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c CCLRC
Section 6.1
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 non-bonded interactions.
(However this is not a universal requirement of all force fields .) The same considerations are
needed in dealing with charged excluded atoms.
The modifications necessary to handle the excluded atoms are as follows. A distributed excluded
atoms list is constructed by the DL POLY 3 routine build excl intra at the start of the simu-
lation and is then used in conjunction with the Verlet neighbour list builder link cell pairs to
ensure that excluded interactions are left out of the pair force calculations. The excluded atoms
list is also updated during the atom relocation process described above (DL POLY 3 routine ex-
change particles).
Once the neighbour list has been constructed, each node of the parallel computer may pro-
ceed independently to calculate the pair force contributions to the atomic forces (see routine
two body forces).
The potential energy and forces arising from the non-bonded interactions, as well as metal and
Tersoff interactions are calculated using interpolation tables. These are generated in the following
routines: vdw generate, metal generate and tersoff generate.
6.1.4
Modifications for the Ewald Sum
For systems with periodic boundary conditions DL POLY 3 employs the Ewald Sum to calculate
the coulombic interactions (see Section
2.4.5
). It should be noted that DL POLY 3 uses only the
Smoothed Particle Mesh (SPME) form of the Ewald sum.
Calculation of the real space component in DL POLY 3 employs the algorithm for the calculation of
the non-bonded interactions outlined above, since the real space interactions are now short ranged
(implemented in ewald real forces routine).
The reciprocal space component is calculated using Fast Fourier Transform (FFT) scheme of the
SMPE method [
34
], Section
2.4.5
. The parallelisation of this scheme is entirely handled within the
DL POLY 3 by the 3D FFT routine parallel fft, which is known as the Daresbury Advanced
Fourier Transform, due to I.J. Bush [
46
]. This FFT distributes the SPME charge array over the
processors in a manner that is completely commensurate with the distribution of the configuration
data under the DD strategy. As a consequence the FFT handles all the necessary communication
implicit in a distributed SPME application. The DL POLY 3 subroutine ewald spme forces
perfoms the bulk of the FFT operations and charge array construction, while spme forces calcu-
lates the forces.
Other routines required to calculate the Ewald sum include ewald excl forces and
ewald frozen forces.
6.1.5
Metal Potentials
The simulation of metals (
2.3.2
) by DL POLY 3 makes use of density dependent potentials of
the Sutton-Chen type [
10
]. The dependence on the atomic density presents no difficulty however,
as this class of potentials can be resolved into pair contributions. This permits the use of the
distributed Verlet neighbour list as outlined above. DL POLY 3 implements these potentials in
various subroutines with names beginning with metal .
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