2006-09-22 00:22:34 +08:00
|
|
|
<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 dpd command
|
|
|
|
</H3>
|
2014-03-20 22:50:17 +08:00
|
|
|
<H3>pair_style dpd/gpu command
|
|
|
|
</H3>
|
2011-10-07 01:32:51 +08:00
|
|
|
<H3>pair_style dpd/omp command
|
|
|
|
</H3>
|
2010-05-06 22:37:29 +08:00
|
|
|
<H3>pair_style dpd/tstat command
|
|
|
|
</H3>
|
2014-03-20 22:50:17 +08:00
|
|
|
<H3>pair_style dpd/tstat/gpu command
|
|
|
|
</H3>
|
2011-10-07 01:32:51 +08:00
|
|
|
<H3>pair_style dpd/tstat/omp command
|
|
|
|
</H3>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P><B>Syntax:</B>
|
|
|
|
</P>
|
2010-05-06 22:37:29 +08:00
|
|
|
<PRE>pair_style dpd T cutoff seed
|
|
|
|
pair_style dpd/tstat Tstart Tstop cutoff seed
|
2006-09-22 00:22:34 +08:00
|
|
|
</PRE>
|
|
|
|
<UL><LI>T = temperature (temperature units)
|
2010-05-06 22:37:29 +08:00
|
|
|
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
|
2006-09-22 00:22:34 +08:00
|
|
|
<LI>cutoff = global cutoff for DPD interactions (distance units)
|
2007-10-10 07:40:45 +08:00
|
|
|
<LI>seed = random # seed (positive integer)
|
2006-09-22 00:22:34 +08:00
|
|
|
</UL>
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
</P>
|
|
|
|
<PRE>pair_style dpd 1.0 2.5 34387
|
|
|
|
pair_coeff * * 3.0 1.0
|
|
|
|
pair_coeff 1 1 3.0 1.0 1.0
|
|
|
|
</PRE>
|
2010-05-06 22:37:29 +08:00
|
|
|
<PRE>pair_style dpd/tstat 1.0 1.0 2.5 34387
|
|
|
|
pair_coeff * * 1.0
|
|
|
|
pair_coeff 1 1 1.0 1.0
|
|
|
|
</PRE>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P><B>Description:</B>
|
|
|
|
</P>
|
|
|
|
<P>Style <I>dpd</I> computes a force field for dissipative particle dynamics
|
2010-05-06 22:37:29 +08:00
|
|
|
(DPD) following the exposition in <A HREF = "#Groot">(Groot)</A>.
|
|
|
|
</P>
|
|
|
|
<P>Style <I>dpd/tstat</I> invokes a DPD thermostat on pairwise interactions,
|
|
|
|
which is equivalent to the non-conservative portion of the DPD force
|
2013-08-24 00:08:03 +08:00
|
|
|
field. This pair-wise thermostat can be used in conjunction with any
|
|
|
|
<A HREF = "pair_style.html">pair style</A>, and in leiu of per-particle thermostats
|
|
|
|
like <A HREF = "fix_langevin.html">fix langevin</A> or ensemble thermostats like
|
|
|
|
Nose Hoover as implemented by <A HREF = "fix_nh.html">fix nvt</A>. To use
|
|
|
|
<I>dpd/stat</I> as a thermostat for another pair style, use the <A HREF = "pair_hybrid.html">pair_style
|
2010-05-06 22:37:29 +08:00
|
|
|
hybrid/overlay</A> command to compute both the desired
|
2010-05-08 00:29:19 +08:00
|
|
|
pair interaction and the thermostat for each pair of particles.
|
2010-05-06 22:37:29 +08:00
|
|
|
</P>
|
|
|
|
<P>For style <I>dpd</I>, the force on atom I due to atom J is given as a sum
|
|
|
|
of 3 terms
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
<CENTER><IMG SRC = "Eqs/pair_dpd.jpg">
|
|
|
|
</CENTER>
|
2008-06-25 03:47:40 +08:00
|
|
|
<P>where Fc is a conservative force, Fd is a dissipative force, and Fr is
|
2006-09-22 00:22:34 +08:00
|
|
|
a random force. Rij is a unit vector in the direction Ri - Rj, Vij is
|
|
|
|
the vector difference in velocities of the two atoms = Vi - Vj, alpha
|
|
|
|
is a Gaussian random number with zero mean and unit variance, dt is
|
|
|
|
the timestep size, and w(r) is a weighting factor that varies between
|
2009-11-03 02:25:19 +08:00
|
|
|
0 and 1. Rc is the cutoff. Sigma is set equal to sqrt(2 Kb T gamma),
|
|
|
|
where Kb is the Boltzmann constant and T is the temperature parameter
|
|
|
|
in the pair_style command.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2010-05-06 22:37:29 +08:00
|
|
|
<P>For style <I>dpd/tstat</I>, the force on atom I due to atom J is the same
|
|
|
|
as the above equation, except that the conservative Fc term is
|
|
|
|
dropped. Also, during the run, T is set each timestep to a ramped
|
|
|
|
value from Tstart to Tstop.
