DL_POLY

Author

W. Smith, T. R. Forester and I. T. Todorov, STFC Daresbury Laboratory.

Origin

W. Smith, STFC Daresbury Laboratory.

Version

DL_POLY_2 (version 2.20) and DL_POLY_3 (versions 3.10)

Official Web Site

http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/

Brief Program Description

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 Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC's Collaborative Computational Project for the Computer Simulation of Condensed Phases (CCP5) and the Computational Chemistry Group (CPG) at the Daresbury Laboratory. The package is the property of Science and Technology Facilities Council (STFC). Two versions of DL_POLY are currently available. DL_POLY_2 is the original version which has been parallelised using the Replicated Data strategy and is useful for simulations of up to 30,000 atoms. DL_POLY_3 is a version which uses Domain Decomposition to achieve parallelism and is suitable for simulations of the order 1 million atoms which run on more than 8 processors.

The DL_POLY force field includes:

• All common forms of non-bonded atom-atom potentialsmand
• Atom-atom (site-site) Coulombic potentials
• Valence angle potentials
• Dihedral angle potentials
• Inversion potentials
• Improper dihedral angle potentials
• 3-body valence angle and hydrogen bond potentials
• 4-body inversion potentials
• Sutton-Chen density dependent potentials (for metals)
• The Tersoff density dependent potential for covalent systems

DL_POLY can accommodate the following boundary conditions:

• None e.g. isolated molecules in vacuo
• Cubic periodic boundaries
• Orthorhombic periodic boundaries
• Parallelepiped periodic boundaries
• Truncated octahedral periodic boundaries (DL_POLY_2 only)
• Rhombic dodecahedral periodic boundaries (DL_POLY_2 only)
• Slab (x,y periodic, z non-periodic)
• Hexagonal prism periodic boundaries (DL_POLY_2 only)

In both DL_POLY_2 and DL_POLY_3, molecular dynamics can now be carried out using either the Verlet Leapfrog or the Velocity Verlet integration algorithms (the Velocity Verlet algorithm is new since version 2.16). In the leapfrog scheme, a parallel version of the SHAKE algorithm is used for bond constraints and a similar adaptation of the RATTLE algorithm is implmented in the velocity Verlet scheme.

For more details regarding the functionality of the two programs, users are referred to the user manuals which can be downloaded in pdf format from the DL_POLY website.

Areas of Application

DL_POLY can be used to simulate the following molecular species:

• Simple atomic systems and mixtures
• Simple unpolarisable point ions
• Polarisable point ions and molecules
• Simple rigid molecules (DL_POLY_2 only)
• Rigid molecular ions with point charges (DL_POLY_2 only)
• Polymers with rigid bonds
• Polymers with rigid bonds and point charges
• Macromolecules and biological systems (DL_POLY_2 only)
• Molecules with flexible bonds (DL_POLY_2 only)
• Silicate glasses and zeolites
• Simple metals and alloys
• Covalent systems (new since version 2.16)

Implementation and Access

DL_POLY_2 (version 2.20) and DL_POLY_3 (version 3.10) are available on Magellan. Both programs run in serial and in parallel on up to 64 processors.

To run a DL_POLY job, one of the following commands should be used:

$CHEM/rundlpoly220

$CHEM/rundlpoly310

The program requires three or four types of input file with set names:

1. CONTROL is for providing instructions for the type of run, etc.
2. CONFIG is for the specification of the starting coordinates for the run.
3. FIELD is for the provision of the force field for the run.
4. TABLE is for the specification of potentials (optional).

An additional file, REVOLD, may be required for restart calculations. These files need to be present in the current directory. During the run a number of output files will be deposited in the current directory. All file names need to be in upper case.

The DLPOLYGUI has now also been installed on Magellan. This may be used to view molecular structures and to edit them, however, please note that users should not submit their jobs directly via the graphical interface.

Machines

Available on Magellan.

Documentation

There are Unix-style man pages containing information on the local implementation of DL_POLY_2 (2.20) and DL_POLY_3 (3.10) accessible by typing: man rundlpoly220 and man rundlpoly310 respectively. A full description of DL_POLY_2 and DL_POLY_3 are available from the DL_POLY web site where the User Manuals are available in online form as well as in various printable forms.

For DL_POLY_2 (2.20), please refer to the man page rundlpoly220.

For DL_POLY_3 (3.10), please refer to the man page rundlpoly310.

Test cases for both versions of the code can be found in the directory $CHEM/doc/dlpoly/ .

Literature References

References are listed in the User Manuals.

Specialist Support

Dr. W. Smith. Address: Computational Science and Engineering Department, STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD. Email: W.Smith@dl.ac.uk.

Program Restrictions and Comments

N/A