mirror of https://github.com/lammps/lammps.git
Axel Kohlmeyer
GitHub
commit
5928389c5e
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@ -187,6 +187,7 @@ OPT.
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* :doc:`qeq/slater <fix_qeq>`
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* :doc:`qmmm <fix_qmmm>`
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* :doc:`qtb <fix_qtb>`
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* :doc:`qtpie/reaxff <fix_qtpie_reaxff>`
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* :doc:`rattle <fix_shake>`
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* :doc:`reaxff/bonds (k) <fix_reaxff_bonds>`
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* :doc:`reaxff/species (k) <fix_reaxff_species>`
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@ -366,6 +366,7 @@ accelerated styles exist.
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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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* :doc:`qtb <fix_qtb>` - implement quantum thermal bath scheme
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* :doc:`qtpie/reaxff <fix_qtpie_reaxff>` - apply QTPIE charge equilibration
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* :doc:`rattle <fix_shake>` - RATTLE constraints on bonds and/or angles
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* :doc:`reaxff/bonds <fix_reaxff_bonds>` - write out ReaxFF bond information
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* :doc:`reaxff/species <fix_reaxff_species>` - write out ReaxFF molecule information
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@ -111,7 +111,8 @@ LAMMPS was built with that package. See the :doc:`Build package
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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 less than :math:`10~\AA`.
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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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@ -122,7 +123,8 @@ 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:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
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:doc:`fix qtpi/reaxff <fix_qtpie_reaxff>`
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Default
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"""""""
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@ -124,7 +124,8 @@ LAMMPS was built with that package. See the :doc:`Build package
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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 less than 10 Angstroms.
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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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@ -138,7 +139,8 @@ as an atom-style variable using the *potential* keyword for `fix efield`.
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Related commands
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""""""""""""""""
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:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/shielded <fix_qeq>`
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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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Default
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"""""""
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@ -0,0 +1,198 @@
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.. index:: fix qtpie/reaxff
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fix qtpie/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 qtpie/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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* qtpie/reaxff = style name of this fix command
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* Nevery = perform QTPIE 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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.. parsed-literal::
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keyword = *maxiter*
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*maxiter* N = limit the number of iterations to *N*
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 reaxff exp.qtpie
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fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 params.qtpie exp.qtpie maxiter 500
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Description
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"""""""""""
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The QTPIE charge equilibration method is an extension of the QEq charge
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equilibration method. With QTPIE, the partial charges on individual atoms
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are computed by minimizing the electrostatic energy of the system in the
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same way as the QEq method but where the absolute electronegativity,
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:math:`\chi_i`, of each atom in the QEq charge equilibration scheme
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:ref:`(Rappe and Goddard) <Rappe3>` is replaced with an effective
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electronegativity given by :ref:`(Chen) <qtpie-Chen>`
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.. math::
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\chi_{\mathrm{eff},i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j) S_{ij}}
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{\sum_{m=1}^{N}S_{im}},
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which acts to penalize long-range charge transfer seen with the QEq charge
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equilibration scheme. In this equation, :math:`N` is the number of atoms in
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the system and :math:`S_{ij}` is the overlap integral between atom :math:`i`
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and atom :math:`j`.
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The effect of an external electric field can be incorporated into the QTPIE
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method by modifying the absolute or effective electronegativities of each
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atom :ref:`(Chen) <qtpie-Chen>`. This fix models the effect of an external
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electric field by using the effective electronegativity given in
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:ref:`(Gergs) <Gergs>`:
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.. math::
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\chi_{\mathrm{eff},i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j + \phi_i - \phi_j) S_{ij}}
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{\sum_{m=1}^{N}S_{im}},
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where :math:`\phi_i` and :math:`\phi_j` are the electric
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potentials at the positions of atom :math:`i` and :math:`j`
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due to the external electric field.
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This fix is typically used in conjunction with the ReaxFF force
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field model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
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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
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charge equilibration performed by `fix qtpie/reaxff`, which is the same as in
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:doc:`fix qeq/reaxff <fix_qeq_reaxff>` except for the use of
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:math:`\chi_{\mathrm{eff},i}`, please refer to :ref:`(Aktulga) <qeq-Aktulga2>`.
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To be explicit, this fix replaces :math:`\chi_k` of eq. 3 in
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:ref:`(Aktulga) <qeq-Aktulga2>` with :math:`\chi_{\mathrm{eff},k}`.
