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Merge pull request #2705 from akohlmey/collected-small-changes

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Collected small changes and fixes
This commit is contained in:
Axel Kohlmeyer
2021-04-16 17:07:39 -04:00
committed by GitHub
parent 9ea465f56a 7a97331e51
commit 4ed57cb757
87 changed files with 386 additions and 411 deletions
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8
doc/src/Build_extras.rst
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@ -1253,8 +1253,8 @@ be built for the most part with all major versions of the C++ language.
USER-PACE package
-----------------------------
This package requires a library that can be downloaded and built
in lib/pace or somewhere else, which must be done before building
This package requires a library that can be downloaded and built
in lib/pace or somewhere else, which must be done before building
LAMMPS with this package. The code for the library can be found
at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
@ -1276,8 +1276,8 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
.. tab:: Traditional make
You can download and build the USER-PACE library
in one step from the ``lammps/src`` dir, using these commands,
which invoke the ``lib/pace/Install.py`` script.
in one step from the ``lammps/src`` dir, using these commands,
which invoke the ``lib/pace/Install.py`` script.
.. code-block:: bash

125
doc/src/fix_qeq.rst
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@ -56,27 +56,28 @@ Examples
Description
"""""""""""
Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) <Rappe1>` and formulated in :ref:`(Nakano) <Nakano1>` (also known
as the matrix inversion method) and in :ref:`(Rick and Stuart) <Rick1>` (also
known as the extended Lagrangian method) based on the
electronegativity equilization principle.
Perform the charge equilibration (QEq) method as described in
:ref:`(Rappe and Goddard) <Rappe1>` and formulated in :ref:`(Nakano)
<Nakano1>` (also known as the matrix inversion method) and in
:ref:`(Rick and Stuart) <Rick1>` (also known as the extended Lagrangian
method) based on the electronegativity equilization principle.
These fixes can be used with any :doc:`pair style <pair_style>` in
LAMMPS, so long as per-atom charges are defined. The most typical
use-case is in conjunction with a :doc:`pair style <pair_style>` that
performs charge equilibration periodically (e.g. every timestep), such
as the ReaxFF or Streitz-Mintmire potential.
But these fixes can also be used with
potentials that normally assume per-atom charges are fixed, e.g. a
:doc:`Buckingham <pair_buck>` or :doc:`LJ/Coulombic <pair_lj>` potential.
as the ReaxFF or Streitz-Mintmire potential. But these fixes can also
be used with potentials that normally assume per-atom charges are fixed,
e.g. a :doc:`Buckingham <pair_buck>` or :doc:`LJ/Coulombic <pair_lj>`
potential.
Because the charge equilibration calculation is effectively
independent of the pair style, these fixes can also be used to perform
a one-time assignment of charges to atoms. For example, you could
define the QEq fix, perform a zero-timestep run via the :doc:`run <run>`
command without any pair style defined which would set per-atom
charges (based on the current atom configuration), then remove the fix
via the :doc:`unfix <unfix>` command before performing further dynamics.
Because the charge equilibration calculation is effectively independent
of the pair style, these fixes can also be used to perform a one-time
assignment of charges to atoms. For example, you could define the QEq
fix, perform a zero-timestep run via the :doc:`run <run>` command
without any pair style defined which would set per-atom charges (based
on the current atom configuration), then remove the fix via the
:doc:`unfix <unfix>` command before performing further dynamics.
.. note::
@ -87,11 +88,14 @@ via the :doc:`unfix <unfix>` command before performing further dynamics.
.. note::
The :doc:`fix qeq/comb <fix_qeq_comb>` command must still be used
to perform charge equilibration with the :doc:`COMB potential <pair_comb>`. The :doc:`fix qeq/reax <fix_qeq_reax>`
command can be used to perform charge equilibration with the :doc:`ReaxFF force field <pair_reaxc>`, although fix qeq/shielded yields the
same results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance*
are the same. Eventually the fix qeq/reax command will be deprecated.
The :doc:`fix qeq/comb <fix_qeq_comb>` command must still be used to
perform charge equilibration with the :doc:`COMB potential
<pair_comb>`. The :doc:`fix qeq/reax <fix_qeq_reax>` command can be
used to perform charge equilibration with the :doc:`ReaxFF force
field <pair_reaxc>`, although fix qeq/shielded yields the same
results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance*
are the same. Eventually the fix qeq/reax command will be
deprecated.
The QEq method minimizes the electrostatic energy of the system (or
equalizes the derivative of energy with respect to charge of all the
@ -134,55 +138,57 @@ usually a good number.