|
2008-06-25 03:47:40 +08:00
|
|
|
</P>
|
2010-05-06 22:37:29 +08:00
|
|
|
<P>For style <I>dpd</I>, the pairwise energy associated with style <I>dpd</I> is
|
2010-05-07 23:28:16 +08:00
|
|
|
only due to the conservative force term Fc, and is shifted to be zero
|
|
|
|
at the cutoff distance Rc. The pairwise virial is calculated using
|
|
|
|
all 3 terms. For style <I>dpd/tstat</I> there is no pairwise energy, but
|
|
|
|
the last two terms of the formula make a contribution to the virial.
|
2010-05-06 22:37:29 +08:00
|
|
|
</P>
|
|
|
|
<P>For style <I>dpd</I>, 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
|
2006-09-22 00:22:34 +08:00
|
|
|
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
|
|
|
|
commands:
|
|
|
|
</P>
|
|
|
|
<UL><LI>A (force units)
|
|
|
|
<LI>gamma (force/velocity units)
|
|
|
|
<LI>cutoff (distance units)
|
|
|
|
</UL>
|
|
|
|
<P>The last coefficient is optional. If not specified, the global DPD
|
|
|
|
cutoff is used. Note that sigma is set equal to sqrt(2 T gamma),
|
|
|
|
where T is the temperature set by the <A HREF = "pair_style.html">pair_style</A>
|
|
|
|
command so it does not need to be specified.
|
|
|
|
</P>
|
2010-05-06 22:37:29 +08:00
|
|
|
<P>For style <I>dpd/tstat</I>, the coefficiencts defined for each pair of
|
|
|
|
atoms types via the <A HREF = "pair_coeff.html">pair_coeff</A> command is the same,
|
|
|
|
except that A is not included.
|
|
|
|
</P>
|
2014-03-20 22:50:17 +08:00
|
|
|
<P>The GPU-accelerated versions of these styles are implemented based on
|
|
|
|
the work of <A HREF = "#Afshar">(Afshar)</A> and <A HREF = "#Phillips">(Phillips)</A>.
|
|
|
|
</P>
|
2014-11-22 08:36:53 +08:00
|
|
|
<P>IMPORTANT NOTE: If you are modeling DPD polymer chains, you may want
|
|
|
|
to use the <A HREF = "pair_srp.html">pair_style srp</A> command in conjuction with
|
|
|
|
these pair styles. It is a soft segmental repulsive potential (SRP)
|
|
|
|
that can prevent DPD polymer chains from crossing each other.
|
|
|
|
</P>
|
2007-06-25 22:36:36 +08:00
|
|
|
<HR>
|
|
|
|
|
2014-08-15 00:30:25 +08:00
|
|
|
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
|
|
|
|
functionally the same as the corresponding style without the suffix.
|
|
|
|
They have been optimized to run faster, depending on your available
|
|
|
|
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
|
|
|
|
of the manual. The accelerated styles take the same arguments and
|
|
|
|
should produce the same results, except for round-off and precision
|
|
|
|
issues.
|
|
|
|
</P>
|
|
|
|
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
|
|
|
|
KOKKOS, USER-OMP and OPT packages, respectively. They are only
|
|
|
|
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
|
|
|
|
LAMMPS</A> section for more info.
|
2011-10-07 01:32:51 +08:00
|
|
|
</P>
|
|
|
|
<P>You can specify the accelerated styles explicitly in your input script
|
2012-01-28 07:39:14 +08:00
|
|
|
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
|
2011-10-07 01:32:51 +08:00
|
|
|
switch</A> when you invoke LAMMPS, or you can
|
|
|
|
use the <A HREF = "suffix.html">suffix</A> command in your input script.
|
|
|
|
</P>
|
2011-12-14 04:35:35 +08:00
|
|
|
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
|
|
|
|
more instructions on how to use the accelerated styles effectively.
|
2011-10-07 01:32:51 +08:00
|
|
|
</P>
|
|
|
|
<HR>
|
|
|
|
|
2008-01-22 02:12:34 +08:00
|
|
|
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2010-05-06 22:37:29 +08:00
|
|
|
<P>These pair styles do not support mixing. Thus, coefficients for all
|
2007-06-25 22:36:36 +08:00
|
|
|
I,J pairs must be specified explicitly.
|
|
|
|
</P>
|
2010-05-06 22:37:29 +08:00
|
|
|
<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
|
2010-05-07 23:28:16 +08:00
|
|
|
shift option for the energy of the pair interaction. Note that as
|
|
|
|
discussed above, the energy due to the conservative Fc term is already
|
|
|
|
shifted to be 0.0 at the cutoff distance Rc.
|
2007-06-25 22:36:36 +08:00
|
|
|
</P>
|
|
|
|
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
|
2010-05-06 22:37:29 +08:00
|
|
|
for these pair styles.
