forked from lijiext/lammps
231 lines
7.8 KiB
Plaintext
231 lines
7.8 KiB
Plaintext
.. index:: pair_style comb
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pair_style comb command
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=======================
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pair_style comb/omp command
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===========================
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pair_style comb3 command
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========================
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Syntax
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""""""
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.. parsed-literal::
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pair_style comb
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pair_style comb3 keyword
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.. parsed-literal::
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keyword = *polar*
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*polar* value = *polar_on* or *polar_off* = whether or not to include atomic polarization
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Examples
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""""""""
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.. parsed-literal::
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pair_style comb
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pair_coeff * * ../potentials/ffield.comb Si
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pair_coeff * * ../potentials/ffield.comb Hf Si O
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.. parsed-literal::
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pair_style comb3 polar_off
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pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
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Description
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"""""""""""
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Style *comb* computes the second-generation variable charge COMB
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(Charge-Optimized Many-Body) potential. Style *comb3* computes the
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third-generation COMB potential. These COMB potentials are described
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in :ref:`(COMB) <COMB>` and :ref:`(COMB3) <COMB3>`. Briefly, the total energy
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*E<sub>T</sub>* of a system of atoms is given by
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.. image:: Eqs/pair_comb1.jpg
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:align: center
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where *E<sub>i</sub><sup>self</sup>* is the self-energy of atom *i*
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(including atomic ionization energies and electron affinities),
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*E<sub>ij</sub><sup>short</sup>* is the bond-order potential between
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atoms *i* and *j*\ ,
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*E<sub>ij</sub><sup>Coul</sup>* is the Coulomb interactions,
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*E<sup>polar</sup>* is the polarization term for organic systems
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(style *comb3* only),
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*E<sup>vdW</sup>* is the van der Waals energy (style *comb3* only),
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*E<sup>barr</sup>* is a charge barrier function, and
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*E<sup>corr</sup>* are angular correction terms.
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The COMB potentials (styles *comb* and *comb3*\ ) are variable charge
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potentials. The equilibrium charge on each atom is calculated by the
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electronegativity equalization (QEq) method. See :ref:`Rick <Rick>` for
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further details. This is implemented by the :doc:`fix qeq/comb <fix_qeq_comb>` command, which should normally be
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specified in the input script when running a model with the COMB
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potential. The :doc:`fix qeq/comb <fix_qeq_comb>` command has options
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that determine how often charge equilibration is performed, its
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convergence criterion, and which atoms are included in the
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calculation.
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Only a single pair_coeff command is used with the *comb* and *comb3*
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styles which specifies the COMB potential file with parameters for all
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needed elements. These are mapped to LAMMPS atom types by specifying
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N additional arguments after the potential file in the pair_coeff
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command, where N is the number of LAMMPS atom types.
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For example, if your LAMMPS simulation of a Si/SiO<sub>2</sub>/
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HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and
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last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
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use the following pair_coeff command:
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.. parsed-literal::
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pair_coeff * * ../potentials/ffield.comb Si Hf O Si
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The first two arguments must be * * so as to span all LAMMPS atom
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types. The first and last Si arguments map LAMMPS atom types 1 and 4
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to the Si element in the *ffield.comb* file. The second Hf argument
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maps LAMMPS atom type 2 to the Hf element, and the third O argument
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maps LAMMPS atom type 3 to the O element in the potential file. If a
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mapping value is specified as NULL, the mapping is not performed.
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This can be used when a *comb* potential is used as part of the
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*hybrid* pair style. The NULL values are placeholders for atom types
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that will be used with other potentials.
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For style *comb*\ , the provided potential file *ffield.comb* contains
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all currently-available 2nd generation COMB parameterizations: for Si,
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Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style
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*comb3*\ , the potential file *ffield.comb3* contains all
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currently-available 3rd generation COMB paramterizations: O, Cu, N, C,
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H, Ti, Zn and Zr. The status of the optimization of the compounds, for
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example Cu<sub>2</sub>O, TiN and hydrocarbons, are given in the
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following table:
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.. image:: Eqs/pair_comb2.jpg
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:align: center
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For style *comb3*\ , in addition to ffield.comb3, a special parameter
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file, *lib.comb3*\ , that is exclusively used for C/O/H systems, will be
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automatically loaded if carbon atom is detected in LAMMPS input
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structure. This file must be in your working directory or in the
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directory pointed to by the environment variable LAMMPS_POTENTIALS, as
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described on the :doc:`pair_coeff <pair_coeff>` command doc page.
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Keyword *polar* indicates whether the force field includes
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the atomic polarization. Since the equilibration of the polarization
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has not yet been implemented, it can only set polar_off at present.
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.. note::
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You can not use potential file *ffield.comb* with style *comb3*\ ,
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nor file *ffield.comb3* with style *comb*\ .
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----------
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Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in :doc:`Section_accelerate <Section_accelerate>`
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. See the :ref:`Making LAMMPS <start_3>` section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
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use the :doc:`suffix <suffix>` command in your input script.
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See :doc:`Section_accelerate <Section_accelerate>` of the manual for
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more instructions on how to use the accelerated styles effectively.
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----------
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**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
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For atom type pairs I,J and I != J, where types I and J correspond to
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two different element types, mixing is performed by LAMMPS as
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described above from values in the potential file.
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These pair styles does not support the :doc:`pair_modify <pair_modify>`
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shift, table, and tail options.
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These pair styles do not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files. Thus, you
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need to re-specify the pair_style, pair_coeff, and :doc:`fix qeq/comb <fix_qeq_comb>` commands in an input script that reads a
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restart file.
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These pair styles can only be used via the *pair* keyword of the
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:doc:`run_style respa <run_style>` command. It does not support the
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*inner*\ , *middle*\ , *outer* keywords.
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----------
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Restrictions
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""""""""""""
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These pair styles are part of the MANYBODY package. It is only enabled
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if LAMMPS was built with that package (which it is by default). See
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the :ref:`Making LAMMPS <start_3>` section for more info.
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These pair styles requires the :doc:`newton <newton>` setting to be "on"
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for pair interactions.
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The COMB potentials in the *ffield.comb* and *ffield.comb3* files provided
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with LAMMPS (see the potentials directory) are parameterized for metal
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:doc:`units <units>`. You can use the COMB potential with any LAMMPS
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units, but you would need to create your own COMB potential file with
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coefficients listed in the appropriate units if your simulation
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doesn't use "metal" units.
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Related commands
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""""""""""""""""
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:doc:`pair_style <pair_style>`, :doc:`pair_coeff <pair_coeff>`,
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:doc:`fix qeq/comb <fix_qeq_comb>`
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**Default:** none
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----------
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.. _COMB:
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**(COMB)** T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and
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S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)
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.. _COMB3:
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**(COMB3)** T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek,
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Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74,
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255-279 (2013).
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.. _Rick:
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**(Rick)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
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(1994).
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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