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This fix requires the absolute electronegativity, :math:`\chi`, in eV, the
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self-Coulomb potential, :math:`\eta`, in eV, and the shielded Coulomb
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constant, :math:`\gamma`, in :math:`\AA^{-1}`. If the *params* setting above
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is the word "reaxff", then these are extracted from the
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:doc:`pair_style reaxff <pair_reaxff>` command and the ReaxFF force field
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file it reads in. If a file name is specified for *params*, then the
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parameters are taken from the specified file and the file must contain
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one line for each atom type. The latter form must be used when performing
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QTPIE with a non-ReaxFF potential. Each line should be formatted as follows,
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ensuring that the parameters are given in units of eV, eV, and :math:`\AA^{-1}`,
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respectively:
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.. parsed-literal::
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itype chi eta gamma
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where *itype* is the atom type from 1 to Ntypes. Note that eta is
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defined here as twice the eta value in the ReaxFF file.
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The overlap integrals in the equation for :math:`\chi_{\mathrm{eff},i}`
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are computed by using normalized 1s Gaussian type orbitals. The Gaussian
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orbital exponents, :math:`\alpha`, that are needed to compute the overlap
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integrals are taken from the file given by *gfile*.
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This file must contain one line for each atom type and provide the Gaussian
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orbital exponent for each atom type in units of inverse square Bohr radius.
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Each line should be formatted as follows:
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.. parsed-literal::
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itype alpha
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Empty lines or any text following the pound sign (#) are ignored. An example
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*gfile* for a system with two atom types is
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.. parsed-literal::
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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 *maxiter* keyword allows changing the max number
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of iterations in the linear solver. The default value is 200.
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.. note::
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In order to solve the self-consistent equations for electronegativity
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equalization, LAMMPS imposes the additional constraint that all the
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charges in the fix group must add up to zero. The initial charge
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assignments should also satisfy this constraint. LAMMPS will print a
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warning if that is not the case.
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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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
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iterations) and a per-atom vector (the effective electronegativity), which
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can be accessed by various :doc:`output commands <Howto_output>`.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command.
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This fix is invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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This fix is part of the REAXFF package. It is only enabled if
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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 field
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must be applied to all atoms in the system. Consequently, `fix efield` must
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be used with *group-ID* all and must not be used with the keyword *region*.
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Equal-style variables can be used for electric field vector
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components without any further settings. Atom-style variables can be used
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for spatially-varying electric field vector components, but the resulting
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electric potential must be specified as an atom-style variable using
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the *potential* keyword for `fix efield`.
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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 acks2/reaxff <fix_acks2_reaxff>`
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Default
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"""""""
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maxiter 200
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----------
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.. _Rappe3:
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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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.. _qtpie-Chen:
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**(Chen)** Chen, Jiahao. Theory and applications of fluctuating-charge models.
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University of Illinois at Urbana-Champaign, 2009.
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.. _Gergs:
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**(Gergs)** Gergs, Dirkmann and Mussenbrock.
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Journal of Applied Physics 123.24 (2018).
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.. _qeq-Aktulga2:
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**(Aktulga)** Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
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245-259 (2012).
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@ -20,7 +20,7 @@ Syntax
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.. parsed-literal::
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keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds* or *tabulate* or *list/blocking*
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*checkqeq* value = *yes* or *no* = whether or not to require qeq/reaxff or acks2/reaxff fix
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*checkqeq* value = *yes* or *no* = whether or not to require one of fix qeq/reaxff, fix acks2/reaxff or fix qtpie/reaxff
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*enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds
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*lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction
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*safezone* = factor used for array allocation
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@ -120,20 +120,22 @@ up that process.
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The ReaxFF parameter files provided were created using a charge
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equilibration (QEq) model for handling the electrostatic interactions.
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Therefore, by default, LAMMPS requires that either the
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:doc:`fix qeq/reaxff <fix_qeq_reaxff>` or the
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:doc:`fix qeq/shielded <fix_qeq>` or :doc:`fix acks2/reaxff <fix_acks2_reaxff>`
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command be used with
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*pair_style reaxff* when simulating a ReaxFF model, to equilibrate
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the charges each timestep.
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Therefore, by default, LAMMPS requires that
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:doc:`fix qeq/reaxff <fix_qeq_reaxff>` or :doc:`fix qeq/shielded <fix_qeq>`
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or :doc:`fix acks2/reaxff <fix_acks2_reaxff>`
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or :doc:`fix qtpie/reaxff <fix_qtpie_reaxff>`
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is used with *pair_style reaxff* when simulating a ReaxFF model,
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to equilibrate the charges at each timestep.
