deploy: 193a17f

Author: simongravelle

sphinx/build/doctrees/environment.pickle

@@ -23,10 +23,9 @@ following content corresponding to **mixing.lmp**:
 
 The ``class2`` styles compute a 6/9 Lennard-Jones potential :cite:`sun1998compass`.
 The ``class2`` bond, angle, dihedral, and improper styles are used as
-well, see the documentation for a description of their respective potentials.
+well, see the documentation for a description the respective potential form they, each, prescribe.
 The ``tail yes`` option adds long-range van der Waals tail corrections to the
-energy and pressure.
-The ``mix sixthpower`` imposes the following mixing rule for the calculation
+energy and pressure.  The ``mix sixthpower`` imposes the following mixing rule for the calculation
 of the cross coefficients:
 
 .. math::
@@ -71,8 +70,10 @@ Finally, let us use the ``minimize`` command to reduce the potential energy of t
     minimize 1.0e-4 1.0e-6 100 1000
     reset_timestep 0
 
+These commands were covered in earlier tutorials and should already be familiar.
+
 Then, let us densify the system to a target value of :math:`0.9~\text{g/cm}^3`
-by manually shrinking the simulation box at a constant rate.  The dimension parallel
+by imposing the shrinking of the simulation box at a constant rate.  The dimension parallel
 to the CNT axis is maintained fixed because the CNT is periodic in that direction.
 Add the following commands to **mixing.lmp**:
 
@@ -91,7 +92,8 @@ Add the following commands to **mixing.lmp**:
     run 9000
 
 The ``fix halt`` command is used to stop the box shrinkage once the
-target density is reached.
+target density is reached, and the other commands
+should be familiar from previous tutorials.
 
 For the next stage of the simulation, we will use ``dump image`` to
 output images every 200 steps:
@@ -120,7 +122,7 @@ system in a file named **mixing.data**:
 
     write_data mixing.data
 
-For visualization purposes, the atoms from the CNT ``group`` is moved
+For visualization purposes, the atoms of the CNT ``group`` are moved
 to the center of the box using ``fix recenter``.
 As the time progresses, the system density,
 :math:`\rho`, gradually converges toward the target value
@@ -291,7 +293,10 @@ line to **polymerize.lmp**:
 
 With the ``stabilization`` keyword, the ``bond/react`` command will
 stabilize the atoms involved in the reaction using the ``nve/limit``
-command with a maximum displacement of :math:`0.03\,\text{Å}`.  By default,
+command with a maximum displacement of :math:`0.03\,\text{Å}`.  
+The ``fix nve/limit`` command functions similar to
+``fix nve``, but restricts how far atoms can move in a single
+time step, even with very large forces. By default,
 each reaction is stabilized for 60 time steps.  Each ``react`` keyword
 corresponds to a reaction, e.g., a transformation of ``mol1`` into ``mol2``
 based on the atom map **M-M.rxnmap**.  Implementation details about each reaction,
@@ -329,8 +334,9 @@ reaction sites, are also specified in this command.
     the group ``all``.  Instead, the group of atoms not currently
     undergoing stabilization is named by appending ``_REACT`` to the user-provided prefix.
 
-Add the following commands to **polymerize.lmp** to operate in the NVT ensemble
-while ensuring that the CNT remains centered in the simulation box:
+Add the following commands to **polymerize.lmp** to carry out the dynamics
+using a Nosé-Hoover thermostat while ensuring that the CNT remains centered in
+the simulation box:
 
 .. code-block:: lammps
 
@@ -344,11 +350,11 @@ while ensuring that the CNT remains centered in the simulation box:
     run 25000
 
 Here, the ``thermo custom`` command is used
-to print the cumulative reaction counts from ``fix rxn``.
-Run the simulation using LAMMPS.  As the simulation progresses, polymer chains are
-observed forming.  During this reaction process, the
-temperature of the system remains well-controlled,
-while the number of reactions, :math:`N_r`, increases with time.
+to print the cumulative reaction counts which are calculated by ``fix rxn``
+and thus can be extracted from it.  Run the simulation using LAMMPS.  As the
+simulation progresses, polymer chains are observed forming.  During this reaction
+process, the temperature of the system remains well-controlled, while the number
+of reactions, :math:`N_r`, increases with time.
 
