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.