215 lines
7.7 KiB
ReStructuredText
215 lines
7.7 KiB
ReStructuredText
.. index:: pair\_style exp6/rx
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pair\_style exp6/rx command
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===========================
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pair\_style exp6/rx/kk 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 exp6/rx cutoff ...
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* cutoff = global cutoff for DPD interactions (distance units)
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* weighting = fractional or molecular (optional)
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Examples
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""""""""
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.. parsed-literal::
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pair_style exp6/rx 10.0
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pair_style exp6/rx 10.0 fractional
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pair_style exp6/rx 10.0 molecular
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pair_coeff \* \* exp6.params h2o h2o exponent 1.0 1.0 10.0
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pair_coeff \* \* exp6.params h2o 1fluid exponent 1.0 1.0 10.0
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pair_coeff \* \* exp6.params 1fluid 1fluid exponent 1.0 1.0 10.0
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pair_coeff \* \* exp6.params 1fluid 1fluid none 10.0
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pair_coeff \* \* exp6.params 1fluid 1fluid polynomial filename 10.0
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Description
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"""""""""""
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Style *exp6/rx* is used in reaction DPD simulations, where the
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coarse-grained (CG) particles are composed of *m* species whose
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reaction rate kinetics are determined from a set of *n* reaction rate
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equations through the :doc:`fix rx <fix_rx>` command. The species of
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one CG particle can interact with a species in a neighboring CG
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particle through a site-site interaction potential model. The
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*exp6/rx* style computes an exponential-6 potential given by
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.. image:: Eqs/pair_exp6_rx.jpg
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:align: center
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where the *epsilon* parameter determines the depth of the potential
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minimum located at *Rm*\ , and *alpha* determines the softness of the repulsion.
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The coefficients must be defined for each species in a given particle
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type via the :doc:`pair\_coeff <pair_coeff>` command as in the examples
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above, where the first argument is the filename that includes the
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exponential-6 parameters for each species. The file includes the
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species tag followed by the *alpha*\ , *epsilon* and *Rm*
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parameters. The format of the file is described below.
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The second and third arguments specify the site-site interaction
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potential between two species contained within two different
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particles. The species tags must either correspond to the species
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defined in the reaction kinetics files specified with the :doc:`fix rx <fix_rx>` command or they must correspond to the tag "1fluid",
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signifying interaction with a product species mixture determined
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through a one-fluid approximation. The interaction potential is
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weighted by the geometric average of either the mole fraction concentrations
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or the number of molecules associated with the interacting coarse-grained
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particles (see the *fractional* or *molecular* weighting pair style options).
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The coarse-grained potential is stored before and after the
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reaction kinetics solver is applied, where the difference is defined
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to be the internal chemical energy (uChem).
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The fourth argument specifies the type of scaling that will be used
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to scale the EXP-6 parameters as reactions occur. Currently, there
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are three scaling options: *exponent*\ , *polynomial* and *none*\ .
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Exponent scaling requires two additional arguments for scaling
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the *Rm* and *epsilon* parameters, respectively. The scaling factor
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is computed by phi\^exponent, where phi is the number of molecules
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represented by the coarse-grain particle and exponent is specified
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as a pair coefficient argument for *Rm* and *epsilon*\ , respectively.
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The *Rm* and *epsilon* parameters are multiplied by the scaling
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factor to give the scaled interaction parameters for the CG particle.
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Polynomial scaling requires a filename to be specified as a pair
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coeff argument. The file contains the coefficients to a fifth order
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polynomial for the *alpha*\ , *epsilon* and *Rm* parameters that depend
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upon phi (the number of molecules represented by the CG particle).
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The format of a polynomial file is provided below.
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The *none* option to the scaling does not have any additional pair coeff
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arguments. This is equivalent to specifying the *exponent* option with
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*Rm* and *epsilon* exponents of 0.0 and 0.0, respectively.
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The final argument specifies the interaction cutoff (optional).
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----------
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The format of a tabulated file is as follows (without the
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parenthesized comments):
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.. parsed-literal::
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# exponential-6 parameters for various species (one or more comment or blank lines)
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h2o exp6 11.00 0.02 3.50 (species, exp6, alpha, Rm, epsilon)
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no2 exp6 13.60 0.01 3.70
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...
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co2 exp6 13.00 0.03 3.20
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The format of the polynomial scaling file as follows (without the
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parenthesized comments):
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.. parsed-literal::
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# POLYNOMIAL FILE (one or more comment or blank lines)
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# General Functional Form:
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# A\*phi\^5 + B\*phi\^4 + C\*phi\^3 + D\*phi\^2 + E\*phi + F
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#
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# Parameter A B C D E F
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(blank)
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alpha 0.0000 0.00000 0.00008 0.04955 -0.73804 13.63201
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epsilon 0.0000 0.00478 -0.06283 0.24486 -0.33737 2.60097
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rm 0.0001 -0.00118 -0.00253 0.05812 -0.00509 1.50106
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A section begins with a non-blank line whose 1st character is not a
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"#"; blank lines or lines starting with "#" can be used as comments
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between sections.
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Following a blank line, the next N lines list the species and their
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corresponding parameters. The first argument is the species tag, the
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second argument is the exp6 tag, the 3rd argument is the *alpha*
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parameter (energy units), the 4th argument is the *epsilon* parameter
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(energy-distance\^6 units), and the 5th argument is the *Rm* parameter
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(distance units). If a species tag of "1fluid" is listed as a pair
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coefficient, a one-fluid approximation is specified where a
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concentration-dependent combination of the parameters is computed
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through the following equations:
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.. image:: Eqs/pair_exp6_rx_oneFluid.jpg
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:align: center
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where
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.. image:: Eqs/pair_exp6_rx_oneFluid2.jpg
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:align: center
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and xa and xb are the mole fractions of a and b, respectively, which
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comprise the gas mixture.
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----------
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**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
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This pair style does not support mixing. Thus, coefficients for all
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I,J pairs must be specified explicitly.
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This style does not support the :doc:`pair\_modify <pair_modify>` shift option
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for the energy of the exp() and 1/r\^6 portion of the pair interaction.
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This style does not support the pair\_modify tail option for adding long-range
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tail corrections to energy and pressure for the A,C terms in the
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pair interaction.
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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 on the :doc:`Speed packages <Speed_packages>` doc
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page. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision 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 :doc:`Build package <Build_package>` doc page 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 :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
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:doc:`suffix <suffix>` command in your input script.
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See the :doc:`Speed packages <Speed_packages>` doc page for more
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instructions on how to use the accelerated styles effectively.
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----------
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Restrictions
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""""""""""""
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This command is part of the USER-DPD package. It is only enabled if
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LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
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Related commands
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""""""""""""""""
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:doc:`pair\_coeff <pair_coeff>`
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**Default:** fractional weighting
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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