dstelter92 / polir-lammps

polarizible water potential optimized for IR spectroscopy in LAMMPS

POLIR-lammps

polarizible water potential optimized for IR spectroscopy in LAMMPS

Please cite:

Mankoo, P. K., & Keyes, T. (2008). POLIR: Polarizable, flexible, transferable water potential optimized for IR spectroscopy. Journal of Chemical Physics, 129(3). https://doi.org/10.1063/1.2948966

WARNING!

This code is an unfinished WIP and is not guarenteed to work. Updates will be put here as they happen.

6/5/18 - Initial Commit, only Bond & Pair potential implemented.

6/19/18 - POLIR fix started, only thole smearing and bond-length dependent charges are implemented

Install

git clone https://github.com/dstelter92/POLIR-lammps.git
cp POLIR-lammps/src/* /path/to/lammps/src/

then re-compile LAMMPS.

src/

fix_polir is the main fix associated with POLIR. It (will) handle computation of the induced dipole loop as well as hooks to all the needed helper-computes

compute_polir_charge_atom (polir/charge/atom) computes the bond-length dependent charges on each atom, currently this part of the code is the limitation for 1 MPI rank. Custom communication is needed

compute_polir_tholer_local (polir/thole/local) computes the pairwise thole-smear charge damping coeffs for each atom pair and charge-charge, charge-dipole, or dipole-dipole interaction

pair_polir_vdw (polir/vdw) is the pairwise O-O potential to attract waters, all other nonbonded interactions are electrostatic

O-H bond potential uses a 'table' style, see bond/table for details. The tabulated file is found in the examples directory as "PS_bond_potential.table"

To-Do list:

• Implement electrostatics with Thole damping as fix
• Implement electrostatics with MPI
• Test against previous work

Issues:

Currently only works with 1 MPI rank.

polir-lammps's Issues

Monomer starting conditions have incorrect charge on O

The O in 1wat.data has a charge of .84 instead of -.84.

Per-atom charge isn't calculated for all atoms

need to re-write compute/polir/charge/atom to get all the hydrogen charges, should be a simple fix for later

No MPI with compute/polir/charge/atom

Only works on 1 proc, MPI_Allreduce call for charges on all hydrogens still results in missing info on each proc.