forked from lijiext/lammps
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HTML
212 lines
8.6 KiB
HTML
<HTML>
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<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>
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<H3>pair_style dpd command
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</H3>
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<H3>pair_style dpd/gpu command
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</H3>
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<H3>pair_style dpd/omp command
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</H3>
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<H3>pair_style dpd/tstat command
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</H3>
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<H3>pair_style dpd/tstat/gpu command
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</H3>
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<H3>pair_style dpd/tstat/omp command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style dpd T cutoff seed
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pair_style dpd/tstat Tstart Tstop cutoff seed
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</PRE>
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<UL><LI>T = temperature (temperature units)
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<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
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<LI>cutoff = global cutoff for DPD interactions (distance units)
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<LI>seed = random # seed (positive integer)
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style dpd 1.0 2.5 34387
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pair_coeff * * 3.0 1.0
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pair_coeff 1 1 3.0 1.0 1.0
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</PRE>
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<PRE>pair_style dpd/tstat 1.0 1.0 2.5 34387
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pair_coeff * * 1.0
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pair_coeff 1 1 1.0 1.0
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Style <I>dpd</I> computes a force field for dissipative particle dynamics
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(DPD) following the exposition in <A HREF = "#Groot">(Groot)</A>.
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</P>
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<P>Style <I>dpd/tstat</I> invokes a DPD thermostat on pairwise interactions,
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which is equivalent to the non-conservative portion of the DPD force
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field. This pair-wise thermostat can be used in conjunction with any
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<A HREF = "pair_style.html">pair style</A>, and in leiu of per-particle thermostats
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like <A HREF = "fix_langevin.html">fix langevin</A> or ensemble thermostats like
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Nose Hoover as implemented by <A HREF = "fix_nh.html">fix nvt</A>. To use
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<I>dpd/stat</I> as a thermostat for another pair style, use the <A HREF = "pair_hybrid.html">pair_style
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hybrid/overlay</A> command to compute both the desired
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pair interaction and the thermostat for each pair of particles.
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</P>
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<P>For style <I>dpd</I>, the force on atom I due to atom J is given as a sum
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of 3 terms
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</P>
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<CENTER><IMG SRC = "Eqs/pair_dpd.jpg">
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</CENTER>
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<P>where Fc is a conservative force, Fd is a dissipative force, and Fr is
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a random force. Rij is a unit vector in the direction Ri - Rj, Vij is
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the vector difference in velocities of the two atoms = Vi - Vj, alpha
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is a Gaussian random number with zero mean and unit variance, dt is
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the timestep size, and w(r) is a weighting factor that varies between
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0 and 1. Rc is the cutoff. Sigma is set equal to sqrt(2 Kb T gamma),
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where Kb is the Boltzmann constant and T is the temperature parameter
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in the pair_style command.
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</P>
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<P>For style <I>dpd/tstat</I>, the force on atom I due to atom J is the same
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as the above equation, except that the conservative Fc term is
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dropped. Also, during the run, T is set each timestep to a ramped
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value from Tstart to Tstop.
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</P>
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<P>For style <I>dpd</I>, the pairwise energy associated with style <I>dpd</I> is
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only due to the conservative force term Fc, and is shifted to be zero
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at the cutoff distance Rc. The pairwise virial is calculated using
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all 3 terms. For style <I>dpd/tstat</I> there is no pairwise energy, but
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the last two terms of the formula make a contribution to the virial.
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</P>
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<P>For style <I>dpd</I>, the following coefficients must be defined for each
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pair of atoms types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in
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the examples above, or in the data file or restart files read by the
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<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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commands:
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</P>
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<UL><LI>A (force units)
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<LI>gamma (force/velocity units)
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<LI>cutoff (distance units)
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</UL>
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<P>The last coefficient is optional. If not specified, the global DPD
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cutoff is used. Note that sigma is set equal to sqrt(2 T gamma),
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where T is the temperature set by the <A HREF = "pair_style.html">pair_style</A>
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command so it does not need to be specified.
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</P>
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<P>For style <I>dpd/tstat</I>, the coefficiencts defined for each pair of
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atoms types via the <A HREF = "pair_coeff.html">pair_coeff</A> command is the same,
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except that A is not included.
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</P>
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<P>The GPU-accelerated versions of these styles are implemented based on
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the work of <A HREF = "#Afshar">(Afshar)</A> and <A HREF = "#Phillips">(Phillips)</A>.
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</P>
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<HR>
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<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> 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 <A HREF = "Section_accelerate.html">Section_accelerate</A> 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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</P>
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<P>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 <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
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section for more info.
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</P>
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<P>You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
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switch</A> when you invoke LAMMPS, or you can
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use the <A HREF = "suffix.html">suffix</A> command in your input script.
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</P>
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<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
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more instructions on how to use the accelerated styles effectively.
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</P>
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<HR>
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<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
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</P>
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<P>These pair styles do not support mixing. Thus, coefficients for all
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I,J pairs must be specified explicitly.
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</P>
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<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
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shift option for the energy of the pair interaction. Note that as
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discussed above, the energy due to the conservative Fc term is already
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shifted to be 0.0 at the cutoff distance Rc.
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</P>
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<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
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for these pair styles.
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</P>
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<P>These pair style do not support the <A HREF = "pair_modify.html">pair_modify</A>
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tail option for adding long-range tail corrections to energy and
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pressure.
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</P>
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<P>These pair styles writes their information to <A HREF = "restart.html">binary restart
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files</A>, 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. Note
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that the user-specified random number seed is stored in the restart
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file, so when a simulation is restarted, each processor will
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re-initialize its random number generator the same way it did
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initially. This means the random forces will be random, but will not
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be the same as they would have been if the original simulation had
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continued past the restart time.
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</P>
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<P>These pair styles can only be used via the <I>pair</I> keyword of the
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<A HREF = "run_style.html">run_style respa</A> command. They do not support the
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<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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</P>
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<P>The <I>dpd/tstat</I> style can ramp its target temperature over multiple
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runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
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command. See the <A HREF = "run.html">run</A> command for details of how to do
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this.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>The default frequency for rebuilding neighbor lists is every 10 steps
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(see the <A HREF = "neigh_modify.html">neigh_modify</A> command). This may be too
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infrequent for style <I>dpd</I> simulations since particles move rapidly
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and can overlap by large amounts. If this setting yields a non-zero
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number of "dangerous" reneighborings (printed at the end of a
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simulation), you should experiment with forcing reneighboring more
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often and see if system energies/trajectories change.
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</P>
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<P>These pair styles requires you to use the <A HREF = "communicate.html">communicate vel
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yes</A> option so that velocites are stored by ghost
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atoms.
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</P>
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<P>These pair styles will not restart exactly when using the
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<A HREF = "read_restart.html">read_restart</A> command, though they should provide
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statistically similar results. This is because the forces they
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compute depend on atom velocities. See the
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<A HREF = "read_restart.html">read_restart</A> command for more details.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_langevin.html">fix
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langevin</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Groot"></A>
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<P><B>(Groot)</B> Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
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</P>
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<A NAME = "Afshar"></A>
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<P><B>(Afshar)</B> Afshar, F. Schmid, A. Pishevar, S. Worley, Comput Phys
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Comm, 184, 1119-1128 (2013).
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</P>
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<A NAME = "Phillips"></A>
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<P><B>(Phillips)</B> C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput
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Phys Comm, 230, 7191-7201 (2011).
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</P>
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</HTML>
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