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See the :doc:`fix qeq/reaxff <fix_qeq_reaxff>` or :doc:`fix qeq/shielded <fix_qeq>`
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or :doc:`fix acks2/reaxff <fix_acks2_reaxff>`
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or :doc:`fix qtpie/reaxff <fix_qtpie_reaxff>`
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command documentation for more details.
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Using the keyword *checkqeq* with the value *no* turns off the check
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for the QEq fixes, allowing a simulation to be run without charge
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equilibration. In this case, the static charges you assign to each
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atom will be used for computing the electrostatic interactions in
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the system. See the :doc:`fix qeq/reaxff <fix_qeq_reaxff>` or
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:doc:`fix qeq/shielded <fix_qeq>` or :doc:`fix acks2/reaxff <fix_acks2_reaxff>`
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command documentation for more details.
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the system.
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Using the optional keyword *lgvdw* with the value *yes* turns on the
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low-gradient correction of ReaxFF for long-range London Dispersion,
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@ -372,8 +374,8 @@ Related commands
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""""""""""""""""
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:doc:`pair_coeff <pair_coeff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
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:doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix reaxff/bonds <fix_reaxff_bonds>`,
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:doc:`fix reaxff/species <fix_reaxff_species>`,
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:doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix qtpie/reaxff <fix_qtpie_reaxff>`,
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:doc:`fix reaxff/bonds <fix_reaxff_bonds>`, :doc:`fix reaxff/species <fix_reaxff_species>`,
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:doc:`compute reaxff/atom <compute_reaxff_atom>`
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Default
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|
|
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@ -815,6 +815,7 @@ dipoleflag
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dir
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Direc
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dirname
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Dirkmann
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discoverable
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discretization
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discretized
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@ -976,6 +977,7 @@ elaplong
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elastance
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Electroneg
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electronegative
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electronegativities
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electronegativity
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electroneutral
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electroneutrality
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|
@ -1293,6 +1295,7 @@ Geocomputing
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georg
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Georg
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Geotechnica
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Gergs
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germain
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Germann
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Germano
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|
@ -1305,6 +1308,7 @@ gettimeofday
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geturl
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gewald
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Gezelter
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gfile
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Gflop
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gfortran
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ghostneigh
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|
|
@ -1712,6 +1716,7 @@ Jewett
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jgissing
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ji
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Jiang
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Jiahao
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Jiao
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||||
jik
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||||
JIK
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|
|
@ -2366,6 +2371,7 @@ mui
|
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Mukherjee
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||||
Mulders
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Müller
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Mulliken
|
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mult
|
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multi
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multibody
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|
|
@ -2390,6 +2396,7 @@ Murdick
|
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Murtola
|
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Murty
|
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Muser
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Mussenbrock
|
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mutexes
|
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Muto
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muVT
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|
|
@ -3073,6 +3080,7 @@ qqr
|
|||
qqrd
|
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Qsb
|
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qtb
|
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qtpie
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quadratically
|
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quadrupolar
|
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quadrupole
|
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|
|
|
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|
|
@ -0,0 +1,5 @@
|
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# Gaussian orbital exponents (required for fix qtpie/reaxff) taken from Table 2.2
|
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# of Chen, J. (2009). 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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|
|
@ -0,0 +1,29 @@
|
|||