 .. figure:: figures/REACT-reacting-dm.png
     :class: only-dark

sphinx/build/doctrees/tutorial8/reactive-molecular-dynamics.doctree

@@ -322,10 +322,9 @@ <h2>Creating the system<a class="headerlink" href="#creating-the-system" title="
 </div>
 <p>The <code class="docutils literal notranslate"><span class="pre">class2</span></code> styles compute a 6/9 Lennard-Jones potential <span id="id3">[<a class="reference internal" href="../non-tutorials/bibliography.html#id59" title="Huai Sun. Compass: an ab initio force-field optimized for condensed-phase applications overview with details on alkane and benzene compounds. The Journal of Physical Chemistry B, 102(38):7338–7364, 1998.">59</a>]</span>.
 The <code class="docutils literal notranslate"><span class="pre">class2</span></code> bond, angle, dihedral, and improper styles are used as
-well, see the documentation for a description of their respective potentials.
+well, see the documentation for a description the respective potential form they, each, prescribe.
 The <code class="docutils literal notranslate"><span class="pre">tail</span> <span class="pre">yes</span></code> option adds long-range van der Waals tail corrections to the
-energy and pressure.
-The <code class="docutils literal notranslate"><span class="pre">mix</span> <span class="pre">sixthpower</span></code> imposes the following mixing rule for the calculation
+energy and pressure.  The <code class="docutils literal notranslate"><span class="pre">mix</span> <span class="pre">sixthpower</span></code> imposes the following mixing rule for the calculation
 of the cross coefficients:</p>
 <div class="math-wrapper docutils container">
 <div class="math notranslate nohighlight">
@@ -354,8 +353,9 @@ <h2>Creating the system<a class="headerlink" href="#creating-the-system" title="
 <span class="k">reset_timestep</span><span class="w"> </span><span class="m">0</span>
 </pre></div>
 </div>
+<p>These commands were covered in earlier tutorials and should already be familiar.</p>
 <p>Then, let us densify the system to a target value of <span class="math notranslate nohighlight">\(0.9~\text{g/cm}^3\)</span>
-by manually shrinking the simulation box at a constant rate.  The dimension parallel
+by imposing the shrinking of the simulation box at a constant rate.  The dimension parallel
 to the CNT axis is maintained fixed because the CNT is periodic in that direction.
 Add the following commands to <strong>mixing.lmp</strong>:</p>
 <div class="highlight-lammps notranslate"><div class="highlight"><pre><span></span><span class="k">velocity </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">create</span><span class="w"> </span><span class="m">530</span><span class="w"> </span><span class="m">9845</span><span class="w"> </span><span class="n">dist</span><span class="w"> </span><span class="n">gaussian</span><span class="w"> </span><span class="n">rot</span><span class="w"> </span><span class="n">yes</span>
@@ -372,7 +372,8 @@ <h2>Creating the system<a class="headerlink" href="#creating-the-system" title="
 </pre></div>
 </div>
 <p>The <code class="docutils literal notranslate"><span class="pre">fix</span> <span class="pre">halt</span></code> command is used to stop the box shrinkage once the
-target density is reached.</p>
+target density is reached, and the other commands
+should be familiar from previous tutorials.</p>
 <p>For the next stage of the simulation, we will use <code class="docutils literal notranslate"><span class="pre">dump</span> <span class="pre">image</span></code> to
 output images every 200 steps:</p>
 <div class="highlight-lammps notranslate"><div class="highlight"><pre><span></span><span class="k">dump </span><span class="nv nv-Identifier">viz</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">image</span><span class="w"> </span><span class="m">200</span><span class="w"> </span><span class="n">myimage</span><span class="o">-*</span><span class="n">.ppm</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="n">shiny</span><span class="w"> </span><span class="m">0.1</span><span class="w"> </span><span class="n">box</span><span class="w"> </span><span class="n">no</span><span class="w"> </span><span class="m">0.01</span><span class="w"> </span><span class="n">size</span><span class="w"> </span><span class="m">1000</span><span class="w"> </span><span class="m">1000</span><span class="w"> </span><span class="n">view</span><span class="w"> </span><span class="m">90</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="n">zoom</span><span class="w"> </span><span class="m">1.8</span><span class="w"> </span><span class="n">fsaa</span><span class="w"> </span><span class="n">yes</span><span class="w"> </span><span class="n">bond</span><span class="w"> </span><span class="n">atom</span><span class="w"> </span><span class="m">0.5</span>
@@ -396,7 +397,7 @@ <h2>Creating the system<a class="headerlink" href="#creating-the-system" title="
 <span class="k">write_data </span><span class="nv nv-Identifier">mixing.data</span>
 </pre></div>
 </div>
-<p>For visualization purposes, the atoms from the CNT <code class="docutils literal notranslate"><span class="pre">group</span></code> is moved
