deploy: 89e9a3a

sphinx/build/html/_sources/tutorials/level1/breaking-a-carbon-nanotube.rst.txt

@@ -28,16 +28,16 @@ Pulling on a carbon nanotube
 
     In this tutorial, a small carbon nanotube (CNT) is simulated
     within an empty box using LAMMPS. An external 
-    forcing is imposed on the CNT, and its deformation is measured with time.
+    force is imposed on the CNT, and its deformation is measured over time.
 
 ..  container:: abstract
 
-    The difference between classical and reactive force fields
-    is illustrated in this tutorial. With a classical force field, the bonds
-    between atoms are unbreakable. With the reactive
-    force field (named AIREBO :cite:`stuart2000reactive`),
-    the breaking of the chemical bonds is possible when
-    the imposed deformation is strong enough.
+    To illustrate the difference between classical and reactive force fields,
+    this tutorial is divided into two parts. Within the first part, a classical
+    force field is used and the bonds between the atoms of the CNT are
+    unbreakable. Within the second part, a reactive force field
+    (named AIREBO :cite:`stuart2000reactive`) is used, allowing for the breaking
+    of chemical bonds when the CNT undergoes strong deformation.
 
 .. include:: ../../non-tutorials/recommand-lj.rst
 
@@ -240,8 +240,7 @@ The LAMMPS input
     Atoms connected by a bond do not typically interact through
     Lennard-Jones interaction. Therefore, atoms that are
     bounded must be excluded from the Lennard-Jones potential calculation.  
-    Here, this is done by the
-    *special_bonds* command. The three numbers of the
+    Here, this is done by the *special_bonds* command. The three numbers of the
     *special_bonds* command are weighting factors for the
     Lennard-Jones interaction between atoms connected by a bond
     (respectively directly bounded :math:`C-C`, separated by two bonds :math:`C-C-C`,
@@ -296,8 +295,8 @@ The LAMMPS input
 
     include parm.lammps
 
-Prepare initial state
----------------------
+Prepare the initial state
+-------------------------
 
 .. container:: justify
 
@@ -374,15 +373,18 @@ Prepare initial state
     The variable :math:`z_\mathrm{max}` corresponds to
     the coordinate of the last atoms along :math:`z` minus 0.5
     Ångstroms, and :math:`z_\mathrm{min}` to the coordinate of
-    the first atoms along :math:`z` plus 0.5 Ångstroms. Then, 3
-    regions are defined, and correspond respectively to: :math:`z < z_\mathrm{min}`, (bottom)
-    :math:`z_\mathrm{min} > z > z_\mathrm{max}` (middle), and  
-    :math:`z > z_\mathrm{max}` (top).
+    the first atoms along :math:`z` plus 0.5 Ångstroms. Then, three
+    regions are defined, and correspond respectively to: :math:`z < z_\mathrm{min}`,
+    (*rbot*, for region bottom)
+    :math:`z_\mathrm{min} > z > z_\mathrm{max}`
+    (*rmid*, for region middle), and  
+    :math:`z > z_\mathrm{max}`
+    (*rtop*, for region top).
 
 .. container:: justify
 
     Finally, let us define 3 groups of atoms
-    corresponding to the atoms located in each of the 3 regions,
+    corresponding to the atoms located in each of the three regions,
     respectively, by adding to *input.lammps*:
 
 .. code-block:: lammps
@@ -423,7 +425,8 @@ Prepare initial state
 
 .. container:: justify
 
-    Finally, let us randomly delete some of the carbon atoms.
+    Finally, to start from a less ideal state and create a system with some defects, 
+    let us randomly delete some of the carbon atoms.
     In order to avoid deleting atoms that are too close to the edges,
     let us define a new region name *rdel* that
     starts :math:`2\,Å`
@@ -626,6 +629,8 @@ Data extraction
 .. container:: justify
 
     The chosen velocity for the deformation is :math:`100\,\text{m/s}`.
+    The length :math:`L` of the CNT increase linearly over
+    time for :math:`t > 5\,\text{ps}`, as expected from the imposed constant velocity.
 
 .. figure:: ../figures/level1/breaking-a-carbon-nanotube/length-unbreakable-dark.png
     :alt: length of the CNT with time - lammps molecular dynamics
@@ -637,7 +642,7 @@ Data extraction
 
 ..  container:: figurelegend
 
-    Figure: Evolution of the length of the CNT with time.
+    Figure: Evolution of the length :math:`L` of the CNT with time.
     The CNT starts deforming at :math:`t = 5\,\text{ps}`.
 
