forked from lijiext/lammps
186 lines
7.4 KiB
Plaintext
186 lines
7.4 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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pair_style exp6/rx command :h3
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pair_style exp6/rx/kk command :h3
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[Syntax:]
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pair_style exp6/rx cutoff ... :pre
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cutoff = global cutoff for DPD interactions (distance units)
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weighting = fractional or molecular (optional) :ul
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[Examples:]
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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 :pre
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[Description:]
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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 "fix rx"_fix_rx.html 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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:c,image(Eqs/pair_exp6_rx.jpg)
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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 "pair_coeff"_pair_coeff.html 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 "fix
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rx"_fix_rx.html 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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:line
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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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# exponential-6 parameters for various species (one or more comment or blank lines) :pre
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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 :pre
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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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# POLYNOMIAL FILE (one or more comment or blank lines) :pre
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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 :pre
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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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:c,image(Eqs/pair_exp6_rx_oneFluid.jpg)
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where
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:c,image(Eqs/pair_exp6_rx_oneFluid2.jpg)
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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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:line
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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 "pair_modify"_pair_modify.html 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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:line
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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 "Speed packages"_Speed_packages.html 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 "Build
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package"_Build_package.html 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 "-suffix command-line
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switch"_Run_options.html when you invoke LAMMPS, or you can use the
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"suffix"_suffix.html command in your input script.
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See the "Speed packages"_Speed_packages.html doc page for more
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instructions on how to use the accelerated styles effectively.
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:line
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[Restrictions:]
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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 "Build
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package"_Build_package.html doc page for more info.
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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[Default:] fractional weighting
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