git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15133 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/Section_packages.html

@@ -493,7 +493,7 @@ name links to a sub-section below with more details.</p>
 <td>python</td>
 <td>lib/python</td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="Section_tools.html#reax"><span class="std std-ref">REAX</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="#reax"><span class="std std-ref">REAX</span></a></td>
 <td>ReaxFF potential</td>
 <td>Aidan Thompson (Sandia)</td>
 <td><a class="reference internal" href="pair_reax.html"><span class="doc">pair_style reax</span></a></td>
@@ -1624,7 +1624,7 @@ src/Make.py -h -voronoi&#8221; to see the details.</p>
 </td>
 </tr>
 <tr class="row-odd"><td><a class="reference internal" href="#user-dpd"><span class="std std-ref">USER-DPD</span></a></td>
-<td>dissipative particle dynamics (DPD)</td>
+<td>reactive dissipative particle dynamics (DPD)</td>
 <td>Larentzos &amp; Mattox &amp; Brennan (5)</td>
 <td>src/USER-DPD/README</td>
 <td>USER/dpd</td>
@@ -2058,9 +2058,11 @@ questions.</p>
 <span id="user-dpd"></span><h3>4.2.6. USER-DPD package</h3>
 <p>Contents: DPD stands for dissipative particle dynamics, This package
 implements DPD for isothermal, isoenergetic, isobaric and isenthalpic
-conditions.  The DPD equations of motion are integrated efficiently
+conditions.  It also has extensions for performing reactive DPD, where
-through the Shardlow splitting algorithm.  See src/USER-DPD/README for
+each particle has internal state for multiple species and a coupled
-more details.</p>
+set of chemical reaction ODEs are integrated each timestep.  The DPD
+equations of motion are integrated efficiently through the Shardlow
+splitting algorithm.  See src/USER-DPD/README for more details.</p>
 <p>Supporting info: /src/USER-DPD/README, <a class="reference internal" href="compute_dpd.html"><span class="doc">compute dpd</span></a>
 <a class="reference internal" href="compute_dpd_atom.html"><span class="doc">compute dpd/atom</span></a>
 <a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/cv</span></a> <a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/table</span></a>

doc/html/_sources/Section_packages.txt

@@ -1521,7 +1521,7 @@ The current list of user-contributed packages is as follows:
 +--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
 | :ref:`USER-DIFFRACTION <USER-DIFFRACTION>` | virutal x-ray and electron diffraction         | Shawn Coleman (ARL)                             | :doc:`compute xrd <compute_xrd>`                        | USER/diffraction | -                       | -           |
 +--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
-| :ref:`USER-DPD <USER-DPD>`                 | dissipative particle dynamics (DPD)            | Larentzos & Mattox & Brennan (5)                | src/USER-DPD/README                                     | USER/dpd         | -                       | -           |
+| :ref:`USER-DPD <USER-DPD>`                 | reactive dissipative particle dynamics (DPD)   | Larentzos & Mattox & Brennan (5)                | src/USER-DPD/README                                     | USER/dpd         | -                       | -           |
 +--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
 | :ref:`USER-DRUDE <USER-DRUDE>`             | Drude oscillators                              | Dequidt & Devemy & Padua (3)                    | :doc:`tutorial <tutorial_drude>`                        | USER/drude       | -                       | -           |
 +--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
@@ -1779,9 +1779,11 @@ USER-DPD package
 
 Contents: DPD stands for dissipative particle dynamics, This package
 implements DPD for isothermal, isoenergetic, isobaric and isenthalpic
-conditions.  The DPD equations of motion are integrated efficiently
+conditions.  It also has extensions for performing reactive DPD, where
-through the Shardlow splitting algorithm.  See src/USER-DPD/README for
+each particle has internal state for multiple species and a coupled
-more details.
+set of chemical reaction ODEs are integrated each timestep.  The DPD
+equations of motion are integrated efficiently through the Shardlow
+splitting algorithm.  See src/USER-DPD/README for more details.
 
 Supporting info: /src/USER-DPD/README, :doc:`compute dpd <compute_dpd>`
 :doc:`compute dpd/atom <compute_dpd_atom>`

doc/src/Section_packages.txt

@@ -1144,7 +1144,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
 "USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
 "USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
-"USER-DPD"_#USER-DPD, dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
+"USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
 "USER-DRUDE"_#USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, -
 "USER-EFF"_#USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
 "USER-FEP"_#USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
@@ -1328,9 +1328,11 @@ USER-DPD package :link(USER-DPD),h5
 
 Contents: DPD stands for dissipative particle dynamics, This package
 implements DPD for isothermal, isoenergetic, isobaric and isenthalpic
-conditions.  The DPD equations of motion are integrated efficiently
+conditions.  It also has extensions for performing reactive DPD, where
-through the Shardlow splitting algorithm.  See src/USER-DPD/README for
+each particle has internal state for multiple species and a coupled
-more details.
+set of chemical reaction ODEs are integrated each timestep.  The DPD
+equations of motion are integrated efficiently through the Shardlow
+splitting algorithm.  See src/USER-DPD/README for more details.
 
 Supporting info: /src/USER-DPD/README, "compute dpd"_compute_dpd.html
 "compute dpd/atom"_compute_dpd_atom.html