 .. container:: justify
@@ -686,9 +691,9 @@ Breakable bonds
 
 .. container:: justify
 
-    When using a classical force field, as we just did, the bonds between atoms 
-    are non-breakable. Let us perform a similar simulation, 
-    but this time using a reactive force field instead, allowing for the bonds to break
+    When using a classical force field, as we just did, the bonds between the atoms 
+    are non-breakable. Let us perform a similar simulation and deform a small CNT again,
+    but this time using a reactive force field that allows for the bonds to break
     if the applied deformation is large enough.
 
 Input file initialization

sphinx/build/html/_sources/tutorials/level1/lennard-jones-fluid.rst.txt

@@ -742,17 +742,23 @@ Control the initial atom positions
 
 ..  container:: justify
 
-    Run the *input.min.lammps* script using LAMMPS. A new dump file named
-    *dump.min.lammpstrj* will appear in the folder, allowing you to visualize
-    the atom's trajectories during minimization. In
-    addition, a file named *minimized_coordinate.data* will be created. 
-
+    Run the *input.min.lammps* script using LAMMPS.
+
 ..  container:: justify
+
+    As soon as the simulation starts, a new dump file named
+    *dump.min.lammpstrj* must appear in the folder.
+    This *.lammpstrj* can be used to visualize the
+    atom's trajectories during minimization using VMD.
+    At the end of the simulation, a file named
+    *minimized_coordinate.data* is created by LAMMPS.
 
-    If you open *minimized_coordinate.data* with a text editor, you can see
-    that it contains all the information necessary to restart the
-    simulation, such as the number of atoms and the box size, the
-    *masses*, the *pair_coeffs*:
+..  container:: justify
+
+    If you open *minimized_coordinate.data* with a text editor,
+    you can see that it contains all the information necessary to
+    restart the simulation, such as the number of atoms, the box
+    size, the *masses*, and the *pair_coeffs*:
 
 ..  code-block:: lammps
 
@@ -863,7 +869,8 @@ Restarting from a saved configuration
 
 ..  container:: justify
 
-    The first two *group* commands create atom groups based on their types.
+    The first two *group* commands are used to create groups containing
+    all the atoms of type 1 and all the atoms of type 2, respectively.
     The next two *group* commands create atom groups based on their
     positions at the beginning of the simulation, i.e. when the commands
     are being read by LAMMPS.
@@ -873,9 +880,8 @@ Restarting from a saved configuration
 ..  container:: justify
 
     Finally, the two *delete_atoms* commands delete the
-    atoms of type 1 that are located within the cylinder, as
-    well as the atoms of type 2 that are located outside the
-    cylinder, respectively. 
+    atoms of type 1 that are located within the cylinder and the atoms of
+    type 2 that are located outside the cylinder, respectively. 
 
 ..  container:: justify
 
@@ -936,11 +942,12 @@ Restarting from a saved configuration
 
 ..  container:: justify
 
-    Let us also extract the coordination number per atom between atoms 
-    of type 1 and 2, i.e. the average number of atoms of type 2 in the vicinity 
-    of the atoms of type 1. This coordination number will be used as
-    an indicator of the degree of mixing of our binary mixture. 
-    Add the following lines into *input.md.lammps*:
+    In addition to counting the atoms in each region, let us also extract the
+    coordination number per atom between atoms of types 1 and 2. The
+    coordination number is a measure of the average number of type 2 atoms
+    in the vicinity of type 1 atoms, serving as a good indicator of
+    the degree of mixing in a binary mixture. Add the following lines into
+    *input.md.lammps*:
 
 ..  code-block:: lammps
 
@@ -979,7 +986,7 @@ Restarting from a saved configuration
     momentum (*rot yes*) are given to the system and that the generated
     velocities are distributed as a Gaussian. Another improvement
     is the *zero yes* keyword in the Langevin thermostat, which
-    ensures that the total random force is equal to zero.
+    ensures that the total random force applied to the atoms is equal to zero.
 
 ..  container:: justify
 
@@ -996,7 +1003,10 @@ Restarting from a saved configuration
 
 .. container:: figurelegend
 
-    Figure: Evolution of the system during mixing.
+    Figure: Evolution of the system during mixing. The three snapshots show
+    respectively the system at :math:`t=0` (left panel),
+    :math:`t=75` (middle panel),
+    and :math:`t=1500` (right panel).
 
 ..  container:: justify
 
@@ -1015,7 +1025,8 @@ Restarting from a saved configuration
 .. container:: figurelegend
 
     Figure: Evolution of the number of atoms within the *region_cylinder_in* region
-    as a function of time (a), and evolution of the coordination number (b). 
+    as a function of time (a), and evolution of the coordination number
+    between atoms of types 1 and 2 (b). 
 
