This folder contains some example data and input scripts for the DIELECTRIC package. Please refer to the following reference for more details:
Nguyen TD, Li H, Bagchi D, Solis FJ, Olvera de la Cruz, Incorporating surface polarization effects into large-scale coarse-grained molecular dynamics simulation, Computer Physics Communications 2019, 241, 80--91.
- data.confined : two point opposite charges confined between two interfaces (epsilon1=2/epsilon2=10/epsilon2=2)
- data.sphere : two point opposite charges outside a spherical interface (epsilon_in=1/epsilon2=10)
- in.confined : read in data.confined
- in.nopbc : read in data.* files, using non-periodic boundary conditions, with a large cutoff
For "atom_style dielectric" the Atoms section in the data file contains 15 following columns:
id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature
where
* id, mol, type, q, x, y and z are similar to those in atom_style full
* normx, normy and normz are the three components of the normal unit vector
of the interface at the boundary element (also called vertex, or patch).
For real charges (ions), these 3 values are irrelevant,
and can be anything (e.g. 0,0,1). normx, normy, and normz can be
accessed through mux, muy and muz as if they were dipole components.
* ed = dielectric difference at the vertex along the normal vector direction.
For example, if (normx,normy,normz) points from medium with epsilon_in
to medium with epsilon_out, then ed = epsilon_out - epsilon_in
* em = (epsilon_out + epsilon_in)/2: the mean dielectric value
* epsilon = the local epsilon value at the vertex or at the ion.
For real charges, epsilon is the medium dielectric constant,
and q is the real (unscaled) charges.
For interface particles, epsilon is set to be em
(the mean dielectric value above).
* area_per_patch: the surface area of the patch (element).
For real charges, this value is irrelevant, can be 1.0.
* curvature: surface mean curvature at the patch.
For example, for spherical interfaces, curvature = 1/spherical radius.
For planar interfaces, curvature = 0.