# QTPIE Water
|
||||
|
||||
boundary p p p
|
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units real
|
||||
atom_style charge
|
||||
|
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read_data data.water
|
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|
||||
variable x index 1
|
||||
variable y index 1
|
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variable z index 1
|
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|
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replicate $x $y $z
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|
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pair_style reaxff NULL safezone 3.0 mincap 150
|
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pair_coeff * * qeq_ff.water O H
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neighbor 0.5 bin
|
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neigh_modify every 1 delay 0 check yes
|
||||
|
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velocity all create 300.0 4928459 rot yes dist gaussian
|
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|
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fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt
|
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fix 2 all nvt temp 300 300 50.0
|
||||
|
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timestep 0.5
|
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thermo 10
|
||||
thermo_style custom step temp press density vol
|
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|
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run 20
|
||||
|
|
@ -0,0 +1,30 @@
|
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# QTPIE Water
|
||||
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * qeq_ff.water O H
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
fix 3 all efield 0.0 0.0 0.05
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
|
@ -0,0 +1,127 @@
|
|||
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-76-g3f232caf9b)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# QTPIE Water
|
||||
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.056 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replication is creating a 1x1x1 = 1 times larger system...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * qeq_ff.water O H
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
fix 3 all efield 0.0 0.0 0.05
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qtpie/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 539.2 | 539.2 | 539.2 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 10137.041 1 29915.273
|
||||
10 296.09128 3564.7969 1 29915.273
|
||||
20 293.04308 10299.201 1 29915.273
|
||||
Loop time of 10.7863 on 1 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.080 ns/day, 299.620 hours/ns, 1.854 timesteps/s, 5.563 katom-step/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.7275 | 4.7275 | 4.7275 | 0.0 | 43.83
|
||||
Neigh | 0.17533 | 0.17533 | 0.17533 | 0.0 | 1.63
|
||||
Comm | 0.0017376 | 0.0017376 | 0.0017376 | 0.0 | 0.02
|
||||
Output | 8.2065e-05 | 8.2065e-05 | 8.2065e-05 | 0.0 | 0.00
|
||||
Modify | 5.8812 | 5.8812 | 5.8812 | 0.0 | 54.52
|
||||
Other | | 0.0005226 | | | 0.00
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11077 ave 11077 max 11077 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 971775 ave 971775 max 971775 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 971775
|
||||
Ave neighs/atom = 323.925
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:12
|
||||
|
|
@ -0,0 +1,127 @@
|
|||
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-76-g3f232caf9b)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# QTPIE Water
|
||||
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.053 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replication is creating a 1x1x1 = 1 times larger system...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.002 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * qeq_ff.water O H
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
fix 3 all efield 0.0 0.0 0.05
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qtpie/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 260.5 | 262.2 | 263.6 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 10137.041 1 29915.273
|
||||
10 296.09128 3564.7969 1 29915.273
|
||||
20 293.04308 10299.201 1 29915.273
|
||||
Loop time of 3.14492 on 4 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.275 ns/day, 87.359 hours/ns, 6.359 timesteps/s, 19.078 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6557 | 1.6847 | 1.7281 | 2.1 | 53.57
|
||||
Neigh | 0.086503 | 0.086968 | 0.087627 | 0.2 | 2.77
|
||||
Comm | 0.003309 | 0.046699 | 0.075729 | 12.4 | 1.48
|
||||
Output | 5.0156e-05 | 5.483e-05 | 6.8111e-05 | 0.0 | 0.00
|
||||
Modify | 1.3254 | 1.3261 | 1.3266 | 0.0 | 42.16
|
||||
Other | | 0.0004552 | | | 0.01
|
||||
|
||||
Nlocal: 750 ave 760 max 735 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Nghost: 6230.5 ave 6253 max 6193 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Neighs: 276995 ave 280886 max 271360 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1107981
|
||||
Ave neighs/atom = 369.327
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -0,0 +1,126 @@
|
|||
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-76-g3f232caf9b)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# QTPIE Water
|
||||
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.055 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replication is creating a 1x1x1 = 1 times larger system...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * qeq_ff.water O H
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qtpie/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 539.2 | 539.2 | 539.2 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 10138.375 1 29915.273
|
||||
10 295.97879 3575.2769 1 29915.273
|
||||
20 292.76583 10309.128 1 29915.273
|
||||
Loop time of 10.8138 on 1 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.080 ns/day, 300.383 hours/ns, 1.849 timesteps/s, 5.548 katom-step/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.7177 | 4.7177 | 4.7177 | 0.0 | 43.63
|
||||
Neigh | 0.17607 | 0.17607 | 0.17607 | 0.0 | 1.63
|
||||
Comm | 0.0017295 | 0.0017295 | 0.0017295 | 0.0 | 0.02
|
||||
Output | 8.5431e-05 | 8.5431e-05 | 8.5431e-05 | 0.0 | 0.00
|
||||
Modify | 5.9177 | 5.9177 | 5.9177 | 0.0 | 54.72
|
||||
Other | | 0.0004911 | | | 0.00
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11077 ave 11077 max 11077 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 971830 ave 971830 max 971830 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 971830
|
||||
Ave neighs/atom = 323.94333
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:12
|
||||
|
|
@ -0,0 +1,126 @@
|
|||
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-76-g3f232caf9b)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# QTPIE Water
|
||||
|
||||
boundary p p p
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
read_data CPU = 0.053 seconds
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
Replication is creating a 1x1x1 = 1 times larger system...
