deploy: 6a95a5b

Author: simongravelle

sphinx/build/doctrees/environment.pickle

@@ -412,7 +412,6 @@ types of atoms, and output the charge values into log files:
 
     fix myspec all reaxff/species 5 1 5 decorate.species element Si O H
 
-
 The commands above are, once again, similar to the ones of the previous script.
 Here, the :math:`+1 \mathrm{e}{-10}` was added to the denominator of the ``variable qH``
 to avoid dividing by 0 at the beginning of the simulation, as no hydrogen atoms exists in

sphinx/build/doctrees/tutorial5/reactive-silicon-dioxide.doctree

@@ -36,12 +36,13 @@ Add the following lines to **generate.lmp**:
     create_atoms Si random 240 5802 box overlap 2.0 maxtry 500
     create_atoms O random 480 1072 box overlap 2.0 maxtry 500
 
-The ``create_atoms`` commands are used to place
+In line with what is done in previous tutorials, the 
+``create_atoms`` commands are used to place
 240 Si atoms and 480 O atoms, respectively.  This corresponds to
 an initial density of approximately :math:`2 \, \text{g/cm}^3`, which is close
 to the expected final density of amorphous silica at 300 K.
 
-Now, specify the pair coefficients by indicating that the first atom type
+Now, specify the potential parameters by indicating that the first atom type
 is ``Si`` and the second is ``O``:
 
 .. code-block:: lammps
@@ -103,6 +104,9 @@ to :math:`T = 300\,\text{K}`, is implemented as follows:
     fix mynvt all nvt temp 6000 300 0.1
     run 30000
 
+In this case, the initial and final target temperatures set for
+the Nosé-Hoover thermostat is different, causing it to evolve
+linearly within the number of timesteps evoked in the ``run`` command.
 In the third step, the system is equilibrated at the final desired
 conditions, :math:`T = 300\,\text{K}` and :math:`p = 1\,\text{atm}`,
 using an anisotropic pressure coupling:
@@ -116,15 +120,16 @@ using an anisotropic pressure coupling:
 
     write_data generate.data
 
-Here, an anisotropic barostat is used.
-Anisotropic barostats adjust the dimensions independently, which is
+Here, an anisotropic barostat is used. As previously mentioned,
+anisotropic barostats adjust the dimensions independently, which is
 generally suitable for a solid phase.
 
 Run the simulation using LAMMPS.  From the ``Charts`` window, the temperature
 evolution can be observed, showing that it closely follows the desired annealing procedure.
 The evolution of the box dimensions over time confirms that the box is deforming during the
-last stage of the simulation.  After the simulation completes, the final LAMMPS topology
-file called **generate.data** will be located next to **generate.lmp**.
+last stage of the simulation.  After the simulation completes, the final
+microstate attained during the dynamics and the system topology will be written to a LAMMPS data
+file called **generate.data** which will be located next to **generate.lmp**.
 
 .. figure:: figures/GCMC-dimension-dm.png
     :class: only-dark
@@ -184,7 +189,7 @@ the **cracking.lmp** file:
 
     write_data cracking.data
 
-The ``fix nvt`` command integrates the Nosé-Hoover equations
+As discussed, the ``fix nvt`` command integrates the Nosé-Hoover equations
 of motion and is employed to control the temperature of the system.
 As observed from the generated images, the atoms
 progressively adjust to the changing box dimensions.  At some point,
@@ -217,20 +222,21 @@ Adding water
 
 To add the water molecules to the silica, we will employ the Monte Carlo
 method in the grand canonical ensemble (GCMC).  In short, the system is
-placed into contact with a virtual reservoir of a given chemical
-potential :math:`\mu`, and multiple attempts to insert water molecules at
-random positions are made.  Each attempt is either accepted or rejected
-based on energy considerations.  For further details, please refer to
-classical textbooks like Ref. :cite:`frenkel2023understanding`.
+placed into contact with a virtual reservoir containing pure water at a given
+thermodynamic state, and multiple attempts to insert water molecules at
+random positions are made.  In the grand
+canonical ensemble, each attempt is either accepted or rejected
+based on internal energy and chemical potential considerations.  For further
+details, please refer to classical textbooks like Ref. :cite:`frenkel2023understanding`.
 
