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Improve qtpie/reaxff docs and add qeqr/reaxff docs

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Navraj Lalli
2025-03-20 13:19:50 +00:00
parent e11245d0fd
commit 2e98ae9de9
7 changed files with 238 additions and 16 deletions
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1
doc/src/Commands_fix.rst
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@ -186,6 +186,7 @@ OPT.
* :doc:`qeq/fire <fix_qeq>`
* :doc:`qeq/point <fix_qeq>`
* :doc:`qeq/reaxff (ko) <fix_qeq_reaxff>`
* :doc:`qeqr/reaxff <fix_qeqr_reaxff>`
* :doc:`qeq/shielded <fix_qeq>`
* :doc:`qeq/slater <fix_qeq>`
* :doc:`qmmm <fix_qmmm>`

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doc/src/fix.rst
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@ -365,6 +365,7 @@ accelerated styles exist.
* :doc:`qeq/fire <fix_qeq>` - charge equilibration via FIRE minimizer
* :doc:`qeq/point <fix_qeq>` - charge equilibration via point method
* :doc:`qeq/reaxff <fix_qeq_reaxff>` - charge equilibration for ReaxFF potential
* :doc:`qeqr/reaxff <fix_qeqr_reaxff>` - charge equilibration for ReaxFF potential with alternate efield implementation
* :doc:`qeq/shielded <fix_qeq>` - charge equilibration via shielded method
* :doc:`qeq/slater <fix_qeq>` - charge equilibration via Slater method
* :doc:`qmmm <fix_qmmm>` - functionality to enable a quantum mechanics/molecular mechanics coupling

2
doc/src/fix_acks2_reaxff.rst
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@ -124,7 +124,7 @@ Related commands
""""""""""""""""
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
:doc:`fix qtpi/reaxff <fix_qtpie_reaxff>`
:doc:`fix qtpie/reaxff <fix_qtpie_reaxff>`, :doc:`fix qeqr/reaxff <fix_qeqr_reaxff>`
Default
"""""""

5
doc/src/fix_qeq_reaxff.rst
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@ -59,7 +59,7 @@ extracted from the :doc:`pair_style reaxff <pair_reaxff>` command and
the ReaxFF force field file it reads in. If a file name is specified
for *params*, then the parameters are taken from the specified file
and the file must contain one line for each atom type. The latter
form must be used when performing QeQ with a non-ReaxFF potential.
form must be used when performing QEq with a non-ReaxFF potential.
Each line should be formatted as follows:
.. parsed-literal::
@ -140,7 +140,8 @@ Related commands
""""""""""""""""
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/shielded <fix_qeq>`,
:doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix qtpie/reaxff <fix_qtpie_reaxff>`
:doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix qtpie/reaxff <fix_qtpie_reaxff>`,
:doc:`fix qeqr/reaxff <fix_qeqr_reaxff>`
Default
"""""""

