deploy: 9a9b0fa

Author: simongravelle

sphinx/build/doctrees/environment.pickle

@@ -450,7 +450,8 @@ the following:
         view 80 10 box yes 0.025 axes no 0.0 0.0 center s 0.483725 0.510373 0.510373
     dump_modify viz pad 9 boxcolor royalblue backcolor white adiam 1 1.6 adiam 2 4.8
 
-This command tells LAMMPS to generate NetPBM format images every 100  
+The $\&$ is used to continue the command on a new line.
+These commands tell LAMMPS to generate NetPBM format images every 100  
 steps.  The two ``type`` keywords are for *color* and  
 *diameter*, respectively.  Run the **initial.lmp** using  
 LAMMPS again, and a new window named ``Slide Show`` will pop up.  

sphinx/build/doctrees/tutorial1/lennard-jones-fluid.doctree

@@ -86,6 +86,8 @@ lines into **water.lmp**:
     molecule h2omol water.mol
     create_atoms 0 random 700 87910 NULL mol h2omol 454756 overlap 1.0 maxtry 50
 
+The first parameter is 0, meaning that the atom IDs from
+the **water.mol** file will be used.
 The ``overlap 1.0`` option of the ``create_atoms`` command ensures
 that no atoms are placed exactly in the same position, as this would cause the
 simulation to crash.  The ``maxtry 50`` asks LAMMPS to try at most 50 times
@@ -139,7 +141,9 @@ Resetting the step of the simulation to 0 using the
 ``reset_timestep`` command is optional.
 It is used here because the number of iterations performed by the ``minimize``
 command is usually not a round number, since the minimization stops when one of
-four criteria is reached.  We will use ``fix npt`` to control the temperature
+four criteria is reached, which can disrupt the intended frequency
+of outputs such as ``dump`` commands that depend on the timestep count.
+We will use ``fix npt`` to control the temperature
 and pressure of the molecules with a Nosé-Hoover thermostat and barostat,
 respectively :cite:`nose1984unified, hoover1985canonical, martyna1994constant`.
 Add the following line into **water.lmp**:

sphinx/build/doctrees/tutorial1/tutorial.doctree

@@ -692,7 +692,8 @@ <h3>Trajectory visualization<a class="headerlink" href="#trajectory-visualizatio
 <span class="k">dump_modify </span><span class="nv nv-Identifier">viz</span><span class="w"> </span><span class="n">pad</span><span class="w"> </span><span class="m">9</span><span class="w"> </span><span class="n">boxcolor</span><span class="w"> </span><span class="n">royalblue</span><span class="w"> </span><span class="n">backcolor</span><span class="w"> </span><span class="n">white</span><span class="w"> </span><span class="n">adiam</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">1.6</span><span class="w"> </span><span class="n">adiam</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">4.8</span>
 </pre></div>
 </div>
-<p>This command tells LAMMPS to generate NetPBM format images every 100
+<p>The $&amp;$ is used to continue the command on a new line.
+These commands tell LAMMPS to generate NetPBM format images every 100
 steps.  The two <code class="docutils literal notranslate"><span class="pre">type</span></code> keywords are for <em>color</em> and
 <em>diameter</em>, respectively.  Run the <strong>initial.lmp</strong> using
 LAMMPS again, and a new window named <code class="docutils literal notranslate"><span class="pre">Slide</span> <span class="pre">Show</span></code> will pop up.

sphinx/build/doctrees/tutorial3/polymer-in-water.doctree

@@ -662,7 +662,8 @@ <h2>Trajectory visualization<a class="headerlink" href="#trajectory-visualizatio
 <span class="k">dump_modify </span><span class="nv nv-Identifier">viz</span><span class="w"> </span><span class="n">pad</span><span class="w"> </span><span class="m">9</span><span class="w"> </span><span class="n">boxcolor</span><span class="w"> </span><span class="n">royalblue</span><span class="w"> </span><span class="n">backcolor</span><span class="w"> </span><span class="n">white</span><span class="w"> </span><span class="n">adiam</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">1.6</span><span class="w"> </span><span class="n">adiam</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">4.8</span>
 </pre></div>
 </div>
-<p>This command tells LAMMPS to generate NetPBM format images every 100
+<p>The $&amp;$ is used to continue the command on a new line.
+These commands tell LAMMPS to generate NetPBM format images every 100
 steps.  The two <code class="docutils literal notranslate"><span class="pre">type</span></code> keywords are for <em>color</em> and
 <em>diameter</em>, respectively.  Run the <strong>initial.lmp</strong> using
 LAMMPS again, and a new window named <code class="docutils literal notranslate"><span class="pre">Slide</span> <span class="pre">Show</span></code> will pop up.