 Adapting the pair style
 -----------------------
 
 For this next step, we need to specify the force field used to
 model the interactions in the system. The TIP4P/2005 model is employed
 for the water :cite:`abascal2005general`, while no interaction within
-silica is defined, as it will be seen farther below. This is be-
-cause atoms of the silica will remain frozen during this part of the simulation.
+silica is defined, as it will be seen farther below. This is because atoms of
+the silica will remain frozen during this part of the simulation.
 Only the cross-interactions between water and silica need
 to be defined. Create a new file called **gcmc.lmp**, and copy the following
 lines into it:
@@ -344,8 +350,8 @@ We can now proceed to complete the **gcmc.lmp** file by adding the system defini
 After reading the data file and defining the ``h2omol`` molecule from the **H2O.mol**
 file, the ``create_atoms`` command is used to include three water molecules
 in the system.  Then, add the following ``pair_coeff`` (and
-``bond_coeff`` and ``angle_coeff``) commands
-to **gcmc.lmp**:
+``bond_coeff`` and ``angle_coeff``) commands to **gcmc.lmp**
+in order to set the potential parameters:
 
 .. code-block:: lammps
         
@@ -357,7 +363,7 @@ to **gcmc.lmp**:
     bond_coeff OW-HW 0 0.9572
     angle_coeff HW-OW-HW 0 104.52
 
-Pair coefficients for the ``lj/cut/tip4p/long``
+Pair coefficients for the ``lj/cut/tip4p/long`` pair style
 potential are defined between O(:math:`\text{H}_2\text{O}`) and between H(:math:`\text{H}_2\text{O}`)
 atoms, as well as between O(:math:`\text{SiO}_2`)-O(:math:`\text{H}_2\text{O}`) and
 Si(:math:`\text{SiO}_2`)-O(:math:`\text{H}_2\text{O}`).  Thus, the fluid-fluid and the
@@ -393,8 +399,9 @@ Add the following lines to **gcmc.lmp** as well:
     their properties or types.
 
 The number of oxygen atoms from water molecules (i.e. the number of molecules)
-is calculated by the ``nO`` variable.  The SHAKE algorithm is used to
-maintain the shape of the water molecules over time :cite:`ryckaert1977numerical, andersen1983rattle`.
+is calculated by the ``nO`` variable.  As already discussed in other tutorials,
+the SHAKE algorithm is used to maintain the shape of the water molecules
+over time :cite:`ryckaert1977numerical, andersen1983rattle`.
 
 Finally, let us create images
 of the system using ``dump image``:

