rename fix qeqr/reaxff to fix qeq/rel/reaxff
This commit is contained in:
Axel Kohlmeyer
@ -186,7 +186,7 @@ OPT.
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* :doc:`qeq/fire <fix_qeq>`
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* :doc:`qeq/point <fix_qeq>`
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* :doc:`qeq/reaxff (ko) <fix_qeq_reaxff>`
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* :doc:`qeqr/reaxff <fix_qeqr_reaxff>`
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* :doc:`qeq/rel/reaxff <fix_qeq_rel_reaxff>`
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* :doc:`qeq/shielded <fix_qeq>`
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* :doc:`qeq/slater <fix_qeq>`
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* :doc:`qmmm <fix_qmmm>`
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@ -365,7 +365,7 @@ accelerated styles exist.
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* :doc:`qeq/fire <fix_qeq>` - charge equilibration via FIRE minimizer
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* :doc:`qeq/point <fix_qeq>` - charge equilibration via point method
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* :doc:`qeq/reaxff <fix_qeq_reaxff>` - charge equilibration for ReaxFF potential
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* :doc:`qeqr/reaxff <fix_qeqr_reaxff>` - charge equilibration for ReaxFF potential with alternate efield implementation
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* :doc:`qeq/rel/reaxff <fix_qeq_rel_reaxff>` - charge equilibration for ReaxFF potential with alternate efield implementation
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* :doc:`qeq/shielded <fix_qeq>` - charge equilibration via shielded method
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* :doc:`qeq/slater <fix_qeq>` - charge equilibration via Slater method
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* :doc:`qmmm <fix_qmmm>` - functionality to enable a quantum mechanics/molecular mechanics coupling
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@ -123,8 +123,10 @@ components in non-periodic directions.
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Related commands
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""""""""""""""""
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:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
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:doc:`fix qtpie/reaxff <fix_qtpie_reaxff>`, :doc:`fix qeqr/reaxff <fix_qeqr_reaxff>`
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:doc:`pair_style reaxff <pair_reaxff>`,
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:doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
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:doc:`fix qtpie/reaxff <fix_qtpie_reaxff>`,
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:doc:`fix qeq/rel/reaxff <fix_qeq_rel_reaxff>`
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Default
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"""""""
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@ -141,7 +141,7 @@ Related commands
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:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/shielded <fix_qeq>`,
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:doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix qtpie/reaxff <fix_qtpie_reaxff>`,
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:doc:`fix qeqr/reaxff <fix_qeqr_reaxff>`
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:doc:`fix qeq/rel/reaxff <fix_qeq_rel_reaxff>`
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Default
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"""""""
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195
doc/src/fix_qeq_rel_reaxff.rst
Normal file
195
doc/src/fix_qeq_rel_reaxff.rst
Normal file
@ -0,0 +1,195 @@
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.. index:: fix qaq/rel/reaxff
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fix qeq/rel/reaxff command
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==========================
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Syntax
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""""""
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.. code-block:: LAMMPS
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fix ID group-ID qeq/rel/reaxff Nevery cutlo cuthi tolerance params gfile args
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* qeq/rel/reaxff = style name of this fix command
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* Nevery = perform QEqR every this many steps
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* cutlo,cuthi = lo and hi cutoff for Taper radius
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* tolerance = precision to which charges will be equilibrated
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* params = reaxff or a filename
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* gfile = the name of a file containing Gaussian orbital exponents
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* one or more keywords or keyword/value pairs may be appended
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|
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.. parsed-literal::
|
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|
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keyword = *scale* or *maxiter* or *nowarn*
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*scale* beta = set value of scaling factor *beta* (determines strength of electric polarization)
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*maxiter* N = limit the number of iterations to *N*
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*nowarn* = do not print a warning message if the maximum number of iterations is reached
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all qeq/rel/reaxff 1 0.0 10.0 1.0e-6 reaxff exp.qeqr
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fix 1 all qeq/rel/reaxff 1 0.0 10.0 1.0e-6 params.qeqr exp.qeqr scale 1.5 maxiter 500 nowarn
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Description
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"""""""""""
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.. versionadded:: 19Nov2024
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This fix implements the QEqR method for charge equilibration, which
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differs from the QEq charge equilibration method :ref:`(Rappe and
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Goddard) <Rappe4>` only in how external electric fields are accounted
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for. This fix therefore raises a warning when used without :doc:`fix
|
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efield <fix_efield>` since :doc:`fix qeq/reaxff <fix_qeq_reaxff>` should