|
2007-06-25 22:36:36 +08:00
|
|
|
</P>
|
2010-05-06 22:37:29 +08:00
|
|
|
<P>These pair style do not support the <A HREF = "pair_modify.html">pair_modify</A>
|
2007-06-25 22:36:36 +08:00
|
|
|
tail option for adding long-range tail corrections to energy and
|
|
|
|
pressure.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2010-05-06 22:37:29 +08:00
|
|
|
<P>These pair styles writes their information to <A HREF = "restart.html">binary restart
|
2007-06-25 22:36:36 +08:00
|
|
|
files</A>, so pair_style and pair_coeff commands do not need
|
|
|
|
to be specified in an input script that reads a restart file. Note
|
2008-02-20 05:47:37 +08:00
|
|
|
that the user-specified random number seed is stored in the restart
|
2007-06-25 22:36:36 +08:00
|
|
|
file, so when a simulation is restarted, each processor will
|
|
|
|
re-initialize its random number generator the same way it did
|
2008-02-20 05:47:37 +08:00
|
|
|
initially. This means the random forces will be random, but will not
|
2007-06-25 22:36:36 +08:00
|
|
|
be the same as they would have been if the original simulation had
|
|
|
|
continued past the restart time.
|
|
|
|
</P>
|
2010-05-06 22:37:29 +08:00
|
|
|
<P>These pair styles can only be used via the <I>pair</I> keyword of the
|
|
|
|
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
|
2007-10-12 07:09:49 +08:00
|
|
|
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
|
2007-10-04 08:21:14 +08:00
|
|
|
</P>
|
2010-05-06 22:37:29 +08:00
|
|
|
<P>The <I>dpd/tstat</I> style can ramp its target temperature over multiple
|
|
|
|
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
|
|
|
|
command. See the <A HREF = "run.html">run</A> command for details of how to do
|
|
|
|
this.
|
|
|
|
</P>
|
2007-06-25 22:36:36 +08:00
|
|
|
<HR>
|
|
|
|
|
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
</P>
|
2007-02-23 00:52:24 +08:00
|
|
|
<P>The default frequency for rebuilding neighbor lists is every 10 steps
|
|
|
|
(see the <A HREF = "neigh_modify.html">neigh_modify</A> command). This may be too
|
2010-05-06 22:37:29 +08:00
|
|
|
infrequent for style <I>dpd</I> simulations since particles move rapidly
|
|
|
|
and can overlap by large amounts. If this setting yields a non-zero
|
|
|
|
number of "dangerous" reneighborings (printed at the end of a
|
|
|
|
simulation), you should experiment with forcing reneighboring more
|
|
|
|
often and see if system energies/trajectories change.
|
2007-02-23 00:52:24 +08:00
|
|
|
</P>
|
2014-06-05 20:50:23 +08:00
|
|
|
<P>These pair styles requires you to use the <A HREF = "comm_modify.html">comm_modify vel
|
|
|
|
yes</A> command so that velocites are stored by ghost
|
2009-11-10 04:18:47 +08:00
|
|
|
atoms.
|
|
|
|
</P>
|
2012-06-19 07:15:48 +08:00
|
|
|
<P>These pair styles will not restart exactly when using the
|
|
|
|
<A HREF = "read_restart.html">read_restart</A> command, though they should provide
|
|
|
|
statistically similar results. This is because the forces they
|
|
|
|
compute depend on atom velocities. See the
|
|
|
|
<A HREF = "read_restart.html">read_restart</A> command for more details.
|
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P><B>Related commands:</B>
|
|
|
|
</P>
|
2010-05-08 00:29:19 +08:00
|
|
|
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_langevin.html">fix
|
2014-11-22 08:36:53 +08:00
|
|
|
langevin</A>, <A HREF = "pair_srp.html">pair_style srp</A>
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
<P><B>Default:</B> none
|
|
|
|
</P>
|
2007-01-30 07:28:45 +08:00
|
|
|
<HR>
|
|
|
|
|
|
|
|
<A NAME = "Groot"></A>
|
|
|
|
|
|
|
|
<P><B>(Groot)</B> Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
|
|
|
|
</P>
|
2014-03-20 22:50:17 +08:00
|
|
|
<A NAME = "Afshar"></A>
|
|
|
|
|
|
|
|
<P><B>(Afshar)</B> Afshar, F. Schmid, A. Pishevar, S. Worley, Comput Phys
|
2014-03-20 22:50:43 +08:00
|
|
|
Comm, 184, 1119-1128 (2013).
|
2014-03-20 22:50:17 +08:00
|
|
|
</P>
|
|
|
|
<A NAME = "Phillips"></A>
|
|
|
|
|
|
|
|
<P><B>(Phillips)</B> C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput
|
2014-03-22 04:46:48 +08:00
|
|
|
Phys Comm, 230, 7191-7201 (2011).
|
2014-03-20 22:50:17 +08:00
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
</HTML>
|