198
doc/src/fix_qeqr_reaxff.rst Normal file
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@ -0,0 +1,198 @@
.. index:: fix qeqr/reaxff
fix qeqr/reaxff command
========================
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID qeqr/reaxff Nevery cutlo cuthi tolerance params gfile args
* ID, group-ID are documented in :doc:`fix <fix>` command
* qeqr/reaxff = style name of this fix command
* Nevery = perform QEqR every this many steps
* cutlo,cuthi = lo and hi cutoff for Taper radius
* tolerance = precision to which charges will be equilibrated
* params = reaxff or a filename
* gfile = the name of a file containing Gaussian orbital exponents
* one or more keywords or keyword/value pairs may be appended
.. parsed-literal::
keyword = *scale* or *maxiter* or *nowarn*
*scale* beta = set value of scaling factor *beta* (determines strength of electric polarization)
*maxiter* N = limit the number of iterations to *N*
*nowarn* = do not print a warning message if the maximum number of iterations is reached
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all qeqr/reaxff 1 0.0 10.0 1.0e-6 reaxff exp.qeqr
fix 1 all qeqr/reaxff 1 0.0 10.0 1.0e-6 params.qeqr exp.qeqr scale 1.5 maxiter 500 nowarn
Description
"""""""""""
.. versionadded:: 19Nov2024
This fix implements QEqR, which only differs from the QEq charge equilibration
method :ref:`(Rappe and Goddard) <Rappe4>` in how external electric fields
are accounted for. This fix therefore raises a warning when used without
:doc:`fix efield <fix_efield>` informing the user to use
:doc:`fix qeq/reaxff <fix_qeq_reaxff>` instead since
:doc:`fix qeq/reaxff <fix_qeq_reaxff>`
leads to the same charges at slightly reduced computational cost. Charges are
computed with QEqR by minimizing the electrostatic energy of the system in the
same way as the QEq method but where the absolute electronegativity,
:math:`\chi_i`, of each atom in the QEq method is replaced with an effective
electronegativity given by
.. math::
\chi_{\mathrm{r}i} = \chi_i + \frac{\sum_{j=1}^{N} \beta(\phi_i - \phi_j) S_{ij}}
{\sum_{m=1}^{N}S_{im}},
where :math:`N` is the number of atoms in the system, :math:`\beta` is a scaling
factor, :math:`\phi_i` and :math:`\phi_j` are the electric potentials at the
positions of atoms :math:`i` and :math:`j` due to the external electric field
and :math:`S_{ij}` is the overlap integral between atoms :math:`i` and :math:`j`.
This formulation is advantageous over the method used by
:doc:`fix qeq/reaxff <fix_qeq_reaxff>` to account for an external electric
field in that it permits periodic boundaries in the direction of an external
electric field and in that it does not worsen long-range charge transfer seen
with QEq.
This fix is typically used in conjunction with the ReaxFF force
field model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
command, but it can be used with any potential in LAMMPS, so long as it
defines and uses charges on each atom. For more technical details about the
charge equilibration performed by `fix qeqr/reaxff`, which is the same as in
:doc:`fix qeq/reaxff <fix_qeq_reaxff>` except for the use of
:math:`\chi_{\mathrm{r}i}`, please refer to :ref:`(Aktulga) <qeq-Aktulga3>`.
To be explicit, `fix qeqr/reaxff` replaces :math:`\chi_k` of eq. 3 in
:ref:`(Aktulga) <qeq-Aktulga3>` with :math:`\chi_{\mathrm{r}k}` when an
external electric field is applied.
This fix requires the absolute electronegativity, :math:`\chi`, in eV, the
self-Coulomb potential, :math:`\eta`, in eV, and the shielded Coulomb
constant, :math:`\gamma`, in :math:`\AA^{-1}`. If the *params* setting above
is the word "reaxff", then these are extracted from the
:doc:`pair_style reaxff <pair_reaxff>` command and the ReaxFF force field
file it reads in. If a file name is specified for *params*, then the
parameters are taken from the specified file and the file must contain
