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whitespace fixes

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This commit is contained in:
Axel Kohlmeyer
2022-10-10 15:26:40 -04:00
parent ba45678528
commit aea3421311
2 changed files with 21 additions and 21 deletions
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16
doc/src/atom_style.rst
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@ -181,19 +181,19 @@ with its orientation.
For the *dielectric* style, each particle can be either a physical
particle (e.g. an ion), or an interface particle representing a boundary
element between two regions of different dielectric constant. For
element between two regions of different dielectric constant. For
interface particles, in addition to the properties associated with
atom_style full, each particle also should be assigned a normal unit vector
(defined by normx, normy, normz), an area (area_per_patch), the difference and
mean of the dielectric constants of two sides of the interface along the
atom_style full, each particle also should be assigned a normal unit vector
(defined by normx, normy, normz), an area (area_per_patch), the difference and
mean of the dielectric constants of two sides of the interface along the
direction of the normal vector (ed and em), the local dielectric constant at the
boundary element (epsilon), and a mean local curvature (curv).
Physical particles must be assigned these values, as well,
but only their local dielectric constants will be used; see documentation for
boundary element (epsilon), and a mean local curvature (curv).
Physical particles must be assigned these values, as well,
but only their local dielectric constants will be used; see documentation for
associated :doc:`pair styles <pair_dielectric>` and :doc:`fixes <fix_polarize>`.
The distinction between the physical and interface
particles is only meaningful when :doc:`fix polarize <fix_polarize>`
commands are applied to the interface particles. This style is part of the
commands are applied to the interface particles. This style is part of the
DIELECTRIC package.
For the *dipole* style, a point dipole is defined for each point

26
doc/src/fix_polarize.rst
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@ -16,7 +16,7 @@ Syntax
.. parsed-literal::
fix ID group-ID style nevery tolerance
fix ID group-ID style nevery tolerance
* ID, group-ID are documented in :doc:`fix <fix>` command
* style = *polarize/bem/gmres* or *polarize/bem/icc* or *polarize/functional*
@ -72,15 +72,15 @@ 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 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 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.
It is assumed that the particles cannot pass through the interface
during the simulation because the value of the local dielectric constant property
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 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.
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.
There are some example scripts for using these fixes
@ -131,7 +131,7 @@ Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to :doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` command provides the ability to modify certain
The :doc:`fix_modify <fix_modify>` command provides the ability to modify certain
settings:
.. parsed-literal::
@ -148,7 +148,7 @@ settings:
max = range of random induced charges to be generated
seed = random number seed to use when generating random charge
*mr* arg
arg = maximum number of q-vectors to use when solving (GMRES only)
arg = maximum number of q-vectors to use when solving (GMRES only)
*omega* arg
arg = relaxation parameter to use when iterating (ICC only)
@ -164,7 +164,7 @@ 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.
Note that the local dielectric constant (epsilon) can also be set independently using the :doc:`set <set>` command.
----------