|
||||
orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
3000 atoms
|
||||
replicate CPU = 0.002 seconds
|
||||
|
||||
pair_style reaxff NULL safezone 3.0 mincap 150
|
||||
pair_coeff * * qeq_ff.water O H
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt
|
||||
fix 2 all nvt temp 300 300 50.0
|
||||
|
||||
timestep 0.5
|
||||
thermo 10
|
||||
thermo_style custom step temp press density vol
|
||||
|
||||
run 20
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/ghost/newtoff
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qtpie/reaxff, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 260.5 | 262.2 | 263.6 Mbytes
|
||||
Step Temp Press Density Volume
|
||||
0 300 10138.375 1 29915.273
|
||||
10 295.97879 3575.2769 1 29915.273
|
||||
20 292.76583 10309.128 1 29915.273
|
||||
Loop time of 3.13598 on 4 procs for 20 steps with 3000 atoms
|
||||
|
||||
Performance: 0.276 ns/day, 87.111 hours/ns, 6.378 timesteps/s, 19.133 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6622 | 1.695 | 1.7252 | 2.2 | 54.05
|
||||
Neigh | 0.086543 | 0.087117 | 0.087848 | 0.2 | 2.78
|
||||
Comm | 0.0048192 | 0.035002 | 0.067754 | 15.4 | 1.12
|
||||
Output | 4.8033e-05 | 5.3375e-05 | 6.6893e-05 | 0.0 | 0.00
|
||||
Modify | 1.3176 | 1.3183 | 1.3189 | 0.0 | 42.04
|
||||
Other | | 0.0004753 | | | 0.02
|
||||
|
||||
Nlocal: 750 ave 760 max 735 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Nghost: 6229.5 ave 6253 max 6191 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Neighs: 277011 ave 280900 max 271380 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1108044
|
||||
Ave neighs/atom = 369.348
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -988,6 +988,8 @@
|
|||
/fix_qeq_reaxff.h
|
||||
/fix_qmmm.cpp
|
||||
/fix_qmmm.h
|
||||
/fix_qtpie_reaxff.cpp
|
||||
/fix_qtpie_reaxff.h
|
||||
/fix_reaxff.cpp
|
||||
/fix_reaxff.h
|
||||
/fix_reaxff_bonds.cpp
|
||||
|
|
|
|||
|
|
@ -1158,7 +1158,7 @@ void FixQEqReaxFF::get_chi_field()
|
|||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & efgroupbit) {
|
||||
if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
|
||||
chi_field[i] = -efield->efield[i][3];
|
||||
chi_field[i] = efield->efield[i][3];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,141 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
// clang-format off
|
||||
FixStyle(qtpie/reaxff,FixQtpieReaxFF);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_QTPIE_REAXFF_H
|
||||
#define LMP_FIX_QTPIE_REAXFF_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixQtpieReaxFF : public Fix {
|
||||
public:
|
||||
FixQtpieReaxFF(class LAMMPS *, int, char **);
|
||||
~FixQtpieReaxFF() override;
|
||||
int setmask() override;
|
||||
void post_constructor() override;
|
||||
void init() override;
|
||||
void init_list(int, class NeighList *) override;
|
||||
void init_storage();
|
||||
void setup_pre_force(int) override;
|
||||
void pre_force(int) override;
|
||||
|
||||
void setup_pre_force_respa(int, int) override;
|
||||
void pre_force_respa(int, int, int) override;
|
||||
|
||||
void min_setup_pre_force(int);
|
||||
void min_pre_force(int) override;
|
||||
|
||||
double compute_scalar() override;
|
||||
|
||||
protected:
|
||||
int nevery, reaxflag;
|
||||
int matvecs;
|
||||
int nn, nt, m_fill;
|
||||
int n_cap, nmax, m_cap;
|
||||
int pack_flag;
|
||||
int nlevels_respa;
|
||||
class NeighList *list;
|
||||
class PairReaxFF *reaxff;
|
||||
class FixEfield *efield;
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
|
||||
double swa, swb; // lower/upper Taper cutoff radius
|
||||
double Tap[8]; // Taper function
|
||||
double tolerance; // tolerance for the norm of the rel residual in CG
