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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4087 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-05-06 14:37:29 +00:00
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24
doc/Section_commands.html
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@ -376,18 +376,18 @@ potentials. Click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_airebo.html">airebo</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/long</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_colloid.html">colloid</A></TD><TD ><A HREF = "pair_coul.html">coul/cut</A></TD><TD ><A HREF = "pair_coul.html">coul/debye</A></TD><TD ><A HREF = "pair_coul.html">coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">dipole/cut</A></TD><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj96_cut.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_peri_pmb.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">dipole/cut</A></TD><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96_cut.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_peri_pmb.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
</TD></TR></TABLE></DIV>
<P>These are pair styles contributed by users, which can be used if

1
doc/Section_commands.txt
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@ -538,6 +538,7 @@ potentials. Click on the style itself for a full description:
"coul/long"_pair_coul.html,
"dipole/cut"_pair_dipole.html,
"dpd"_pair_dpd.html,
"dpd/tstat"_pair_dpd.html,
"dsmc"_pair_dsmc.html,
"eam"_pair_eam.html,
"eam/opt"_pair_eam.html,

32
doc/Section_howto.html
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@ -1262,9 +1262,11 @@ that subtracts a velocity bias. This allows the translational
velocity of extended spherical or aspherical particles to be adjusted
in prescribed ways.
</P>
<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>. Four
thermostatting fixes are currently available: Nose-Hoover (nvt),
Berendsen, Langevin, and direct rescaling (temp/rescale):
<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>, or in one
case by a pair style. Four thermostatting fixes are currently
available: Nose-Hoover (nvt), Berendsen, Langevin, and direct
rescaling (temp/rescale). Dissipative particle dynamics (DPD)
thermostatting can be invoked via the <I>dpd/tstat</I> pair style:
</P>
<UL><LI><A HREF = "fix_nh.html">fix nvt</A>
<LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
@ -1273,6 +1275,7 @@ Berendsen, Langevin, and direct rescaling (temp/rescale):
<LI><A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>
<LI><A HREF = "fix_langevin.html">fix langevin</A>
<LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
<LI><A HREF = "pair_dpd.html">pair_style dpd/tstat</A>
</UL>
<P><A HREF = "fix_nh.html">Fix nvt</A> only thermostats the translational velocity of
particles. <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> also does this, except
@ -1284,15 +1287,20 @@ nvt/asphere</A> thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
</P>
<P>Any of these fixes can use temperature computes that remove bias for
two purposes: (a) computing the current temperature to compare to the
requested target temperature, and (b) adjusting only the thermal
temperature component of the particle's velocities. See the doc pages
for the individual fixes and for the <A HREF = "fix_modify.html">fix_modify</A>
command for instructions on how to assign a temperature compute to a
thermostatting fix. For example, you can apply a thermostat to only
the x and z components of velocity by using it in conjunction with
<A HREF = "compute_temp_partial.html">compute temp/partial</A>.
<P>DPD thermostatting alters pairwise interactions in a manner analagous
to the per-particle thermostatting of <A HREF = "fix_langevin.html">fix
langevin</A>.
</P>
<P>Any of the thermostatting fixes can use temperature computes that
remove bias for two purposes: (a) computing the current temperature to
compare to the requested target temperature, and (b) adjusting only
the thermal temperature component of the particle's velocities. See
the doc pages for the individual fixes and for the
<A HREF = "fix_modify.html">fix_modify</A> command for instructions on how to assign
a temperature compute to a thermostatting fix. For example, you can
apply a thermostat to only the x and z components of velocity by using
it in conjunction with <A HREF = "compute_temp_partial.html">compute
temp/partial</A>.
</P>
<P>IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
they update the velocities and positions of particles due to forces

