forked from lijiext/lammps
158 lines
5.3 KiB
Plaintext
158 lines
5.3 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,Section_commands.html#comm)
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:line
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pair_style gauss command :h3
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pair_style gauss/gpu command :h3
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pair_style gauss/omp command :h3
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pair_style gauss/cut command :h3
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pair_style gauss/cut/omp command :h3
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[Syntax:]
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pair_style gauss cutoff
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pair_style gauss/cut cutoff :pre
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cutoff = global cutoff for Gauss interactions (distance units) :ul
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[Examples:]
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pair_style gauss 12.0
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pair_coeff * * 1.0 0.9
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pair_coeff 1 4 1.0 0.9 10.0 :pre
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pair_style gauss/cut 3.5
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pair_coeff 1 4 0.2805 1.45 0.112 :pre
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[Description:]
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Style {gauss} computes a tethering potential of the form
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:c,image(Eqs/pair_gauss.jpg)
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between an atom and its corresponding tether site which will typically
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be a frozen atom in the simulation. Rc is the cutoff.
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The following coefficients must be defined for each pair of atom types
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via the "pair_coeff"_pair_coeff.html command as in the examples above,
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or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands:
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A (energy units)
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B (1/distance^2 units)
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cutoff (distance units) :ul
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The last coefficient is optional. If not specified, the global cutoff
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is used.
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Style {gauss/cut} computes a generalized Gaussian interaction potential
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between pairs of particles:
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:c,image(Eqs/pair_gauss_cut.jpg)
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where H determines together with the standard deviation sigma_h the
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peak height of the Gaussian function, and r_mh the peak position.
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Examples of the use of the Gaussian potentials include implicit
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solvent simulations of salt ions "(Lenart)"_#Lenart and of surfactants
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"(Jusufi)"_#Jusufi. In these instances the Gaussian potential mimics
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the hydration barrier between a pair of particles. The hydration
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barrier is located at r_mh and has a width of sigma_h. The prefactor
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determines the hight of the potential barrier.
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The following coefficients must be defined for each pair of atom types
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via the "pair_coeff"_pair_coeff.html command as in the example above,
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or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands:
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H (energy * distance units)
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r_mh (distance units)
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sigma_h (distance units) :ul
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The global cutoff (r_c) specified in the pair_style command is used.
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:line
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Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
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the same as the corresponding style without the suffix. They have
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been optimized to run faster, depending on your available hardware, as
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discussed in "Section_accelerate"_Section_accelerate.html of the
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manual. 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 USER-CUDA, GPU, USER-OMP and OPT
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packages, respectively. They are only enabled if LAMMPS was built with
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those packages. See the "Making LAMMPS"_Section_start.html#start_3
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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 "-suffix command-line
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switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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:line
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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These pair style do not support mixing. Thus, coefficients for all
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I,J pairs must be specified explicitly.
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The {gauss} style does not support the "pair_modify"_pair_modify.html
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shift option. There is no effect due to the Gaussian well beyond the
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cutoff; hence reasonable cutoffs need to be specified.
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The {gauss/cut} style supports the "pair_modify"_pair_modify.html shift
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option for the energy of the Gauss-potential portion of the pair
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interaction.
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The "pair_modify"_pair_modify.html table and tail options are not
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relevant for this pair style.
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This pair style does not support the "pair_modify"_pair_modify.html
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table option, since a tabulation capability does not exist for this
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potential.
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This pair style writes its information to "binary restart
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files"_restart.html, so pair_style and pair_coeff commands do not need
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to be specified in an input script that reads a restart file.
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This pair style can only be used via the {pair} keyword of the
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"run_style respa"_run_style.html command. It does not support the
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{inner}, {middle}, {outer} keywords.
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Thes {gauss} pair style tallies an "occupancy" count of how many Gaussian-well
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sites have an atom within the distance at which the force is a maximum
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= sqrt(0.5/b). This quantity can be accessed via the "compute
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pair"_compute_pair.html command as a vector of values of length 1.
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To print this quantity to the log file (with a descriptive column
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heading) the following commands could be included in an input script:
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compute gauss all pair gauss
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variable occ equal c_gauss\[1\]
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thermo_style custom step temp epair v_occ :pre
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:line
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[Restrictions:]
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The {gauss/cut} style is part of the "user-misc" package. It is only enabled
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if LAMMPS is build with that package. See the "Making of LAMMPS"_Section_start.html#3
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section for more info.
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[Related commands:]
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"pair_coeff"_pair_coeff.html,
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"pair_style coul/diel"_pair_coul_diel.html
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[Default:] none
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