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DIELECTRIC package doc and example updates

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ali
2022-10-10 10:54:50 -05:00
parent d834d5cc15
commit ba45678528
3 changed files with 11 additions and 14 deletions
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16
doc/src/fix_polarize.rst
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@ -72,16 +72,14 @@ coming from its area and surface charge density.
For non-interface particles such as atoms and charged particles,
the interface normal vectors, element area, and dielectric mismatch are
irrelevant. Their local dielectric value is used to rescale their given charge
when computing the Coulombic interactions. For instance, to simulate a cation
irrelevant and unused. Their local dielectric value is used internally to rescale their given
charge when computing the Coulombic interactions. For instance, to simulate a cation
carrying a charge of +2 (in simulation charge units) in an implicit solvent with
a dielectric constant of 40, the cation's charge should be set to +2/40 = +0.05 and
its local dielectric constant property (defined in the
:doc:`atom_style dielectric <atom_style>`) should be set to 40. This will produce
a dielectric constant of 40, the cation's charge should be set to +2 and
its local dielectric constant property (defined in the :doc:`atom_style dielectric <atom_style>`)
should be set to 40; there is no need to manually rescale charge. This will produce
the proper force for any :doc:`pair_style <pair_style>` with the dielectric suffix.
As noted in :doc:`pair_style <pair_dielectric>`, the charge (+0.05) will be scaled by the
local dielectric constant (40) to produce the appropriate charge (+2) during
force computation. It is assumed that the particles cannot pass through the interface
It is assumed that the particles cannot pass through the interface
during the simulation because the value of the local dielectric constant property
does not change.
@ -166,6 +164,8 @@ The *mr* keyword only applies to *style* = *polarize/bem/gmres*. It is the maxim
The *omega* keyword only applies when using *style* = *polarize/bem/icc*. It is a relaxation parameter defined in :ref:`(Tyagi) <Tyagi>` that should generally be set between 0 and 2.
Note that the local dielectric constant (epsilon) can also be set independently using the :doc:`set <set>` command.
----------
*polarize/bem/gmres* or *polarize/bem/icc* compute a global 2-element vector

7
doc/src/pair_dielectric.rst
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@ -77,15 +77,12 @@ Description
All these pair styles are derived from the corresponding pair styles
without the *dielectric* suffix. In addition to computing atom forces
and energies, these pair styles compute the electrical field vector
and energies, these pair styles compute the electric field vector
at each atom, which are intended to be used by the :doc:`fix polarize <fix_polarize>` commands
to compute induced charges at interfaces between two regions of different
dielectric constant.
These pair styles should be used with :doc:`atom_style dielectric <atom_style>`,
which uses atom charges rescaled by their local dielectric constant. See the note in
:doc:`fix polarize <fix_polarize>` about properly setting ion charge given a
local dielectric constant.
These pair styles should be used with :doc:`atom_style dielectric <atom_style>`.
The styles lj/cut/coul/long/dielectric, lj/cut/coul/msm/dielectric, and
lj/long/coul/long/dielectric should be used with their kspace style counterparts,

2
examples/PACKAGES/dielectric/in.confined
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@ -7,7 +7,7 @@
# Dielectric constants can be set to be different from the input data file
variable epsilon1 index 20
variable epsilon2 index 10 # must be the same as the local epsilon defined in data.confined
variable epsilon2 index 10
variable data index data.confined