34
doc/Section_howto.txt
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@ -1251,9 +1251,11 @@ that subtracts a velocity bias. This allows the translational
velocity of extended spherical or aspherical particles to be adjusted
in prescribed ways.
Thermostatting in LAMMPS is performed by "fixes"_fix.html. Four
thermostatting fixes are currently available: Nose-Hoover (nvt),
Berendsen, Langevin, and direct rescaling (temp/rescale):
Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one
case by a pair style. Four thermostatting fixes are currently
available: Nose-Hoover (nvt), Berendsen, Langevin, and direct
rescaling (temp/rescale). Dissipative particle dynamics (DPD)
thermostatting can be invoked via the {dpd/tstat} pair style:
"fix nvt"_fix_nh.html
"fix nvt/sphere"_fix_nvt_sphere.html
@ -1261,7 +1263,8 @@ Berendsen, Langevin, and direct rescaling (temp/rescale):
"fix nvt/sllod"_fix_nvt_sllod.html
"fix temp/berendsen"_fix_temp_berendsen.html
"fix langevin"_fix_langevin.html
"fix temp/rescale"_fix_temp_rescale.html :ul
"fix temp/rescale"_fix_temp_rescale.html
"pair_style dpd/tstat"_pair_dpd.html :ul
"Fix nvt"_fix_nh.html only thermostats the translational velocity of
particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except
@ -1273,15 +1276,20 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
Any of these fixes can use temperature computes that remove bias for
two purposes: (a) computing the current temperature to compare to the
requested target temperature, and (b) adjusting only the thermal
temperature component of the particle's velocities. See the doc pages
for the individual fixes and for the "fix_modify"_fix_modify.html
command for instructions on how to assign a temperature compute to a
thermostatting fix. For example, you can apply a thermostat to only
the x and z components of velocity by using it in conjunction with
"compute temp/partial"_compute_temp_partial.html.
DPD thermostatting alters pairwise interactions in a manner analagous
to the per-particle thermostatting of "fix
langevin"_fix_langevin.html.
Any of the thermostatting fixes can use temperature computes that
remove bias for two purposes: (a) computing the current temperature to
compare to the requested target temperature, and (b) adjusting only
the thermal temperature component of the particle's velocities. See
the doc pages for the individual fixes and for the
"fix_modify"_fix_modify.html command for instructions on how to assign
a temperature compute to a thermostatting fix. For example, you can
apply a thermostat to only the x and z components of velocity by using
it in conjunction with "compute
temp/partial"_compute_temp_partial.html.
IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
they update the velocities and positions of particles due to forces

9
doc/Section_tools.html
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@ -207,11 +207,10 @@ Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.
</H4>
<P>The matlab sub-directory contains several <A HREF = "http://www.mathworks.com">MATLAB</A> scripts for
post-processing LAMMPS output. The scripts include readers for log
and dump files, a reader for radial distribution output from the <A HREF = "fix_rdf.html">fix
rdf</A> command, a reader for EAM potential files, and a
converter that reads LAMMPS dump files and produces CFG files that can
be visualized with the
<A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> visualizer.
and dump files, a reader for EAM potential files, and a converter that
reads LAMMPS dump files and produces CFG files that can be visualized
with the <A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A>
visualizer.
</P>
<P>See the README.pdf file for more information.
</P>

9
doc/Section_tools.txt
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@ -203,11 +203,10 @@ matlab tool :h4,link(matlab)
The matlab sub-directory contains several "MATLAB"_matlab scripts for
post-processing LAMMPS output. The scripts include readers for log
and dump files, a reader for radial distribution output from the "fix
rdf"_fix_rdf.html command, a reader for EAM potential files, and a
converter that reads LAMMPS dump files and produces CFG files that can
be visualized with the
"AtomEye"_http://164.107.79.177/Archive/Graphics/A visualizer.
and dump files, a reader for EAM potential files, and a converter that
reads LAMMPS dump files and produces CFG files that can be visualized
with the "AtomEye"_http://164.107.79.177/Archive/Graphics/A
visualizer.
See the README.pdf file for more information.

8
doc/fix_langevin.html
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@ -58,7 +58,10 @@ Fr is proportional to sqrt(Kb T m / (dt damp))
interactions (<A HREF = "pair_style.html">pair_style</A>,
<A HREF = "bond_style.html">bond_style</A>, etc).
</P>
<P>The Ff and Fr terms are added by this fix.
<P>The Ff and Fr terms are added by this fix on a per-particle basis.
See the <A HREF = "pair_dpd.html">pair_style dpd/tstat</A> command for a
thermostatting option that adds similar terms on a pairwise basis to
pairs of interacting particles.
</P>
<P>Ff is a frictional drag or viscous damping term proportional to the
particle's velocity. The proportionality constant for each atom is
@ -188,7 +191,8 @@ quantity requires setting the <I>tally</I> keyword to <I>yes</I>.
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_viscous.html">fix
viscous</A>, <A HREF = "fix_nh.html">fix nvt</A>
viscous</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "pair_dpd.html">pair_style
dpd/tstat</A>
</P>
<P><B>Default:</B>
</P>

8
doc/fix_langevin.txt
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@ -48,7 +48,10 @@ Fc is the conservative force computed via the usual inter-particle
interactions ("pair_style"_pair_style.html,
"bond_style"_bond_style.html, etc).
The Ff and Fr terms are added by this fix.
The Ff and Fr terms are added by this fix on a per-particle basis.
See the "pair_style dpd/tstat"_pair_dpd.html command for a
thermostatting option that adds similar terms on a pairwise basis to
pairs of interacting particles.
Ff is a frictional drag or viscous damping term proportional to the
particle's velocity. The proportionality constant for each atom is
@ -178,7 +181,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Related commands:]
"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
viscous"_fix_viscous.html, "fix nvt"_fix_nh.html
viscous"_fix_viscous.html, "fix nvt"_fix_nh.html, "pair_style
dpd/tstat"_pair_dpd.html
[Default:]

