430e7e962f
# Conflicts: # src/DIELECTRIC/Install.sh # src/DIELECTRIC/pppm_disp_dielectric.cpp # src/DIELECTRIC/pppm_disp_dielectric.h
43 lines
2.1 KiB
Plaintext
43 lines
2.1 KiB
Plaintext
This folder contains some example data and input scripts for the DIELECTRIC package. Please refer to the following reference for more details:
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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.
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- data.confined : two point opposite charges confined between two interfaces (epsilon1=2/epsilon2=10/epsilon2=2)
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- data.sphere : two point opposite charges outside a spherical interface (epsilon_in=1/epsilon2=10)
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- in.confined : read in data.confined
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- in.nopbc : read in data.* files, using non-periodic boundary conditions, with a large cutoff
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For "atom_style dielectric" the Atoms section in the data file contains 15 following columns:
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id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature
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where
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* id, mol, type, q, x, y and z are similar to those in atom_style full
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* normx, normy and normz are the three components of the normal unit vector
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of the interface at the boundary element (also called vertex, or patch).
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For real charges (ions), these 3 values are irrelevant,
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and can be anything (e.g. 0,0,1). normx, normy, and normz can be
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accessed through mux, muy and muz as if they were dipole components.
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* ed = dielectric difference at the vertex along the normal vector direction.
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For example, if (normx,normy,normz) points from medium with epsilon_in
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to medium with epsilon_out, then ed = epsilon_out - epsilon_in
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* em = (epsilon_out + epsilon_in)/2: the mean dielectric value
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* epsilon = the local epsilon value at the vertex or at the ion.
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For real charges, epsilon is the medium dielectric constant,
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and q is the real (unscaled) charges.
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For interface particles, epsilon is set to be em
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(the mean dielectric value above).
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* area_per_patch: the surface area of the patch (element).
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For real charges, this value is irrelevant, can be 1.0.
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* curvature: surface mean curvature at the patch.
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For example, for spherical interfaces, curvature = 1/spherical radius.
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For planar interfaces, curvature = 0.
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