Treatment of Frozen Atoms, Rigid Body and Core-Shell Units

Frozen atoms, core-shell units and rigid body units are treated in a manner similar to that of the intra-molecular interactions due to their “by site” definition.

DL_POLY_4 allows for atoms to be completely immobilized ( i.e. “frozen” at a fixed 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 file. DL_POLY_4 does not calculate contributions to the virial or the stress tensor arising from the constraints required to freeze atomic positions. Neither does it calculate contributions from intra- and inter- molecular interactions between frozen atoms. As with the tethering potential, the reference position of a frozen site is scaled with the cell vectors in constant pressure simulations. In the case of frozen rigid bodies, their “centre of mass” is scaled with the cell vectors in constant pressure simulations and the positions of their constituent sites are then moved accordingly.

In DL_POLY_4 the frozen atom option is handled by the subroutine freeze_atoms.

The rigid body dynamics (see Section Rigid Bodies and Rotational Integration Algorithms) is resolved by solving the Eulerian equations of rotational motion. However, their statics includes calculation of the individual contributions of each RB’s centre of mass stress and virial due to the action of the resolved forces on sites/atoms constituting it. These contribute towards the total system stress and pressure.

As seen in Section Polarisation Shell Models core-shell units are dealt with (i) kinetically by the adiabatic shell model or (ii) statically by the dynamic shell model. Both contribute to the total system stress (pressure) but in different manner. The former does it via the kinetic stress (energy) and atomic stress (potential energy) due to the core-shell spring. The latter via atomic stress (potential energy) due to the shells move to minimised configuration.