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be used without an external electric field. Charges are computed with
|
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the QEqR method by minimizing the electrostatic energy of the system in
|
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the same way as the QEq method but where the absolute electronegativity,
|
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:math:`\chi_i`, of each atom in the QEq method is replaced with an
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effective electronegativity given by
|
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.. math::
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\chi_{\mathrm{r}i} = \chi_i + \frac{\sum_{j=1}^{N} \beta(\phi_i - \phi_j) S_{ij}}
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{\sum_{m=1}^{N}S_{im}},
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where :math:`N` is the number of atoms in the system, :math:`\beta` is a
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scaling factor, :math:`\phi_i` and :math:`\phi_j` are the electric
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potentials at the positions of atoms :math:`i` and :math:`j` due to the
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external electric field and :math:`S_{ij}` is the overlap integral
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between atoms :math:`i` and :math:`j`. This formulation is advantageous
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over the method used by :doc:`fix qeq/reaxff <fix_qeq_reaxff>` to
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account for an external electric field in that it permits periodic
|
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boundaries in the direction of an external electric field and in that it
|
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does not worsen long-range charge transfer seen with QEq.
|
||||
|
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This fix is typically used in conjunction with the ReaxFF force field
|
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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
|
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defines and uses charges on each atom. For more technical details about
|
||||
the charge equilibration performed by *fix qeq/rel/reaxff*, which is the
|
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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)
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<qeq-Aktulga3>`. To be explicit, *fix qeq/rel/reaxff* replaces
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:math:`\chi_k` of eq. 3 in :ref:`(Aktulga) <qeq-Aktulga3>` with
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:math:`\chi_{\mathrm{r}k}` when an external electric field is applied.
|
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This fix requires the absolute electronegativity, :math:`\chi`, in eV,
|
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the self-Coulomb potential, :math:`\eta`, in eV, and the shielded
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||||
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
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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
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||||
|
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Empty lines or any text following the pound sign (#) are ignored. An
|
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example *gfile* for a system with two atom types is
|
||||
|
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.. parsed-literal::
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||||
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# An example gfile. Exponents are taken from Table 2.2 of Chen, J. (2009).
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# Theory and applications of fluctuating-charge models.
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# The units of the exponents are 1 / (Bohr radius)^2 .
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1 0.2240 # O
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2 0.5434 # H
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The optional *scale* keyword sets the value of :math:`\beta` in the
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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
|
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<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
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||||
<Build_package>` page for more info.
|
||||
|
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This fix does not correctly handle interactions involving multiple
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periodic images of the same atom. Hence, it should not be used for
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periodic cell dimensions smaller than the non-bonded cutoff radius,
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which is typically :math:`10~\AA` for ReaxFF simulations.
|
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This fix may be used in combination with :doc:`fix efield <fix_efield>`
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and will apply the external electric field during charge equilibration,
|
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but there may be only one fix efield instance used and the electric
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field must be applied to all atoms in the system. Consequently, `fix
|
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efield` must be used with *group-ID* all and must not be used with the
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keyword *region*. Equal-style variables can be used for electric field
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vector components without any further settings. Atom-style variables can
|
||||
be used for spatially-varying electric field vector components, but the
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resulting electric potential must be specified as an atom-style variable
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using the *potential* keyword for `fix efield`.
|
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|
||||
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
|
||||
"""""""
|
||||
|
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scale = 1.0 and maxiter = 200
|
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----------
|
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.. _Rappe4:
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**(Rappe)** Rappe and Goddard III, Journal of Physical Chemistry, 95,
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3358-3363 (1991).
