24, 70, 72, 86, 89,
90, 99, 108, 111, 113, 116, 173
Sutton-Chen, see potential,metal
tabulated, 120, 175
tethered, 35, 36, 115, 126, 138, 150,
151, 181, 204
three-body, 10, 22{24, 26, 36, 40, 41,
72, 89, 117, 126, 150, 151, 174,
181, 183, 184, 204
torsion, see potential,dihedral
218
valence angle, 9, 10, 22{24, 26, 27, 33,
40, 41, 69, 72, 79, 89, 112, 113,
126, 150, 151, 179
van der Waals, 23, 26, 28, 68, 79, 85,
101, 114, 151, 198
quaternions, 11, 54, 64, 100
reaction eld, 50, 51, 100
respa, 12, 17, 68
rigid body, 9, 11, 12, 36, 54, 63, 65, 66, 68,
74, 78, 137, 138, 150, 151, 185,
193{195, 201, 205, 209
rigid bond, see constraints,bond
rigid ion, 12, 68
rigid molecule, see rigid body
stress tensor, 28, 31, 35, 36, 38, 39, 41, 42,
44{46, 48, 51, 52, 56, 59, 201, 202
sub-directory, 144{146
bench, 16
build, 16
data, 16
execute, 16, 171
public, 16
respa, 16
sdk, 16
source, 16
utility, 16
thermostat, 11, 43, 65, 68, 99, 201, 206
Berendsen, 62, 65, 67, 137, 138
Hoover, 138
Nose-Hoover, 59, 60, 65, 67, 80, 137
units
DL POLY, 15, 127
energy, 109
pressure, 15, 60, 99, 127
Verlet neighbour list, 49, 67, 70{72, 79,
102, 187, 188
WWW, 9, 18, 19
X-PLOR, 8
Was this manual useful for you? yes no
Thank you for your participation!

* Your assessment is very important for improving the work of artificial intelligence, which forms the content of this project

Download PDF

advertisement