one line for each atom type. The latter form must be used when using this
fix with a non-ReaxFF potential. Each line should be formatted as follows,
ensuring that the parameters are given in units of eV, eV, and :math:`\AA^{-1}`,
respectively:
.. parsed-literal::
itype chi eta gamma
where *itype* is the atom type from 1 to Ntypes. Note that eta is
defined here as twice the eta value in the ReaxFF file.
The overlap integrals :math:`S_{ij}`
are computed by using normalized 1s Gaussian type orbitals. The Gaussian
orbital exponents, :math:`\alpha`, that are needed to compute the overlap
integrals are taken from the file given by *gfile*.
This file must contain one line for each atom type and provide the Gaussian
orbital exponent for each atom type in units of inverse square Bohr radius.
Each line should be formatted as follows:
.. parsed-literal::
itype alpha
Empty lines or any text following the pound sign (#) are ignored. An example
*gfile* for a system with two atom types is
.. parsed-literal::
# An example gfile. Exponents are taken from Table 2.2 of Chen, J. (2009).
# Theory and applications of fluctuating-charge models.
# The units of the exponents are 1 / (Bohr radius)^2 .
1 0.2240 # O
2 0.5434 # H
The optional *scale* keyword sets the value of :math:`\beta` in the equation for
:math:`\chi_{\mathrm{r}i}`. The default value is 1.0.
The optional *maxiter* keyword allows changing the max number
of iterations in the linear solver. The default value is 200.
The optional *nowarn* keyword silences the warning message printed
when the maximum number of iterations is reached. This can be
useful for comparing serial and parallel results where having the
same fixed number of iterations is desired, which can be achieved
by using a very small tolerance and setting *maxiter* to the desired
number of iterations.
.. note::
In order to solve the self-consistent equations for electronegativity
equalization, LAMMPS imposes the additional constraint that all the
charges in the fix group must add up to zero. The initial charge
assignments should also satisfy this constraint. LAMMPS will print a
warning if that is not the case.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files
<restart>`. This fix computes a global scalar (the number of
iterations) and a per-atom vector (the effective electronegativity), which
can be accessed by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
This fix is invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the REAXFF package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This fix does not correctly handle interactions involving multiple
periodic images of the same atom. Hence, it should not be used for
periodic cell dimensions smaller than the non-bonded cutoff radius,
which is typically :math:`10~\AA` for ReaxFF simulations.
This fix may be used in combination with :doc:`fix efield <fix_efield>`
and will apply the external electric field during charge equilibration,
but there may be only one fix efield instance used and the electric field
must be applied to all atoms in the system. Consequently, `fix efield` must
be used with *group-ID* all and must not be used with the keyword *region*.
Equal-style variables can be used for electric field vector
components without any further settings. Atom-style variables can be used
for spatially-varying electric field vector components, but the resulting
electric potential must be specified as an atom-style variable using
the *potential* keyword for `fix efield`.
Related commands
""""""""""""""""
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
:doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix qtpie/reaxff <fix_qtpie_reaxff>`
Default
"""""""
scale = 1.0 and maxiter = 200
----------
.. _Rappe4:
**(Rappe)** Rappe and Goddard III, Journal of Physical Chemistry, 95,
3358-3363 (1991).
.. _qeq-Aktulga3:
**(Aktulga)** Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
245-259 (2012).