+<p>For visualization purposes, the atoms of the CNT <code class="docutils literal notranslate"><span class="pre">group</span></code> are moved
 to the center of the box using <code class="docutils literal notranslate"><span class="pre">fix</span> <span class="pre">recenter</span></code>.
 As the time progresses, the system density,
 <span class="math notranslate nohighlight">\(\rho\)</span>, gradually converges toward the target value
@@ -514,7 +515,10 @@ <h3>Simulating the reaction<a class="headerlink" href="#simulating-the-reaction"
 </div>
 <p>With the <code class="docutils literal notranslate"><span class="pre">stabilization</span></code> keyword, the <code class="docutils literal notranslate"><span class="pre">bond/react</span></code> command will
 stabilize the atoms involved in the reaction using the <code class="docutils literal notranslate"><span class="pre">nve/limit</span></code>
-command with a maximum displacement of <span class="math notranslate nohighlight">\(0.03\,\text{Å}\)</span>.  By default,
+command with a maximum displacement of <span class="math notranslate nohighlight">\(0.03\,\text{Å}\)</span>.
+The <code class="docutils literal notranslate"><span class="pre">fix</span> <span class="pre">nve/limit</span></code> command functions similar to
+<code class="docutils literal notranslate"><span class="pre">fix</span> <span class="pre">nve</span></code>, but restricts how far atoms can move in a single
+time step, even with very large forces. By default,
 each reaction is stabilized for 60 time steps.  Each <code class="docutils literal notranslate"><span class="pre">react</span></code> keyword
 corresponds to a reaction, e.g., a transformation of <code class="docutils literal notranslate"><span class="pre">mol1</span></code> into <code class="docutils literal notranslate"><span class="pre">mol2</span></code>
 based on the atom map <strong>M-M.rxnmap</strong>.  Implementation details about each reaction,
@@ -546,8 +550,9 @@ <h3>Simulating the reaction<a class="headerlink" href="#simulating-the-reaction"
 the group <code class="docutils literal notranslate"><span class="pre">all</span></code>.  Instead, the group of atoms not currently
 undergoing stabilization is named by appending <code class="docutils literal notranslate"><span class="pre">_REACT</span></code> to the user-provided prefix.</p>
 </div>
-<p>Add the following commands to <strong>polymerize.lmp</strong> to operate in the NVT ensemble
-while ensuring that the CNT remains centered in the simulation box:</p>
+<p>Add the following commands to <strong>polymerize.lmp</strong> to carry out the dynamics
+using a Nosé-Hoover thermostat while ensuring that the CNT remains centered in
+the simulation box:</p>
 <div class="highlight-lammps notranslate"><div class="highlight"><pre><span></span><span class="k">fix </span><span class="nv nv-Identifier">mynvt</span><span class="w"> </span><span class="nv nv-Identifier">statted_grp_REACT</span><span class="w"> </span><span class="n">nvt</span><span class="w"> </span><span class="n">temp</span><span class="w"> </span><span class="m">530</span><span class="w"> </span><span class="m">530</span><span class="w"> </span><span class="m">100</span>
 <span class="k">group </span><span class="nv nv-Identifier">CNT</span><span class="w"> </span><span class="n">molecule</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">3</span>
 <span class="k">fix </span><span class="nv nv-Identifier">myrec</span><span class="w"> </span><span class="nv nv-Identifier">CNT</span><span class="w"> </span><span class="n">recenter</span><span class="w"> </span><span class="n">NULL</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="n">shift</span><span class="w"> </span><span class="n">all</span>
@@ -559,11 +564,11 @@ <h3>Simulating the reaction<a class="headerlink" href="#simulating-the-reaction"
 </pre></div>
 </div>
 <p>Here, the <code class="docutils literal notranslate"><span class="pre">thermo</span> <span class="pre">custom</span></code> command is used
-to print the cumulative reaction counts from <code class="docutils literal notranslate"><span class="pre">fix</span> <span class="pre">rxn</span></code>.
-Run the simulation using LAMMPS.  As the simulation progresses, polymer chains are
-observed forming.  During this reaction process, the
-temperature of the system remains well-controlled,
-while the number of reactions, <span class="math notranslate nohighlight">\(N_r\)</span>, increases with time.</p>
+to print the cumulative reaction counts which are calculated by <code class="docutils literal notranslate"><span class="pre">fix</span> <span class="pre">rxn</span></code>
+and thus can be extracted from it.  Run the simulation using LAMMPS.  As the
+simulation progresses, polymer chains are observed forming.  During this reaction
+process, the temperature of the system remains well-controlled, while the number
+of reactions, <span class="math notranslate nohighlight">\(N_r\)</span>, increases with time.</p>
 <figure class="align-default">
 <img alt="Evolution of reacting species" class="only-dark" src="../_images/REACT-reacting-dm.png" />
 </figure>