DL_POLY Quantum v1.0

DL_POLY quantum v1.0 is an extensively modified code based on the open-source DL_POLY classic v1.10 for large-scale long-time molecular dynamics simulations in condensed phases. This code is available to public through our GitHub repository.

Some of most significant modifications in DL_POLY quantum v1.0 are as following:

1. Implementing Nose-Hoover Chain (NHC) thermostat for classical simulations in canonical ensemble based on Suzuki-Yoshida scheme [1-3]. The thermodynamic control variables in the canonical ensemble are constant particle number N, constant volume V, and constant temperature T, which characterize a system in thermal contact with an infinite heat source [4]. Different thermostats were already available in DL_POLY classic for creating an NVT ensemble, including Nose-Hoover thermostat. However, Nose–Hoover equations fail when more than one conservation law is obeyed by the system, i.e., the equations of motion do not contain a sufficient number of variables in the extended phase space to offset the restrictions placed on the accessible phase space caused by multiple conservation laws [4]. Each conservation law restricts the accessible phase space by one dimension resulting in an unphysical distribution. In order to counterbalance this effect, more phase space dimensions must be introduced, which can be accomplished by introducing a chain of interconnected Nose-Hoover thermostats. In DL_POLY quantum, this is achieved through adding a subroutine called NVTVV_NHC in vv_motion_module.f which calls for subroutine NHC_part in integrator_module.f.

2. Implementing Nose-Hoover Chain thermostat/barostat for isothermal-isobaric ensemble through Martyna-Tobias-Klein (MTK) algorithm [5,6] for classical MD simulations. Experiments are more commonly performed at conditions of constant pressure P, rather than constant volume, hence the NPT NHC ensemble is also implemented in DL_POLY quantum v1.0. The canonical ensemble nevertheless forms the basis for the NPT ensemble. To maintain a fixed internal pressure, the volume of the system is allowed to fluctuate isotropically. This implementation is achieved through adding a subroutine called NPTVV_NHC in vv_motion_module.f which calls for two subroutines NHC_part and NHC_baro in integrator_module.f.

3. Implementing the four-site flexible quantum water potential model qTIP4P/f [8], both classical and PIMDsimulations. It is a fixed point charge model for liquid water in which the O–H stretches are described by Morse-type functions. Two positive charges of magnitude qM/2 are placed on the hydrogen atoms of each water molecule with a negative charge of −qM placed on a mass-less M-site located at point rM along the vector connecting the oxygen atom to the center of mass of the two hydrogens. Since qTIP4P/f model has been parameterized on the basis of quantum calculations, one might wonder whether it is appropriate to use this model in classical simulations. However, it has been already shown that the results of classical and quantum simulations of qTIP4P/f water are in reasonably close agreement owing to an approximate cancellation of inter- and intra-molecular quantum effects [7]. For comparison between classical and quantum dynamics simulations, two test cases are provided for bulk water. TEST42 uses qTIP4P/f water potential in classical molecular dynamics simulations and TEST45 uses it in Path Integral Molecular Dynamics (PIMD) simulations with 35 beads. A new module called water_module.f is added to DL_POLY quantum v1.0 which includes several subroutines needed for simulation of water dynamics. The input files should be changed accordingly, CONTROL file should contain keyword “qtip4pf”. In the CONFIG file, each water molecule should include M-site as the 4th atom with mass of zero. The FIELD file should use keyword “qmor” for O-H bonds as well as a new section called “voids” for DL_POLY quantum to exclude intramolecular interactions including M-site from the list of pairwise electrostatic interactions. 

4. Implementing a 12-6 Lennard-Jones as external potential for confinement simulations. Two Lennard-Jones walls are implemented in external_field_module.f at distances -Z and +Z. The initial configuration file should pack water molecules between -Z and +Z.

Note: The DL_POLY quantum project is ongoing with new implementations underway; a manual will be available in near future. For suggestions, feedbacks and questions please contact Dr. Farnaz Shakib at shakib@njit.edu. 

References

[1] Yoshida, H. Phys. Lett. A 1990, 150, 262.

[2] Suzuki, M. J. math. Phys. 1991, 32, 400.

[3] Martyna, G.J.; Tuckerman, M.E.; Tobias, D.J.; Klein, M.L. Molecular Physics 1996, 87, 1117.

[4] Tuckerman, M.E. Statistical Mechanics: Theory and Molecular Simulation, Oxford University Press, 2010.

[5] Martyna, G.J.; Tobias, D.J.; Klein, M.L. J. Chem. Phys. 1994, 101, 4177.

[6] Tuckerman, M.E.; Alejandre, J.; López-Rendón, R.; Jochim, A.L.; Martyna, G.J. J. Phys. A: Math. Gen. 2006, 39, 5629.

[7] Habershon, S.; Markland, T.E.; Manolopoulos, D.E. J. Chem. Phys. 2009, 131, 024501.