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

doc/Section_commands.html

@@ -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_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/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</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/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_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/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_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/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_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/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_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/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.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_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_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_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_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/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_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_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_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_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_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

doc/Section_commands.txt

@@ -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,

doc/Section_howto.html

@@ -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
+<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>, or in one
-thermostatting fixes are currently available: Nose-Hoover (nvt),
+case by a pair style.  Four thermostatting fixes are currently
-Berendsen, Langevin, and direct rescaling (temp/rescale):
+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>
@@ -1272,7 +1274,8 @@ Berendsen, Langevin, and direct rescaling (temp/rescale):
 <LI><A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
 <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 = "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
+<P>DPD thermostatting alters pairwise interactions in a manner analagous
-two purposes: (a) computing the current temperature to compare to the
+to the per-particle thermostatting of <A HREF = "fix_langevin.html">fix
-requested target temperature, and (b) adjusting only the thermal
+langevin</A>.
-temperature component of the particle's velocities.  See the doc pages
+</P>
-for the individual fixes and for the <A HREF = "fix_modify.html">fix_modify</A>
+<P>Any of the thermostatting fixes can use temperature computes that
-command for instructions on how to assign a temperature compute to a
+remove bias for two purposes: (a) computing the current temperature to
-thermostatting fix.  For example, you can apply a thermostat to only
+compare to the requested target temperature, and (b) adjusting only
-the x and z components of velocity by using it in conjunction with
+the thermal temperature component of the particle's velocities.  See
-<A HREF = "compute_temp_partial.html">compute temp/partial</A>.
+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

doc/Section_howto.txt

@@ -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 in LAMMPS is performed by "fixes"_fix.html, or in one
-thermostatting fixes are currently available: Nose-Hoover (nvt),
+case by a pair style.  Four thermostatting fixes are currently
-Berendsen, Langevin, and direct rescaling (temp/rescale):
+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
+DPD thermostatting alters pairwise interactions in a manner analagous
-two purposes: (a) computing the current temperature to compare to the
+to the per-particle thermostatting of "fix
-requested target temperature, and (b) adjusting only the thermal
+langevin"_fix_langevin.html.
-temperature component of the particle's velocities.  See the doc pages
+
-for the individual fixes and for the "fix_modify"_fix_modify.html
+Any of the thermostatting fixes can use temperature computes that
-command for instructions on how to assign a temperature compute to a
+remove bias for two purposes: (a) computing the current temperature to
-thermostatting fix.  For example, you can apply a thermostat to only
+compare to the requested target temperature, and (b) adjusting only
-the x and z components of velocity by using it in conjunction with
+the thermal temperature component of the particle's velocities.  See
-"compute temp/partial"_compute_temp_partial.html.
+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

doc/Section_tools.html

@@ -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
+and dump files, a reader for EAM potential files, and a converter that
-rdf</A> command, a reader for EAM potential files, and a
+reads LAMMPS dump files and produces CFG files that can be visualized
-converter that reads LAMMPS dump files and produces CFG files that can
+with the <A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A>
-be visualized with the
+visualizer.
-<A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> visualizer.
 </P>
 <P>See the README.pdf file for more information.
 </P>

doc/Section_tools.txt

@@ -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
+and dump files, a reader for EAM potential files, and a converter that
-rdf"_fix_rdf.html command, a reader for EAM potential files, and a
+reads LAMMPS dump files and produces CFG files that can be visualized
-converter that reads LAMMPS dump files and produces CFG files that can
+with the "AtomEye"_http://164.107.79.177/Archive/Graphics/A
-be visualized with the
+visualizer.
-"AtomEye"_http://164.107.79.177/Archive/Graphics/A visualizer.
 
 See the README.pdf file for more information.
 

doc/fix_langevin.html

@@ -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>

doc/fix_langevin.txt

@@ -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:]
 

doc/pair_coeff.html

@@ -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

doc/pair_coeff.txt

@@ -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

doc/pair_dpd.html

@@ -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 
+<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
+(DPD) following the exposition in <A HREF = "#Groot">(Groot)</A>.
-on atom I due to atom J is given as a sum of 3 terms
+</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
+<P>For style <I>dpd/tstat</I>, the force on atom I due to atom J is the same
-conservative force term Fc.
+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
+<P>For style <I>dpd</I>, the pairwise energy associated with style <I>dpd</I> is
-types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+only due to the conservative force term Fc.  The pairwise virial is
-above, or in the data file or restart files read by the
+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
+<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.  It does not support 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
+infrequent for style <I>dpd</I> simulations since particles move rapidly
-overlap by large amounts.  If this setting yields a non-zero number of
+and can overlap by large amounts.  If this setting yields a non-zero
-"dangerous" reneighborings (printed at the end of a simulation), you
+number of "dangerous" reneighborings (printed at the end of a
-should experiment with forcing reneighboring more often and see if
+simulation), you should experiment with forcing reneighboring more
-system energies/trajectories change.
+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>

doc/pair_dpd.txt

@@ -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
+(DPD) following the exposition in "(Groot)"_#Groot.
-on atom I due to atom J is given as a sum of 3 terms
+
+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
+For style {dpd/tstat}, the force on atom I due to atom J is the same
-conservative force term Fc.
+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
+For style {dpd}, the pairwise energy associated with style {dpd} is
-types via the "pair_coeff"_pair_coeff.html command as in the examples
+only due to the conservative force term Fc.  The pairwise virial is
-above, or in the data file or restart files read by the
+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
+These pair styles can only be used via the {pair} keyword of the
-"run_style respa"_run_style.html command.  It does not support 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
+infrequent for style {dpd} simulations since particles move rapidly
-overlap by large amounts.  If this setting yields a non-zero number of
+and can overlap by large amounts.  If this setting yields a non-zero
-"dangerous" reneighborings (printed at the end of a simulation), you
+number of "dangerous" reneighborings (printed at the end of a
-should experiment with forcing reneighboring more often and see if
+simulation), you should experiment with forcing reneighboring more
-system energies/trajectories change.
+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
 

doc/pair_style.html

@@ -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

doc/pair_style.txt

@@ -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