|
||||
|
||||
double *chi, *eta, *gamma; // qeq parameters
|
||||
double **shld;
|
||||
|
||||
// fictitious charges
|
||||
|
||||
double *s, *t;
|
||||
double **s_hist, **t_hist;
|
||||
int nprev;
|
||||
|
||||
typedef struct {
|
||||
int n, m;
|
||||
int *firstnbr;
|
||||
int *numnbrs;
|
||||
int *jlist;
|
||||
double *val;
|
||||
} sparse_matrix;
|
||||
|
||||
sparse_matrix H;
|
||||
double *Hdia_inv;
|
||||
double *b_s, *b_t;
|
||||
double *b_prc, *b_prm;
|
||||
double *chi_eff; // array of effective electronegativities
|
||||
|
||||
//CG storage
|
||||
double *p, *q, *r, *d;
|
||||
int imax, maxwarn;
|
||||
|
||||
char *pertype_option; // argument to determine how per-type info is obtained
|
||||
char *gauss_file; // input file for gaussian orbital exponents
|
||||
double *gauss_exp; // array of gaussian orbital exponents for each atom type
|
||||
double dist_cutoff; // separation distance beyond which to neglect overlap integrals
|
||||
|
||||
void pertype_parameters(char *);
|
||||
void init_shielding();
|
||||
void init_taper();
|
||||
void allocate_storage();
|
||||
void deallocate_storage();
|
||||
void reallocate_storage();
|
||||
void allocate_matrix();
|
||||
void deallocate_matrix();
|
||||
void reallocate_matrix();
|
||||
|
||||
void init_matvec();
|
||||
void init_H();
|
||||
void compute_H();
|
||||
double calculate_H(double, double);
|
||||
void calculate_Q();
|
||||
|
||||
int CG(double *, double *);
|
||||
void sparse_matvec(sparse_matrix *, double *, double *);
|
||||
|
||||
int pack_forward_comm(int, int *, double *, int, int *) override;
|
||||
void unpack_forward_comm(int, int, double *) override;
|
||||
int pack_reverse_comm(int, int, double *) override;
|
||||
void unpack_reverse_comm(int, int *, double *) override;
|
||||
double memory_usage() override;
|
||||
void grow_arrays(int) override;
|
||||
void copy_arrays(int, int, int) override;
|
||||
int pack_exchange(int, double *) override;
|
||||
int unpack_exchange(int, double *) override;
|
||||
|
||||
double parallel_norm(double *, int);
|
||||
double parallel_dot(double *, double *, int);
|
||||
double parallel_vector_acc(double *, int);
|
||||
|
||||
void vector_sum(double *, double, double *, double, double *, int);
|
||||
void vector_add(double *, double, double *, int);
|
||||
|
||||
void calc_chi_eff();
|
||||
double find_min_exp(const double*, const int);
|
||||
double distance(const double*, const double*);
|
||||
|
||||
int matvecs_s, matvecs_t; // Iteration count for each system
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -340,11 +340,13 @@ void PairReaxFF::init_style()
|
|||
|
||||
auto acks2_fixes = modify->get_fix_by_style("^acks2/reax");
|
||||
int have_qeq = modify->get_fix_by_style("^qeq/reax").size()
|
||||
+ modify->get_fix_by_style("^qeq/shielded").size() + acks2_fixes.size();
|
||||
+ modify->get_fix_by_style("^qeq/shielded").size() + acks2_fixes.size()
|
||||
+ modify->get_fix_by_style("^qtpie/reax").size();
|
||||
|
||||
if (qeqflag && (have_qeq != 1))
|
||||
error->all(FLERR,"Pair style reaxff requires use of exactly one of the "
|
||||
"fix qeq/reaxff or fix qeq/shielded or fix acks2/reaxff commands");
|
||||
"fix qeq/reaxff or fix qeq/shielded or fix acks2/reaxff or "
|
||||
"fix qtpie/reaxff commands");
|
||||
|
||||
api->system->acks2_flag = acks2_fixes.size();
|
||||
if (api->system->acks2_flag)
|
||||
|
|
|
|||
|
|
@ -26,6 +26,7 @@ namespace LAMMPS_NS {
|
|||
|
||||
class FixEfield : public Fix {
|
||||
friend class FixQEqReaxFF;
|
||||
friend class FixQtpieReaxFF;
|
||||
|
||||
public:
|
||||
FixEfield(class LAMMPS *, int, char **);
|
||||
|
|
|
|||
Loading…
Reference in New Issue