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.. _qeq-Aktulga3:
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**(Aktulga)** Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
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||||
245-259 (2012).
|
||||
@ -1,198 +0,0 @@
|
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.. 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).
|
||||
@ -186,7 +186,8 @@ Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
|
||||
:doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix qeqr/reaxff <fix_qeqr_reaxff>`
|
||||
:doc:`fix acks2/reaxff <fix_acks2_reaxff>`,
|
||||
:doc:`fix qeq/rel/reaxff <fix_qeq_rel_reaxff>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
4
src/.gitignore
vendored
4
src/.gitignore
vendored
@ -996,8 +996,8 @@
|
||||
/fix_qeq_fire.h
|
||||
/fix_qeq_reaxff.cpp
|
||||
/fix_qeq_reaxff.h
|
||||
/fix_qeqr_reaxff.cpp
|
||||
/fix_qeqr_reaxff.h
|
||||
/fix_qeq_rel_reaxff.cpp
|
||||
/fix_qeq_rel_reaxff.h
|
||||
/fix_qmmm.cpp
|
||||
/fix_qmmm.h
|
||||
/fix_qtpie_reaxff.cpp
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -18,7 +17,7 @@
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_qeqr_reaxff.h"
|
||||
#include "fix_qeq_rel_reaxff.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
@ -40,46 +39,45 @@ static constexpr double ANGSTROM_TO_BOHRRADIUS = 1.8897261259;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixQEqrReaxFF::FixQEqrReaxFF(LAMMPS *lmp, int narg, char **arg) :
|
||||
FixQtpieReaxFF(lmp, narg, arg)
|
||||
FixQEqRelReaxFF::FixQEqRelReaxFF(LAMMPS *lmp, int narg, char **arg) : FixQtpieReaxFF(lmp, narg, arg)
|
||||
{
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixQEqrReaxFF::calc_chi_eff()
|
||||
void FixQEqRelReaxFF::calc_chi_eff()
|
||||
{
|
||||
memset(&chi_eff[0],0,atom->nmax*sizeof(double));
|
||||
memset(&chi_eff[0], 0, atom->nmax * sizeof(double));
|
||||
|
||||
const auto x = (const double * const *)atom->x;
|
||||
const auto x = (const double *const *) atom->x;
|
||||
const int *type = atom->type;
|
||||
|
||||
double dist,overlap,sum_n,sum_d,expa,expb,chia,phia,phib,p,m;
|
||||
int i,j;
|
||||
double dist, overlap, sum_n, sum_d, expa, expb, chia, phia, phib, p, m;
|
||||
int i, j;
|
||||
|
||||
// check ghost atoms are stored up to the distance cutoff for overlap integrals
|
||||
const double comm_cutoff = MAX(neighbor->cutneighmax,comm->cutghostuser);
|
||||
if(comm_cutoff < dist_cutoff/ANGSTROM_TO_BOHRRADIUS) {
|
||||
error->all(FLERR,"comm cutoff = {} Angstrom is smaller than distance cutoff = {} Angstrom "
|
||||
"for overlap integrals in {}. Increase comm cutoff with comm_modify",
|
||||
comm_cutoff, dist_cutoff/ANGSTROM_TO_BOHRRADIUS, style);
|
||||
const double comm_cutoff = MAX(neighbor->cutneighmax, comm->cutghostuser);
|
||||
if (comm_cutoff < dist_cutoff / ANGSTROM_TO_BOHRRADIUS) {
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Comm cutoff {} is smaller than distance cutoff {} for overlap integrals in fix {}. "
|
||||
"Increase accordingly using comm_modify cutoff",
|
||||
comm_cutoff, dist_cutoff / ANGSTROM_TO_BOHRRADIUS, style);
|
||||
}
|
