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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_accelerate.html" > 5. Accelerating LAMMPS performance< / a > < / li >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_modify.html" > 10. Modifying & extending LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_python.html" > 11. Python interface to LAMMPS< / a > < / li >
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< div class = "section" id = "pair-style-lj-gromacs-command" >
< span id = "index-0" > < / span > < h1 > pair_style lj/gromacs command< a class = "headerlink" href = "#pair-style-lj-gromacs-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "pair-style-lj-gromacs-cuda-command" >
< h1 > pair_style lj/gromacs/cuda command< a class = "headerlink" href = "#pair-style-lj-gromacs-cuda-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "pair-style-lj-gromacs-gpu-command" >
< h1 > pair_style lj/gromacs/gpu command< a class = "headerlink" href = "#pair-style-lj-gromacs-gpu-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "pair-style-lj-gromacs-omp-command" >
< h1 > pair_style lj/gromacs/omp command< a class = "headerlink" href = "#pair-style-lj-gromacs-omp-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "pair-style-lj-gromacs-coul-gromacs-command" >
< h1 > pair_style lj/gromacs/coul/gromacs command< a class = "headerlink" href = "#pair-style-lj-gromacs-coul-gromacs-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "pair-style-lj-gromacs-coul-gromacs-cuda-command" >
< h1 > pair_style lj/gromacs/coul/gromacs/cuda command< a class = "headerlink" href = "#pair-style-lj-gromacs-coul-gromacs-cuda-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "pair-style-lj-gromacs-coul-gromacs-omp-command" >
< h1 > pair_style lj/gromacs/coul/gromacs/omp command< a class = "headerlink" href = "#pair-style-lj-gromacs-coul-gromacs-omp-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > pair_style style args
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > style = < em > lj/gromacs< / em > or < em > lj/gromacs/coul/gromacs< / em > < / li >
< li > args = list of arguments for a particular style< / li >
< / ul >
< pre class = "literal-block" >
< em > lj/gromacs< / em > args = inner outer
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inner, outer = global switching cutoffs for Lennard Jones
< em > lj/gromacs/coul/gromacs< / em > args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
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< / pre >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > pair_style lj/gromacs 9.0 12.0
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pair_coeff * * 100.0 2.0
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pair_coeff 2 2 100.0 2.0 8.0 10.0
< / pre > < / div >
< / div >
< div class = "highlight-python" > < div class = "highlight" > < pre > pair_style lj/gromacs/coul/gromacs 9.0 12.0
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pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The < em > lj/gromacs< / em > styles compute shifted LJ and Coulombic interactions
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with an additional switching function S(r) that ramps the energy and force
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smoothly to zero between an inner and outer cutoff. It is a commonly
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used potential in the < a class = "reference external" href = "http://www.gromacs.org" > GROMACS< / a > MD code and for
the coarse-grained models of < a class = "reference internal" href = "#marrink" > < span > (Marrink)< / span > < / a > .< / p >
< img alt = "_images/pair_gromacs.jpg" class = "align-center" src = "_images/pair_gromacs.jpg" / >
< p > r1 is the inner cutoff; rc is the outer cutoff. The coefficients A, B,
and C are computed by LAMMPS to perform the shifting and smoothing.
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The function
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S(r) is actually applied once to each term of the LJ formula and once
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to the Coulombic formula, so there are 2 or 3 sets of A,B,C coefficients
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depending on which pair_style is used. The boundary conditions
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applied to the smoothing function are as follows: S’ (r1) = S’ ‘ (r1) = 0,
S(rc) = -E(rc), S’ (rc) = -E’ (rc), and S’ ‘ (rc) = -E’ ‘ (rc),
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where E(r) is the corresponding term
in the LJ or Coulombic potential energy function.