The *qeq/shielded* style describes partial charges on atoms also as
point charges, but uses a shielded Coulomb potential to describe the
interaction between a pair of charged particles. Interaction through
the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force field <vanDuin>` paper. The shielding accounts for charge overlap
the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force
field <vanDuin>` paper. The shielding accounts for charge overlap
between charged particles at small separation. This style is the same
as :doc:`fix qeq/reax <fix_qeq_reax>`, and can be used with :doc:`pair_style reax/c <pair_reaxc>`. Only the *chi*\ , *eta*\ , and *gamma*
parameters from the *qfile* file are used. When using the string
*reax/c* as filename, these parameters are extracted directly from
an active *reax/c* pair style. This style solves partial
charges on atoms via the matrix inversion method. A tolerance of
1.0e-6 is usually a good number.
as :doc:`fix qeq/reax <fix_qeq_reax>`, and can be used with
:doc:`pair_style reax/c <pair_reaxc>`. Only the *chi*\ , *eta*\ , and
*gamma* parameters from the *qfile* file are used. When using the string
*reax/c* as filename, these parameters are extracted directly from an
active *reax/c* pair style. This style solves partial charges on atoms
via the matrix inversion method. A tolerance of 1.0e-6 is usually a
good number.
The *qeq/slater* style describes partial charges on atoms as spherical
charge densities centered around atoms via the Slater 1\ *s* orbital, so
that the interaction between a pair of charged particles is the
product of two Slater 1\ *s* orbitals. The expression for the Slater
1\ *s* orbital is given under equation (6) of the
:ref:`Streitz-Mintmire <Streitz1>` paper. Only the *chi*\ , *eta*\ , *zeta*\ , and
*qcore* parameters from the *qfile* file are used. When using the string
that the interaction between a pair of charged particles is the product
of two Slater 1\ *s* orbitals. The expression for the Slater 1\ *s*
orbital is given under equation (6) of the :ref:`Streitz-Mintmire
<Streitz1>` paper. Only the *chi*\ , *eta*\ , *zeta*\ , and *qcore*
parameters from the *qfile* file are used. When using the string
*coul/streitz* as filename, these parameters are extracted directly from
an active *coul/streitz* pair style. This style solves
partial charges on atoms via the matrix inversion method. A tolerance
of 1.0e-6 is usually a good number. Keyword *alpha* can be used to
change the Slater type orbital exponent.
an active *coul/streitz* pair style. This style solves partial charges
on atoms via the matrix inversion method. A tolerance of 1.0e-6 is
usually a good number. Keyword *alpha* can be used to change the Slater
type orbital exponent.
The *qeq/dynamic* style describes partial charges on atoms as point
charges that interact through 1/r, but the extended Lagrangian method
is used to solve partial charges on atoms. Only the *chi* and *eta*
charges that interact through 1/r, but the extended Lagrangian method is
used to solve partial charges on atoms. Only the *chi* and *eta*
parameters from the *qfile* file are used. Note that Coulomb
catastrophe can occur if repulsion between the pair of charged
particles is too weak. A tolerance of 1.0e-3 is usually a good
number. Keyword *qdamp* can be used to change the damping factor, while
keyword *qstep* can be used to change the time step size.
catastrophe can occur if repulsion between the pair of charged particles
is too weak. A tolerance of 1.0e-3 is usually a good number. Keyword
*qdamp* can be used to change the damping factor, while keyword *qstep*
can be used to change the time step size.
The :ref:`\ *qeq/fire*\ <Shan>` style describes the same charge model and charge
solver as the *qeq/dynamic* style, but employs a FIRE minimization
algorithm to solve for equilibrium charges.
Keyword *qdamp* can be used to change the damping factor, while
keyword *qstep* can be used to change the time step size.
The :ref:`\ *qeq/fire*\ <Shan>` style describes the same charge model
and charge solver as the *qeq/dynamic* style, but employs a FIRE
minimization algorithm to solve for equilibrium charges. Keyword
*qdamp* can be used to change the damping factor, while keyword *qstep*
can be used to change the time step size.
Note that *qeq/point*\ , *qeq/shielded*\ , and *qeq/slater* describe
different charge models, whereas the matrix inversion method and the
extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are
different solvers.
Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all describe
charges as point charges that interact through 1/r relationship, but
solve partial charges on atoms using different solvers. These three
styles should yield comparable results if
the QEq parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the
same. Style *qeq/point* is typically faster, *qeq/dynamic* scales
better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all
describe charges as point charges that interact through 1/r
relationship, but solve partial charges on atoms using different
solvers. These three styles should yield comparable results if the QEq
parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the same.
Style *qeq/point* is typically faster, *qeq/dynamic* scales better on
larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
.. note::
@ -200,9 +206,11 @@ better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about these fixes is written to :doc:`binary restart files <restart>`. No global scalar or vector or per-atom
quantities are stored by these fixes for access by various :doc:`output commands <Howto_output>`. No parameter of these fixes can be used
with the *start/stop* keywords of the :doc:`run <run>` command.
No information about these fixes is written to :doc:`binary restart
files <restart>`. No global scalar or vector or per-atom quantities are
stored by these fixes for access by various :doc:`output commands
<Howto_output>`. No parameter of these fixes can be used with the
*start/stop* keywords of the :doc:`run <run>` command.
Thexe fixes are invoked during :doc:`energy minimization <minimize>`.
@ -210,7 +218,8 @@ Restrictions
""""""""""""
These fixes are part of the QEQ package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
Related commands
""""""""""""""""