1
doc/pair_coeff.html
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@ -98,6 +98,7 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_coul.html">pair_style coul/long</A> - long-range Coulombic potential
<LI><A HREF = "pair_dipole.html">pair_style dipole/cut</A> - point dipoles with cutoff
<LI><A HREF = "pair_dpd.html">pair_style dpd</A> - dissipative particle dynamics (DPD)
<LI><A HREF = "pair_dpd.html">pair_style dpd/tstat</A> - DPD thermostatting
<LI><A HREF = "pair_dsmc.html">pair_style dsmc</A> - Direct Simulation Monte Carlo (DSMC)
<LI><A HREF = "pair_eam.html">pair_style eam</A> - embedded atom method (EAM)
<LI><A HREF = "pair_eam.html">pair_style eam/opt</A> - optimized version of EAM

1
doc/pair_coeff.txt
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@ -95,6 +95,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style coul/long"_pair_coul.html - long-range Coulombic potential
"pair_style dipole/cut"_pair_dipole.html - point dipoles with cutoff
"pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
"pair_style dpd/tstat"_pair_dpd.html - DPD thermostatting
"pair_style dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC)
"pair_style eam"_pair_eam.html - embedded atom method (EAM)
"pair_style eam/opt"_pair_eam.html - optimized version of EAM

79
doc/pair_dpd.html
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@ -11,11 +11,15 @@
<H3>pair_style dpd command
</H3>
<H3>pair_style dpd/tstat command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style dpd T cutoff seed
pair_style dpd/tstat Tstart Tstop cutoff seed
</PRE>
<UL><LI>T = temperature (temperature units)
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
<LI>cutoff = global cutoff for DPD interactions (distance units)
<LI>seed = random # seed (positive integer)
</UL>
@ -25,11 +29,27 @@
pair_coeff * * 3.0 1.0
pair_coeff 1 1 3.0 1.0 1.0
</PRE>
<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>
<P><B>Description:</B>
</P>
<P>Style <I>dpd</I> computes a force field for dissipative particle dynamics
(DPD) following the exposition in <A HREF = "#Groot">(Groot)</A>. The force
on atom I due to atom J is given as a sum of 3 terms
(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
field. This thermostat can be used in conjunction with any <A HREF = "doc/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_nvt.html">fix nvt</A>. To use
<I>dpd/stat</I> with another pair style, use the <A HREF = "pair_hybrid.html">pair_style
hybrid/overlay</A> command to compute both the desired
pair interaction and the thermostat for each pair of particles.
</P>
<P>For style <I>dpd</I>, the force on atom I due to atom J is given as a sum
of 3 terms
</P>
<CENTER><IMG SRC = "Eqs/pair_dpd.jpg">
</CENTER>
@ -42,12 +62,19 @@ the timestep size, and w(r) is a weighting factor that varies between
where Kb is the Boltzmann constant and T is the temperature parameter
in the pair_style command.
</P>
<P>The pairwise energy associated with this potential is only due to the
conservative force term Fc.
<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.
</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
<P>For style <I>dpd</I>, the pairwise energy associated with style <I>dpd</I> is
only due to the conservative force term Fc. The pairwise virial is
calculated using all 3 terms. For style <I>dpd/tstat</I> there is no
pairwise energy or virial.
</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
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands:
</P>
@ -60,24 +87,28 @@ 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>
<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>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>This pair style does not support mixing. Thus, coefficients for all
<P>These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
for these pair styles.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
<P>These pair style do not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
<P>These pair styles writes 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. Note
that the user-specified random number seed is stored in the restart
@ -87,29 +118,35 @@ initially. This means the random forces will be random, but will not
be the same as they would have been if the original simulation had
continued past the restart time.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<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
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<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>
<HR>
<P><B>Restrictions:</B>
</P>
<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
infrequent for DPD 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.
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.
</P>
<P>This pair style requires you to use the <A HREF = "communicate.html">communicate vel
<P>These pair styles requires you to use the <A HREF = "communicate.html">communicate vel
yes</A> option so that velocites are stored by ghost
atoms.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_langevin.html">fix
langevin</A>
</P>
<P><B>Default:</B> none
</P>