||||
|
||||
// efield energy is in real units of kcal/mol, factor needed for conversion to eV
|
||||
const double qe2f = force->qe2f;
|
||||
const double factor = 1.0/qe2f;
|
||||
const double factor = 1.0 / qe2f;
|
||||
|
||||
if (efield) {
|
||||
if (efield->varflag != FixEfield::CONSTANT)
|
||||
efield->update_efield_variables();
|
||||
if (efield->varflag != FixEfield::CONSTANT) efield->update_efield_variables();
|
||||
|
||||
// compute chi_eff for each local atom
|
||||
for (i = 0; i < nn; i++) {
|
||||
expa = gauss_exp[type[i]];
|
||||
chia = chi[type[i]];
|
||||
if (efield->varflag != FixEfield::ATOM) {
|
||||
phia = -factor*(x[i][0]*efield->ex + x[i][1]*efield->ey + x[i][2]*efield->ez);
|
||||
} else { // atom-style potential from FixEfield
|
||||
phia = -factor * (x[i][0] * efield->ex + x[i][1] * efield->ey + x[i][2] * efield->ez);
|
||||
} else { // atom-style potential from FixEfield
|
||||
phia = efield->efield[i][3];
|
||||
}
|
||||
|
||||
@ -87,7 +85,7 @@ void FixQEqrReaxFF::calc_chi_eff()
|
||||
sum_d = 0.0;
|
||||
|
||||
for (j = 0; j < nt; j++) {
|
||||
dist = distance(x[i],x[j])*ANGSTROM_TO_BOHRRADIUS; // in atomic units
|
||||
dist = distance(x[i], x[j]) * ANGSTROM_TO_BOHRRADIUS; // in atomic units
|
||||
|
||||
if (dist < dist_cutoff) {
|
||||
expb = gauss_exp[type[j]];
|
||||
@ -95,11 +93,11 @@ void FixQEqrReaxFF::calc_chi_eff()
|
||||
// overlap integral of two normalised 1s Gaussian type orbitals
|
||||
p = expa + expb;
|
||||
m = expa * expb / p;
|
||||
overlap = pow((4.0*m/p),0.75) * exp(-m*dist*dist);
|
||||
overlap = pow((4.0 * m / p), 0.75) * exp(-m * dist * dist);
|
||||
|
||||
if (efield->varflag != FixEfield::ATOM) {
|
||||
phib = -factor*(x[j][0]*efield->ex + x[j][1]*efield->ey + x[j][2]*efield->ez);
|
||||
} else { // atom-style potential from FixEfield
|
||||
phib = -factor * (x[j][0] * efield->ex + x[j][1] * efield->ey + x[j][2] * efield->ez);
|
||||
} else { // atom-style potential from FixEfield
|
||||
phib = efield->efield[j][3];
|
||||
}
|
||||
sum_n += (chia + scale * (phia - phib)) * overlap;
|
||||
@ -109,8 +107,6 @@ void FixQEqrReaxFF::calc_chi_eff()
|
||||
chi_eff[i] = sum_n / sum_d;
|
||||
}
|
||||
} else {
|
||||
for (i = 0; i < nn; i++) {
|
||||
chi_eff[i] = chi[type[i]];
|
||||
}
|
||||
for (i = 0; i < nn; i++) { chi_eff[i] = chi[type[i]]; }
|
||||
}
|
||||
}
|
||||
@ -13,20 +13,20 @@
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
// clang-format off
|
||||
FixStyle(qeqr/reaxff,FixQEqrReaxFF);
|
||||
FixStyle(qeq/rel/reaxff,FixQEqRelReaxFF);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_QEQR_REAXFF_H
|
||||
#define LMP_FIX_QEQR_REAXFF_H
|
||||
#ifndef LMP_FIX_QEQ_REL_REAXFF_H
|
||||
#define LMP_FIX_QEQ_REL_REAXFF_H
|
||||
|
||||
#include "fix_qtpie_reaxff.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixQEqrReaxFF : public FixQtpieReaxFF {
|
||||
class FixQEqRelReaxFF : public FixQtpieReaxFF {
|
||||
public:
|
||||
FixQEqrReaxFF(class LAMMPS *, int, char **);
|
||||
FixQEqRelReaxFF(class LAMMPS *, int, char **);
|
||||
|
||||
protected:
|
||||
void calc_chi_eff() override;
|
||||
Reference in New Issue
Block a user