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c CCLRC
Section 4.2
occurrence of atoms in the excluded atoms list when building the link-cell lists. Lastly, the ther-
modynamic properties of the system are checked and set intact by the set temperature routine
(which also generates the initial velocities if required to do so).
The calculation of the pair forces represents the main part of any simulation. A Verlet neighbour list
is used by DL POLY 3 in calculating the atomic forces. The routine that constructs this this from
the link-cell lists and calculates all pair forces is called two body forces. Variety of subroutines
are called within this one to calculate specific contributions by different interactions. For example;
vdw forces for the short-range (van der Waals) forces (Section
2.3.1
), metal ld compute and
metal forces for the Sutton-Chen metal interactions (Section
2.3.2
), and ewald spme forces
and ewald real forces for the Coulombic forces (Section
2.4
).
Higher order intermolecular, site related and intramolecular forces require the routines; ter-
soff forces, three body forces, four body forces, core shell forces, tethers forces,
bonds forces, angles forces, dihedrals forces and inversions forces. The routine ex-
ternal field is required if the simulated system has an external force field (e.g. electrostatic field)
operating. To help with equilibration simulations, routines such as cap forces and zero k optimise
are sometimes required to reduce the magnitude of badly equilibrated forces.
Integration of the equations of motion is handled by one of the routines listed and described in
Chapter
3
.
As mentioned elsewhere, DL POLY 3 does not contain many routines for computing system prop-
erties during a simulation. Radial distributions may be calculated however, by using the routines
rdf collect and rdf compute. Similarly Z-density distribution may be calculated by using the
routines z density collect and z density compute. Ordinary thermodynamic quantities are
calculated by the routine statistics collect, which also writes the STATIS file (Section
5.2.8
).
Routine trajectory write writes the HISTORY (Section
5.2.1
) file for later (postmortem) anal-
ysis.
Job termination is handled by the routine statistics result which writes the final summaries in
the OUTPUT file and dumps the restart files REVIVE and REVCON (Sections
5.2.5
and
5.2.4
respectively).
4.2
Compiling and Running DL POLY 3
4.2.1
Compiling the DL POLY 3 Source Code
When you have obtained DL POLY 3 from Daresbury Laboratory and unpacked it, your next
task will be to compile it. To aid compilation two general makefiles (called "Makefile VV" and
"Makefile LFV" for compiling VV and LFV integration versions of DL POLY 3 respectively) have
been provided in the sub-directory build (see Appendix
C
to this document). After choosing what
the default integration schema is to be, the appropriate makefile is to be coped as "Makefile" in the
sub-directory source. The general DL POLY 3 makefile will build an executable with the full range
of functionality - sufficient for the test cases and for most users' requirements. In most cases, the
user will have to modify few entries in the specification part of their makefile to match the location
of certain software on their system architecture. Note that only FORTRAN 90 compiler and MPI
implementation are required for a successful build of DL POLY 3 . Should the user add additional
functionality to the code, major changes of the makefile may be required!
In UNIX environment the compilation of the program is initiated by typing the command:
make target
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