42
doc/src/fix_qtpie_reaxff.rst
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@ -21,8 +21,10 @@ Syntax
.. parsed-literal::
keyword = *maxiter*
keyword = *scale* or *maxiter* or *nowarn*
*scale* beta = set value of scaling factor *beta* (determines strength of electric polarization)
*maxiter* N = limit the number of iterations to *N*
*nowarn* = do not print a warning message if the maximum number of iterations is reached
Examples
""""""""
@ -30,7 +32,7 @@ Examples
.. code-block:: LAMMPS
fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 reaxff exp.qtpie
fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 params.qtpie exp.qtpie maxiter 500
fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 params.qtpie exp.qtpie scale 1.5 maxiter 500 nowarn
Description
"""""""""""
@ -46,7 +48,7 @@ same way as the QEq method but where the absolute electronegativity,
electronegativity given by :ref:`(Chen) <qtpie-Chen>`
.. math::
\chi_{\mathrm{eff},i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j) S_{ij}}
\tilde{\chi}_{i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j) S_{ij}}
{\sum_{m=1}^{N}S_{im}},
which acts to penalize long-range charge transfer seen with the QEq charge
@ -61,11 +63,11 @@ electric field by using the effective electronegativity given in
:ref:`(Gergs) <Gergs>`:
.. math::
\chi_{\mathrm{eff},i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j + \phi_i - \phi_j) S_{ij}}
\tilde{\chi}_{\mathrm{r}i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j + \beta(\phi_i - \phi_j)) S_{ij}}
{\sum_{m=1}^{N}S_{im}},
where :math:`\phi_i` and :math:`\phi_j` are the electric
potentials at the positions of atom :math:`i` and :math:`j`
where :math:`\beta` is a scaling factor and :math:`\phi_i` and :math:`\phi_j`
are the electric potentials at the positions of atoms :math:`i` and :math:`j`
due to the external electric field.
This fix is typically used in conjunction with the ReaxFF force
@ -74,9 +76,12 @@ command, but it can be used with any potential in LAMMPS, so long as it
defines and uses charges on each atom. For more technical details about the
charge equilibration performed by `fix qtpie/reaxff`, which is the same as in
:doc:`fix qeq/reaxff <fix_qeq_reaxff>` except for the use of
:math:`\chi_{\mathrm{eff},i}`, please refer to :ref:`(Aktulga) <qeq-Aktulga2>`.
:math:`\tilde{\chi}_{i}` or :math:`\tilde{\chi}_{\mathrm{r}i}`,
please refer to :ref:`(Aktulga) <qeq-Aktulga2>`.
To be explicit, this fix replaces :math:`\chi_k` of eq. 3 in
:ref:`(Aktulga) <qeq-Aktulga2>` with :math:`\chi_{\mathrm{eff},k}`.
:ref:`(Aktulga) <qeq-Aktulga2>` with :math:`\tilde{\chi}_{k}` when no external
electric field is applied and with :math:`\tilde{\chi}_{\mathrm{r}k}` when an
external electric field is applied.
This fix requires the absolute electronegativity, :math:`\chi`, in eV, the
self-Coulomb potential, :math:`\eta`, in eV, and the shielded Coulomb
@ -97,7 +102,7 @@ respectively:
where *itype* is the atom type from 1 to Ntypes. Note that eta is
defined here as twice the eta value in the ReaxFF file.
The overlap integrals in the equation for :math:`\chi_{\mathrm{eff},i}`
The overlap integrals :math:`S_{ij}`
are computed by using normalized 1s Gaussian type orbitals. The Gaussian
orbital exponents, :math:`\alpha`, that are needed to compute the overlap
integrals are taken from the file given by *gfile*.
@ -120,15 +125,26 @@ Empty lines or any text following the pound sign (#) are ignored. An example
1 0.2240 # O
2 0.5434 # H
The optional *scale* keyword sets the value of :math:`\beta` in the equation for
:math:`\tilde{\chi}_{\mathrm{r}i}`. This keyword only affects the computed charges
when :doc:`fix efield <fix_efield>` is used. The default value is 1.0.
The optional *maxiter* keyword allows changing the max number
of iterations in the linear solver. The default value is 200.
The optional *nowarn* keyword silences the warning message printed
when the maximum number of iterations is reached. This can be
useful for comparing serial and parallel results where having the
same fixed number of iterations is desired, which can be achieved
by using a very small tolerance and setting *maxiter* to the desired
number of iterations.
.. note::
In order to solve the self-consistent equations for electronegativity
equalization, LAMMPS imposes the additional constraint that all the
charges in the fix group must add up to zero. The initial charge
assignments should also satisfy this constraint. LAMMPS will print a
charges in the fix group must add up to zero. The initial charge
assignments should also satisfy this constraint. LAMMPS will print a
warning if that is not the case.
Restart, fix_modify, output, run start/stop, minimize info
@ -170,12 +186,12 @@ Related commands
""""""""""""""""
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
:doc:`fix acks2/reaxff <fix_acks2_reaxff>`
:doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix qeqr/reaxff <fix_qeqr_reaxff>`
Default
"""""""
maxiter 200
scale = 1.0 and maxiter = 200
----------

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doc/utils/sphinx-config/false_positives.txt
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@ -725,6 +725,7 @@ dashpot
dat
datafile
datatype
dataset
datums
Davidchack
Daw
@ -856,6 +857,7 @@ DNi
Dobnikar
Dobson
docenv
docstring
Dodds
dodgerblue
dof
@ -3116,9 +3118,11 @@ qE
qeff
qelectron
qeq
qeqr
Qamar
QeQ
QEq
QEqR
qfactor
qfile
qi
@ -3261,6 +3265,7 @@ resquared
REsquared
restartfile
restartinfo
reStructuredText
Restrepo
rethrowing
Revenga