forked from lijiext/lammps
194 lines
6.1 KiB
Plaintext
194 lines
6.1 KiB
Plaintext
.. index:: pair_style lj/gromacs
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pair_style lj/gromacs command
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=============================
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pair_style lj/gromacs/cuda command
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==================================
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pair_style lj/gromacs/gpu command
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=================================
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pair_style lj/gromacs/omp command
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=================================
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pair_style lj/gromacs/coul/gromacs command
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==========================================
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pair_style lj/gromacs/coul/gromacs/cuda command
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===============================================
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pair_style lj/gromacs/coul/gromacs/omp 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 style args
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* style = *lj/gromacs* or *lj/gromacs/coul/gromacs*
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* args = list of arguments for a particular style
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.. parsed-literal::
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*lj/gromacs* args = inner outer
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inner, outer = global switching cutoffs for Lennard Jones
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*lj/gromacs/coul/gromacs* args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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Examples
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""""""""
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.. parsed-literal::
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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
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.. parsed-literal::
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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
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Description
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"""""""""""
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The *lj/gromacs* 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 `GROMACS <http://www.gromacs.org>`_ MD code and for
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the coarse-grained models of :ref:`(Marrink) <Marrink>`.
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.. image:: Eqs/pair_gromacs.jpg
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:align: center
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r1 is the inner cutoff; rc is the outer cutoff. The coefficients A, B,
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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,
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S(rc) = -E(rc), S'(rc) = -E'(rc), and S''(rc) = -E''(rc),
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where E(r) is the corresponding term
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in the LJ or Coulombic potential energy function.
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Single and double primes denote first and second
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derivatives with respect to r, respectively.
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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
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inner Coulombic cutoff can be >= 0.
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The following coefficients must be defined for each pair of atoms
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types via the :doc:`pair_coeff <pair_coeff>` 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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:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
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commands, or by mixing as described below:
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* epsilon (energy units)
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* sigma (distance units)
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* inner (distance units)
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* outer (distance units)
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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.
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The last 2 coefficients are optional inner and outer cutoffs for style
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*lj/gromacs*. If not specified, the global *inner* and *outer* values
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are used.
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The last 2 coefficients cannot be used with style
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*lj/gromacs/coul/gromacs* 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.
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----------
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Styles *intel*, *kk*, with a *cuda*, *gpu*, *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 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 :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, 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 *geometric*. See the "pair_modify" command
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for details.
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None of the GROMACS pair styles support the
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:doc:`pair_modify <pair_modify>` 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.
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The :doc:`pair_modify <pair_modify>` table option is not relevant
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for this pair style.
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None of the GROMACS pair styles support the
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:doc:`pair_modify <pair_modify>` 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.
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All of the GROMACS pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
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not need to be specified in an input script that reads a restart file.
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All of the GROMACS pair styles can only be used via the *pair*
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keyword of the :doc:`run_style respa <run_style>` command. They do not
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support the *inner*, *middle*, *outer* keywords.
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----------
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`pair_coeff <pair_coeff>`
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**Default:** none
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----------
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.. _Marrink:
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**(Marrink)** Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).
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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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