sphinx/build/doctrees/tutorial5/tutorial.doctree

@@ -302,11 +302,12 @@ <h1>Generation of the silica block<a class="headerlink" href="#generation-of-the
 <span class="k">create_atoms</span><span class="w"> </span><span class="n">O</span><span class="w"> </span><span class="n">random</span><span class="w"> </span><span class="m">480</span><span class="w"> </span><span class="m">1072</span><span class="w"> </span><span class="n">box</span><span class="w"> </span><span class="n">overlap</span><span class="w"> </span><span class="m">2.0</span><span class="w"> </span><span class="n">maxtry</span><span class="w"> </span><span class="m">500</span>
 </pre></div>
 </div>
-<p>The <code class="docutils literal notranslate"><span class="pre">create_atoms</span></code> commands are used to place
+<p>In line with what is done in previous tutorials, the
+<code class="docutils literal notranslate"><span class="pre">create_atoms</span></code> commands are used to place
 240 Si atoms and 480 O atoms, respectively.  This corresponds to
 an initial density of approximately <span class="math notranslate nohighlight">\(2 \, \text{g/cm}^3\)</span>, which is close
 to the expected final density of amorphous silica at 300 K.</p>
-<p>Now, specify the pair coefficients by indicating that the first atom type
+<p>Now, specify the potential parameters by indicating that the first atom type
 is <code class="docutils literal notranslate"><span class="pre">Si</span></code> and the second is <code class="docutils literal notranslate"><span class="pre">O</span></code>:</p>
 <div class="highlight-lammps notranslate"><div class="highlight"><pre><span></span><span class="k">pair_coeff</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">SiO.1990.vashishta</span><span class="w"> </span><span class="n">Si</span><span class="w"> </span><span class="n">O</span>
 </pre></div>
@@ -350,7 +351,10 @@ <h1>Generation of the silica block<a class="headerlink" href="#generation-of-the
 <span class="k">run</span><span class="w"> </span><span class="m">30000</span>
 </pre></div>
 </div>
-<p>In the third step, the system is equilibrated at the final desired
+<p>In this case, the initial and final target temperatures set for
+the Nosé-Hoover thermostat is different, causing it to evolve
+linearly within the number of timesteps evoked in the <code class="docutils literal notranslate"><span class="pre">run</span></code> command.
+In the third step, the system is equilibrated at the final desired
 conditions, <span class="math notranslate nohighlight">\(T = 300\,\text{K}\)</span> and <span class="math notranslate nohighlight">\(p = 1\,\text{atm}\)</span>,
 using an anisotropic pressure coupling:</p>
 <div class="highlight-lammps notranslate"><div class="highlight"><pre><span></span><span class="k">unfix </span><span class="nv nv-Identifier">mynvt</span>
@@ -361,14 +365,15 @@ <h1>Generation of the silica block<a class="headerlink" href="#generation-of-the
 <span class="k">write_data </span><span class="nv nv-Identifier">generate.data</span>
 </pre></div>
 </div>
-<p>Here, an anisotropic barostat is used.
-Anisotropic barostats adjust the dimensions independently, which is
+<p>Here, an anisotropic barostat is used. As previously mentioned,
+anisotropic barostats adjust the dimensions independently, which is
 generally suitable for a solid phase.</p>
 <p>Run the simulation using LAMMPS.  From the <code class="docutils literal notranslate"><span class="pre">Charts</span></code> window, the temperature
 evolution can be observed, showing that it closely follows the desired annealing procedure.
 The evolution of the box dimensions over time confirms that the box is deforming during the
-last stage of the simulation.  After the simulation completes, the final LAMMPS topology
-file called <strong>generate.data</strong> will be located next to <strong>generate.lmp</strong>.</p>
+last stage of the simulation.  After the simulation completes, the final
+microstate attained during the dynamics and the system topology will be written to a LAMMPS data
+file called <strong>generate.data</strong> which will be located next to <strong>generate.lmp</strong>.</p>
 <figure class="align-default">
 <img alt="Temperature and density of the silicon" class="only-dark" src="../_images/GCMC-dimension-dm.png" />
 </figure>
@@ -419,7 +424,7 @@ <h1>Cracking the silica<a class="headerlink" href="#cracking-the-silica" title="
 <span class="k">write_data </span><span class="nv nv-Identifier">cracking.data</span>
 </pre></div>
 </div>
-<p>The <code class="docutils literal notranslate"><span class="pre">fix</span> <span class="pre">nvt</span></code> command integrates the Nosé-Hoover equations
+<p>As discussed, the <code class="docutils literal notranslate"><span class="pre">fix</span> <span class="pre">nvt</span></code> command integrates the Nosé-Hoover equations
 of motion and is employed to control the temperature of the system.
 As observed from the generated images, the atoms
 progressively adjust to the changing box dimensions.  At some point,
@@ -447,18 +452,19 @@ <h1>Cracking the silica<a class="headerlink" href="#cracking-the-silica" title="
 <h1>Adding water<a class="headerlink" href="#adding-water" title="Link to this heading">¶</a></h1>
 <p>To add the water molecules to the silica, we will employ the Monte Carlo
 method in the grand canonical ensemble (GCMC).  In short, the system is
-placed into contact with a virtual reservoir of a given chemical
-potential <span class="math notranslate nohighlight">\(\mu\)</span>, and multiple attempts to insert water molecules at
-random positions are made.  Each attempt is either accepted or rejected
-based on energy considerations.  For further details, please refer to
-classical textbooks like Ref. <span id="id3">[<a class="reference internal" href="../non-tutorials/bibliography.html#id9" title="Daan Frenkel and Berend Smit. Understanding molecular simulation: from algorithms to applications. Elsevier, 2023.">6</a>]</span>.</p>
+placed into contact with a virtual reservoir containing pure water at a given
+thermodynamic state, and multiple attempts to insert water molecules at
+random positions are made.  In the grand
+canonical ensemble, each attempt is either accepted or rejected
+based on internal energy and chemical potential considerations.  For further