80
doc/pair_dpd.txt
View File

@ -7,12 +7,15 @@
:line
pair_style dpd command :h3
pair_style dpd/tstat command :h3
[Syntax:]
pair_style dpd T cutoff seed :pre
pair_style dpd T cutoff seed
pair_style dpd/tstat Tstart Tstop cutoff seed :pre
T = temperature (temperature units)
Tstart,Tstop = desired temperature at start/end of run (temperature units)
cutoff = global cutoff for DPD interactions (distance units)
seed = random # seed (positive integer) :ul
@ -22,11 +25,27 @@ 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
pair_style dpd/tstat 1.0 1.0 2.5 34387
pair_coeff * * 1.0
pair_coeff 1 1 1.0 1.0 :pre
[Description:]
Style {dpd} computes a force field for dissipative particle dynamics
(DPD) following the exposition in "(Groot)"_#Groot. The force
on atom I due to atom J is given as a sum of 3 terms
(DPD) following the exposition in "(Groot)"_#Groot.
Style {dpd/tstat} invokes a DPD thermostat on pairwise interactions,
which is equivalent to the non-conservative portion of the DPD force
field. This thermostat can be used in conjunction with any "pair
style"_doc/pair_style.html, and in leiu of per-particle thermostats
like "fix langevin"_fix_langevin.html or ensemble thermostats like
Nose Hoover as implemented by "fix nvt"_fix_nvt.html. To use
{dpd/stat} with another pair style, use the "pair_style
hybrid/overlay"_pair_hybrid.html command to compute both the desired
pair interaction and the thermostat for each pair of particles.
For style {dpd}, the force on atom I due to atom J is given as a sum
of 3 terms
:c,image(Eqs/pair_dpd.jpg)
@ -39,12 +58,19 @@ the timestep size, and w(r) is a weighting factor that varies between
where Kb is the Boltzmann constant and T is the temperature parameter
in the pair_style command.
The pairwise energy associated with this potential is only due to the
conservative force term Fc.
For style {dpd/tstat}, 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.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
For style {dpd}, the pairwise energy associated with style {dpd} is
only due to the conservative force term Fc. The pairwise virial is
calculated using all 3 terms. For style {dpd/tstat} there is no
pairwise energy or virial.
For style {dpd}, the following coefficients must be defined for each
pair of atoms types via the "pair_coeff"_pair_coeff.html command as in
the examples above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
@ -57,24 +83,28 @@ cutoff is used. Note that sigma is set equal to sqrt(2 T gamma),
where T is the temperature set by the "pair_style"_pair_style.html
command so it does not need to be specified.
For style {dpd/tstat}, the coefficiencts defined for each pair of
atoms types via the "pair_coeff"_pair_coeff.html command is the same,
except that A is not included.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair style does not support mixing. Thus, coefficients for all
These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
This pair style does not support the "pair_modify"_pair_modify.html
These pair styles do not support the "pair_modify"_pair_modify.html
shift option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
for these pair styles.
This pair style does not support the "pair_modify"_pair_modify.html
These pair style do not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes its information to "binary restart
These pair styles writes their information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file. Note
that the user-specified random number seed is stored in the restart
@ -84,29 +114,35 @@ initially. This means the random forces will be random, but will not
be the same as they would have been if the original simulation had
continued past the restart time.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
These pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords.
The {dpd/tstat} style can ramp its target temperature over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html
command. See the "run"_run.html command for details of how to do
this.
:line
[Restrictions:]
The default frequency for rebuilding neighbor lists is every 10 steps
(see the "neigh_modify"_neigh_modify.html command). This may be too
infrequent for DPD 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.
infrequent for style {dpd} 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.
This pair style requires you to use the "communicate vel
These pair styles requires you to use the "communicate vel
yes"_communicate.html option so that velocites are stored by ghost
atoms.
[Related commands:]
"pair_coeff"_pair_coeff.html
"pair_coeff"_pair_coeff.html, "fix nvt"_fix_nvt.html, "fix
langevin"_fix_langevin.html
[Default:] none

1
doc/pair_style.html
View File

@ -100,6 +100,7 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_coul.html">pair_style coul/long</A> - long-range Coulombic potential
<LI><A HREF = "pair_dipole.html">pair_style dipole/cut</A> - point dipoles with cutoff
<LI><A HREF = "pair_dpd.html">pair_style dpd</A> - dissipative particle dynamics (DPD)
<LI><A HREF = "pair_dpd.html">pair_style dpd/tstat</A> - DPD thermostatting
<LI><A HREF = "pair_dsmc.html">pair_style dsmc</A> - Direct Simulation Monte Carlo (DSMC)
<LI><A HREF = "pair_eam.html">pair_style eam</A> - embedded atom method (EAM)
<LI><A HREF = "pair_eam.html">pair_style eam/opt</A> - optimized version of EAM

1
doc/pair_style.txt
View File

@ -97,6 +97,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style coul/long"_pair_coul.html - long-range Coulombic potential
"pair_style dipole/cut"_pair_dipole.html - point dipoles with cutoff
"pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
"pair_style dpd/tstat"_pair_dpd.html - DPD thermostatting
"pair_style dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC)
"pair_style eam"_pair_eam.html - embedded atom method (EAM)
"pair_style eam/opt"_pair_eam.html - optimized version of EAM