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Merge pull request #3040 from akohlmey/collected-small-changes

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Collected small changes and bugfixes
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Axel Kohlmeyer
2021-12-10 15:51:13 -05:00
committed by GitHub
parent fa8e2ccee8 6140503158
commit abd3df0c5a
37 changed files with 1333 additions and 641 deletions
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36
doc/src/pair_local_density.rst
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@ -26,23 +26,25 @@ Examples
Description
"""""""""""
The local density (LD) potential is a mean-field manybody potential, and, in some
sense,a generalization of embedded atom models (EAM). The name "local density
potential" arises from the fact that it assigns an energy to an atom depending
on the number of neighboring atoms of given type around it within a predefined
spherical volume (i.e., within a cutoff). The bottom-up coarse-graining (CG)
literature suggests that such potentials can be widely useful in capturing
effective multibody forces in a computationally efficient manner so as to
improve the quality of CG models of implicit solvation:ref:`(Sanyal1) <Sanyal1>` and
phase-segregation in liquid mixtures:ref:`(Sanyal2) <Sanyal2>`, and provide guidelines
to determine the extent of manybody correlations present in a CG
model.:ref:`(Rosenberger) <Rosenberger>` The LD potential in LAMMPS is primarily
intended to be used as a corrective potential over traditional pair potentials
in bottom-up CG models, i.e., as a hybrid pair style with
other explicit pair interaction terms (e.g., table spline, Lennard Jones, etc.).
Because the LD potential is not a pair potential per se, it is implemented
simply as a single auxiliary file with all specifications that will be read
upon initialization.
The local density (LD) potential is a mean-field manybody potential,
and, in some way, a generalization of embedded atom models (EAM). The
name "local density potential" arises from the fact that it assigns an
energy to an atom depending on the number of neighboring atoms of a
given type around it within a predefined spherical volume (i.e., within
the cutoff). The bottom-up coarse-graining (CG) literature suggests
that such potentials can be widely useful in capturing effective
multibody forces in a computationally efficient manner and thus improve
the quality of CG models of implicit solvation :ref:`(Sanyal1)
<Sanyal1>` and phase-segregation in liquid mixtures :ref:`(Sanyal2)
<Sanyal2>`, and provide guidelines to determine the extent of manybody
correlations present in a CG model :ref:`(Rosenberger) <Rosenberger>`.
The LD potential in LAMMPS is primarily intended to be used as a
corrective potential over traditional pair potentials in bottom-up CG
models via :doc:`hybrid/overlay pair style <pair_hybrid>` with other
explicit pair interaction terms (e.g., tabulated, Lennard-Jones, Morse
etc.). Because the LD potential is not a pair potential per se, it is
implemented simply as a single auxiliary file with all specifications
that will be read upon initialization.
.. note::

2
doc/src/pair_tersoff.rst
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@ -23,7 +23,7 @@ Syntax
pair_style style keywords values
* style = *tersoff* or *tersoff/table* or *tersoff/gpu* or *tersoff/omp* or *tersoff/table/omp*
* style = *tersoff* or *tersoff/table*
* keyword = *shift*
.. parsed-literal::

4
doc/src/pair_thole.rst
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@ -17,7 +17,7 @@ Syntax
pair_style style args
* style = *thole* or *lj/cut/thole/long* or *lj/cut/thole/long/omp*
* style = *thole* or *lj/cut/thole/long*
* args = list of arguments for a particular style
.. parsed-literal::
@ -25,7 +25,7 @@ Syntax
*thole* args = damp cutoff
damp = global damping parameter
cutoff = global cutoff (distance units)
*lj/cut/thole/long* or *lj/cut/thole/long/omp* args = damp cutoff (cutoff2)
*lj/cut/thole/long* args = damp cutoff (cutoff2)
damp = global damping parameter
cutoff = global cutoff for LJ (and Thole if only 1 arg) (distance units)
cutoff2 = global cutoff for Thole (optional) (distance units)

6
doc/src/pair_vashishta.rst
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@ -22,13 +22,13 @@ Syntax
pair_style style args
* style = *vashishta* or *vashishta/table* or *vashishta/omp* or *vashishta/table/omp*
* style = *vashishta* or *vashishta/table*
* args = list of arguments for a particular style
.. parsed-literal::
*vashishta* or *vashishta/omp* args = none
*vashishta/table* or *vashishta/table/omp* args = Ntable cutinner
*vashishta* args = none
*vashishta/table* args = Ntable cutinner
Ntable = # of tabulation points
cutinner = tablulate from cutinner to cutoff