+details, please refer to classical textbooks like Ref. <span id="id3">[<a class="reference internal" href="../non-tutorials/bibliography.html#id9" title="Daan Frenkel and Berend Smit. Understanding molecular simulation: from algorithms to applications. Elsevier, 2023.">6</a>]</span>.</p>
 <section id="adapting-the-pair-style">
 <h2>Adapting the pair style<a class="headerlink" href="#adapting-the-pair-style" title="Link to this heading">¶</a></h2>
 <p>For this next step, we need to specify the force field used to
 model the interactions in the system. The TIP4P/2005 model is employed
 for the water <span id="id4">[<a class="reference internal" href="../non-tutorials/bibliography.html#id54" title="Jose LF Abascal and Carlos Vega. A general purpose model for the condensed phases of water: TIP4P/2005. The Journal of chemical physics, 2005.">4</a>]</span>, while no interaction within
-silica is defined, as it will be seen farther below. This is be-
-cause atoms of the silica will remain frozen during this part of the simulation.
+silica is defined, as it will be seen farther below. This is because atoms of
+the silica will remain frozen during this part of the simulation.
 Only the cross-interactions between water and silica need
 to be defined. Create a new file called <strong>gcmc.lmp</strong>, and copy the following
 lines into it:</p>
@@ -556,8 +562,8 @@ <h2>Adapting the pair style<a class="headerlink" href="#adapting-the-pair-style"
 <p>After reading the data file and defining the <code class="docutils literal notranslate"><span class="pre">h2omol</span></code> molecule from the <strong>H2O.mol</strong>
 file, the <code class="docutils literal notranslate"><span class="pre">create_atoms</span></code> command is used to include three water molecules
 in the system.  Then, add the following <code class="docutils literal notranslate"><span class="pre">pair_coeff</span></code> (and
-<code class="docutils literal notranslate"><span class="pre">bond_coeff</span></code> and <code class="docutils literal notranslate"><span class="pre">angle_coeff</span></code>) commands
-to <strong>gcmc.lmp</strong>:</p>
+<code class="docutils literal notranslate"><span class="pre">bond_coeff</span></code> and <code class="docutils literal notranslate"><span class="pre">angle_coeff</span></code>) commands to <strong>gcmc.lmp</strong>
+in order to set the potential parameters:</p>
 <div class="highlight-lammps notranslate"><div class="highlight"><pre><span></span><span class="k">pair_coeff</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">0</span>
 <span class="k">pair_coeff</span><span class="w"> </span><span class="n">Si</span><span class="w"> </span><span class="n">OW</span><span class="w"> </span><span class="m">0.0057</span><span class="w"> </span><span class="m">4.42</span>
 <span class="k">pair_coeff</span><span class="w"> </span><span class="n">O</span><span class="w"> </span><span class="n">OW</span><span class="w"> </span><span class="m">0.0043</span><span class="w"> </span><span class="m">3.12</span>
@@ -567,7 +573,7 @@ <h2>Adapting the pair style<a class="headerlink" href="#adapting-the-pair-style"
 <span class="k">angle_coeff</span><span class="w"> </span><span class="n">HW</span><span class="o">-</span><span class="n">OW</span><span class="o">-</span><span class="n">HW</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">104.52</span>
 </pre></div>
 </div>
-<p>Pair coefficients for the <code class="docutils literal notranslate"><span class="pre">lj/cut/tip4p/long</span></code>
+<p>Pair coefficients for the <code class="docutils literal notranslate"><span class="pre">lj/cut/tip4p/long</span></code> pair style
 potential are defined between O(<span class="math notranslate nohighlight">\(\text{H}_2\text{O}\)</span>) and between H(<span class="math notranslate nohighlight">\(\text{H}_2\text{O}\)</span>)
 atoms, as well as between O(<span class="math notranslate nohighlight">\(\text{SiO}_2\)</span>)-O(<span class="math notranslate nohighlight">\(\text{H}_2\text{O}\)</span>) and
 Si(<span class="math notranslate nohighlight">\(\text{SiO}_2\)</span>)-O(<span class="math notranslate nohighlight">\(\text{H}_2\text{O}\)</span>).  Thus, the fluid-fluid and the
@@ -598,8 +604,9 @@ <h2>Adapting the pair style<a class="headerlink" href="#adapting-the-pair-style"
 their properties or types.</p>
 </div>
 <p>The number of oxygen atoms from water molecules (i.e. the number of molecules)
-is calculated by the <code class="docutils literal notranslate"><span class="pre">nO</span></code> variable.  The SHAKE algorithm is used to
-maintain the shape of the water molecules over time <span id="id7">[<a class="reference internal" href="../non-tutorials/bibliography.html#id27" title="Jean-Paul Ryckaert, Giovanni Ciccotti, and Herman JC Berendsen. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. Journal of computational physics, 23(3):327–341, 1977.">35</a>, <a class="reference internal" href="../non-tutorials/bibliography.html#id28" title="Hans C Andersen. Rattle: a “velocity” version of the shake algorithm for molecular dynamics calculations. Journal of computational Physics, 52(1):24–34, 1983.">36</a>]</span>.</p>
+is calculated by the <code class="docutils literal notranslate"><span class="pre">nO</span></code> variable.  As already discussed in other tutorials,
+the SHAKE algorithm is used to maintain the shape of the water molecules
+over time <span id="id7">[<a class="reference internal" href="../non-tutorials/bibliography.html#id27" title="Jean-Paul Ryckaert, Giovanni Ciccotti, and Herman JC Berendsen. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. Journal of computational physics, 23(3):327–341, 1977.">35</a>, <a class="reference internal" href="../non-tutorials/bibliography.html#id28" title="Hans C Andersen. Rattle: a “velocity” version of the shake algorithm for molecular dynamics calculations. Journal of computational Physics, 52(1):24–34, 1983.">36</a>]</span>.</p>
 <p>Finally, let us create images
 of the system using <code class="docutils literal notranslate"><span class="pre">dump</span> <span class="pre">image</span></code>:</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">250</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="o">&amp;</span>