Homec4science
Diffusion lammps (master) Browse

lammps/doc/pair_cmm.html
23984ac78b8emaster

Last Change
Raw File

pair_cmm.html
View Options

<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style cg/cmm command
</H3>
<H3>pair_style cg/cmm/gpu command
</H3>
<H3>pair_style cg/cmm/coul/cut command
</H3>
<H3>pair_style cg/cmm/coul/long command
</H3>
<H3>pair_style cg/cmm/coul/long/gpu command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>cg/cmm</I> or <I>cg/cmm/gpu</I> or <I>cg/cmm/coul/cut</I> or <I>cg/cmm/coul/long</I> or <I>cg/cmm/coul/long/gpu</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>cg/cmm</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>cg/cmm/gpu</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>cg/cmm/coul/cut</I> args = cutoff (cutoff2) (kappa)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
kappa = Debye length (optional, defaults to 0.0 = disabled) (inverse distance units)
<I>cg/cmm/coul/long</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<PRE> <I>cg/cmm/coul/long/gpu</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style cg/cmm 2.5
pair_coeff 1 1 lj12_6 1 1.1 2.8
</PRE>
<PRE>pair_style cg/cmm/coul/cut 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 9.0
pair_coeff 1 1 lj12_4 100.0 3.5 9.0 9.0
</PRE>
<PRE>pair_style cg/cmm/coul/long 10.0
pair_style cg/cmm/coul/long 10.0 8.0
pair_coeff 1 1 lj9_6 100.0 3.5 9.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cg/cmm</I> styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
given by
</P>
<CENTER><IMG SRC = "Eqs/pair_cmm.jpg">
</CENTER>
<P>as required for the CMM Coarse-grained MD parametrization discussed in
<A HREF = "#Shinoda">(Shinoda)</A> and <A HREF = "#DeVane">(DeVane)</A>. Rc is the cutoff.
</P>
<P>Style <I>cg/cmm/gpu</I> is a GPU-enabled version of style <I>cg/cmm</I>. See
more details below.
</P>
<P>Style <I>cg/cmm/coul/cut</I> adds a Coulombic pairwise interaction given by
</P>
<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
</CENTER>
<P>where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, and epsilon is the dielectric constant which can be set
by the <A HREF = "dielectric.html">dielectric</A> command. If one cutoff is
specified in the pair_style command, it is used for both the LJ and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively.
</P>
<P>This style also contains an additional exp() damping factor
to the Coulombic term, given by
</P>
<CENTER><IMG SRC = "Eqs/pair_debye.jpg">
</CENTER>
<P>where kappa is the Debye length (kappa=0.0 is the unscreened coulomb).
This potential is another way to mimic the screening effect of a polar
solvent.
</P>
<P>Style <I>cg/cmm/coul/long</I> computes the same Coulombic interactions as
style <I>cg/cmm/coul/cut</I> except that an additional damping factor is
applied to the Coulombic term so it can be used in conjunction with
the <A HREF = "kspace_style.html">kspace_style</A> command and its <I>ewald</I> or <I>pppm</I>
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>Style <I>cg/cmm/coul/long/gpu</I> is a GPU-enabled version of style
<I>cg/cmm/coul/long</I>. See more details below.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>cg_type (lj9_6, lj12_4, or lj12_6)
<LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff1 (distance units)
<LI>cutoff2 (distance units)
</UL>
<P>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum. The prefactors
are chosen so that the potential minimum is at -epsilon.
</P>
<P>The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.
</P>
<P>For <I>cg/cmm/coul/long</I> only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
</P>
<HR>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
</P>
<P>Additional requirements in your input script to run the styles with a
<I>gpu</I> suffix are as follows:
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, and rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the cg/cmm pair styles <I>cannot</I> be mixed,
since different pairs may have different exponents. So all parameters
for all pairs have to be specified explicitly through the "pair_coeff"
command. Defining then in a data file is also not supported, due to
limitations of that file format.
</P>
<P>All of the cg/cmm pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the
Lennard-Jones portion of the pair interaction.
</P>
<P>The <I>cg/cmm/coul/long</I> pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
</P>
<P>All of the cg/cmm pair styles write their information to <A HREF = "restart.html">binary
restart files</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>The cg/cmm, cg/cmm/coul/cut and lj/cut/coul/long pair styles support
the use of the <I>inner</I>, <I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
respa</A> command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
See the <A HREF = "run_style.html">run_style</A> command for details.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>All of the cg/cmm pair styles are part of the "user-cg-cmm"
package. They are only enabled if LAMMPS was built with that package.
The <I>cg/cmm/coul/long</I> style also requires the "kspace" package to be
built (which is enabled by default). The styles with a <I>gpu</I> suffix
are part of the "gpu" package. They are only enabled if LAMMPS was
built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "angle_cmm.html">angle_style cg/cmm</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Shinoda"></A>
<P><B>(Shinoda)</B> Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
</P>
<A NAME = "DeVane"></A>
<P><B>(DeVane)</B> Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
</P>
</HTML>
c4science · Help