DL_POLY_4

Author

I.T. Todorov and W. Smith

Origin

STFC Daresbury Laboratory

Version

DL_POLY_4 version 4.02 & 4.01

Official Web Site

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

Brief Program Description

DL_POLY_4 is a molecular dynamics package developed at the STFC Daresbury Laboratory for UK computational chemists, 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.

Areas of Application

DL_POLY_4 can be used to simulate the following molecular species:

• Simple atomic systems and mixtures, e.g. Ne, Ar, Kr, etc.
• Simple unpolarisable point ions, e.g. NaCl, KCl, etc.
• Polarisable point ions and molecules, e.g. MgO, H2O, etc.
• Simple rigid molecules e.g. CCl4 , SF6 , Benzene, etc.
• Rigid molecular ions with point charges e.g. KNO3, (NH4)2 SO4 , etc.
• Polymers with rigid bonds, e.g. Cn H2n+2
• Polymers with flexible and rigid bonds and point charges, e.g. proteins, macromolecules etc.
• Silicate glasses and zeolites
• Simple metals and metal alloys, e.g. Al, Ni, Cu, Cu3 Au, etc.

The DL_POLY_4 force field includes:

• All common forms of non-bonded atom-atom (van der Waals) potentials
• Atom-atom (and site-site) coulombic potentials
• Metal-metal (local density dependent) potentials
• Tersoff (local density dependent) potentials (for hydro-carbons)
• Three-body valence angle and hydrogen bond potentials
• Four-body inversion potentials
• Ion core-shell polarasation
• Tether potentials
• Chemical bond potentials
• Valence angle potentials
• Dihedral angle (and improper dihedral angle) potentials
• Inversion angle potentials
• External field potentials.

DL_POLY_4 can accommodate the following boundary conditions:

• None e.g. isolated molecules in vacuo
• Cubic periodic boundaries
• Orthorhombic periodic boundaries
• Parallelepiped periodic boundaries
• Slab (x,y periodic, z non-periodic)

Molecular dynamics can be carried out using either the Verlet Leapfrog or the Velocity Verlet integration algorithms. 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 information, users are referred to the DL_POLY website:
http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/

Implementation and Access

DL_POLY_4 is available on Magellan and runs in serial and in parallel on up to 64 processors.

To run a DL_POLY_4 version 4.02 job, one of the following commands should be used:

$CHEM/rundlpoly402

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.

Version 4.01 is still accessible via the following command:

$CHEM/rundlpoly401

Machines

Magellan

Documentation

There is an Unix-style man page containing information on the local implementation of DL_POLY_4 version 4.02 accessible by typing: man rundlpoly402. A full description of DL_POLY_4 is available from the DL_POLY web site where the User Manual is available to download in PDF.

Test cases for the code can be found in the directory $CHEM/doc/dlpoly-4.02.

The Unix-style man page for version 4.01 can be accessed by typing man rundlpoly401.

Literature References

References are listed in the User Manual.

Specialist Support

Program Restrictions and Comments

Due to license restrictions, users must have registered on the DL_POLY website (http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/) before they can be given access to the code. For more information about this, please contact the Service Manager.

Please acknowledge the use of DL_POLY_4 by including the following reference when publishing data obtained using DL_POLY_4: "I.T. Todorov, W. Smith, K. Trachenko & M.T. Dove, J. Mater. Chem., 16, 1611-1618 (2006)".