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Single and double primes denote first and second
derivatives with respect to r, respectively.< / p >
< p > The inner and outer cutoff for the LJ and Coulombic terms can be the
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same or different depending on whether 2 or 4 arguments are used in
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the pair_style command. The inner LJ cutoff must be > 0, but the
inner Coulombic cutoff can be > = 0.< / p >
< p > The following coefficients must be defined for each pair of atoms
types via the < a class = "reference internal" href = "pair_coeff.html" > < em > pair_coeff< / em > < / a > command as in the examples
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above, or in the data file or restart files read by the
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< a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > or < a class = "reference internal" href = "read_restart.html" > < em > read_restart< / em > < / a >
commands, or by mixing as described below:< / p >
< ul class = "simple" >
< li > epsilon (energy units)< / li >
< li > sigma (distance units)< / li >
< li > inner (distance units)< / li >
< li > outer (distance units)< / li >
< / ul >
< p > Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum at 2^(1/6)
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sigma.< / p >
< p > The last 2 coefficients are optional inner and outer cutoffs for style
< em > lj/gromacs< / em > . If not specified, the global < em > inner< / em > and < em > outer< / em > values
are used.< / p >
< p > The last 2 coefficients cannot be used with style
< em > lj/gromacs/coul/gromacs< / em > because this force field does not allow
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varying cutoffs for individual atom pairs; all pairs use the global
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cutoff(s) specified in the pair_style command.< / p >
< hr class = "docutils" / >
< p > Styles < em > intel< / em > , < em > kk< / em > , with a < em > cuda< / em > , < em > gpu< / em > , < em > omp< / em > , or < em > opt< / em > suffix are
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functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
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hardware, as discussed in < a class = "reference internal" href = "Section_accelerate.html" > < em > Section_accelerate< / em > < / a >
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of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
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issues.< / p >
< p > These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if LAMMPS was built with those packages. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section for more info.< / p >
< p > You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the < a class = "reference internal" href = "Section_start.html#start-7" > < span > -suffix command-line switch< / span > < / a > when you invoke LAMMPS, or you can
use the < a class = "reference internal" href = "suffix.html" > < em > suffix< / em > < / a > command in your input script.< / p >
< p > See < a class = "reference internal" href = "Section_accelerate.html" > < em > Section_accelerate< / em > < / a > of the manual for
more instructions on how to use the accelerated styles effectively.< / p >
< hr class = "docutils" / >
< p > < strong > Mixing, shift, table, tail correction, restart, rRESPA info< / strong > :< / p >
< p > For atom type pairs I,J and I != J, the epsilon and sigma coefficients
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and cutoff distance for all of the lj/cut pair styles can be mixed.
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The default mix value is < em > geometric< / em > . See the “ pair_modify” command
for details.< / p >
< p > None of the GROMACS pair styles support the
< a class = "reference internal" href = "pair_modify.html" > < em > pair_modify< / em > < / a > shift option, since the Lennard-Jones
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portion of the pair interaction is already smoothed to 0.0 at the
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cutoff.< / p >
< p > The < a class = "reference internal" href = "pair_modify.html" > < em > pair_modify< / em > < / a > table option is not relevant
for this pair style.< / p >
< p > None of the GROMACS pair styles support the
< a class = "reference internal" href = "pair_modify.html" > < em > pair_modify< / em > < / a > tail option for adding long-range tail
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corrections to energy and pressure, since there are no corrections for
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a potential that goes to 0.0 at the cutoff.< / p >
< p > All of the GROMACS pair styles write their information to < a class = "reference internal" href = "restart.html" > < em > binary restart files< / em > < / a > , so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.< / p >
< p > All of the GROMACS pair styles can only be used via the < em > pair< / em >
keyword of the < a class = "reference internal" href = "run_style.html" > < em > run_style respa< / em > < / a > command. They do not
support the < em > inner< / em > , < em > middle< / em > , < em > outer< / em > keywords.< / p >
< / div >
< hr class = "docutils" / >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< blockquote >
< div > none< / div > < / blockquote >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "pair_coeff.html" > < em > pair_coeff< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
< hr class = "docutils" / >
< p id = "marrink" > < strong > (Marrink)< / strong > Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).< / p >
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