 .. include:: ../../non-tutorials/accessfile.rst
 

sphinx/build/html/tutorials/level1/breaking-a-carbon-nanotube.html

@@ -308,15 +308,15 @@
 <div class="abstract docutils container">
 <p>In this tutorial, a small carbon nanotube (CNT) is simulated
 within an empty box using LAMMPS. An external
-forcing is imposed on the CNT, and its deformation is measured with time.</p>
+force is imposed on the CNT, and its deformation is measured over time.</p>
 </div>
 <div class="abstract docutils container">
-<p>The difference between classical and reactive force fields
-is illustrated in this tutorial. With a classical force field, the bonds
-between atoms are unbreakable. With the reactive
-force field (named AIREBO <span id="id1">[<a class="reference internal" href="../../non-tutorials/bibliography.html#id34" title="Steven J Stuart, Alan B Tutein, and Judith A Harrison. A reactive potential for hydrocarbons with intermolecular interactions. The Journal of chemical physics, 112(14):6472–6486, 2000.">18</a>]</span>),
-the breaking of the chemical bonds is possible when
-the imposed deformation is strong enough.</p>
+<p>To illustrate the difference between classical and reactive force fields,
+this tutorial is divided into two parts. Within the first part, a classical
+force field is used and the bonds between the atoms of the CNT are
+unbreakable. Within the second part, a reactive force field
+(named AIREBO <span id="id1">[<a class="reference internal" href="../../non-tutorials/bibliography.html#id34" title="Steven J Stuart, Alan B Tutein, and Judith A Harrison. A reactive potential for hydrocarbons with intermolecular interactions. The Journal of chemical physics, 112(14):6472–6486, 2000.">18</a>]</span>) is used, allowing for the breaking
+of chemical bonds when the CNT undergoes strong deformation.</p>
 </div>
 <div class="justify docutils container">
 <p>If you are completely new to LAMMPS, I recommend that
@@ -484,8 +484,7 @@ <h3>The LAMMPS input<a class="headerlink" href="#the-lammps-input" title="Link t
 <p>Atoms connected by a bond do not typically interact through
 Lennard-Jones interaction. Therefore, atoms that are
 bounded must be excluded from the Lennard-Jones potential calculation.
-Here, this is done by the
-<em>special_bonds</em> command. The three numbers of the
+Here, this is done by the <em>special_bonds</em> command. The three numbers of the
 <em>special_bonds</em> command are weighting factors for the
 Lennard-Jones interaction between atoms connected by a bond
 (respectively directly bounded <span class="math notranslate nohighlight">\(C-C\)</span>, separated by two bonds <span class="math notranslate nohighlight">\(C-C-C\)</span>,
@@ -535,8 +534,8 @@ <h3>The LAMMPS input<a class="headerlink" href="#the-lammps-input" title="Link t
 </pre></div>
 </div>
 </section>
-<section id="prepare-initial-state">
-<h3>Prepare initial state<a class="headerlink" href="#prepare-initial-state" title="Link to this heading">¶</a></h3>
+<section id="prepare-the-initial-state">
+<h3>Prepare the initial state<a class="headerlink" href="#prepare-the-initial-state" title="Link to this heading">¶</a></h3>
 <div class="justify docutils container">
 <p>Before starting the molecular dynamics simulation,
 let us make sure that we start from a clean initial state
@@ -601,14 +600,17 @@ <h3>Prepare initial state<a class="headerlink" href="#prepare-initial-state" tit
 <p>The variable <span class="math notranslate nohighlight">\(z_\mathrm{max}\)</span> corresponds to
 the coordinate of the last atoms along <span class="math notranslate nohighlight">\(z\)</span> minus 0.5
 Ångstroms, and <span class="math notranslate nohighlight">\(z_\mathrm{min}\)</span> to the coordinate of
-the first atoms along <span class="math notranslate nohighlight">\(z\)</span> plus 0.5 Ångstroms. Then, 3
-regions are defined, and correspond respectively to: <span class="math notranslate nohighlight">\(z &lt; z_\mathrm{min}\)</span>, (bottom)
-<span class="math notranslate nohighlight">\(z_\mathrm{min} &gt; z &gt; z_\mathrm{max}\)</span> (middle), and
-<span class="math notranslate nohighlight">\(z &gt; z_\mathrm{max}\)</span> (top).</p>
+the first atoms along <span class="math notranslate nohighlight">\(z\)</span> plus 0.5 Ångstroms. Then, three
+regions are defined, and correspond respectively to: <span class="math notranslate nohighlight">\(z &lt; z_\mathrm{min}\)</span>,
+(<em>rbot</em>, for region bottom)
+<span class="math notranslate nohighlight">\(z_\mathrm{min} &gt; z &gt; z_\mathrm{max}\)</span>
+(<em>rmid</em>, for region middle), and
+<span class="math notranslate nohighlight">\(z &gt; z_\mathrm{max}\)</span>
+(<em>rtop</em>, for region top).</p>
 </div>
 <div class="justify docutils container">
 <p>Finally, let us define 3 groups of atoms
-corresponding to the atoms located in each of the 3 regions,
+corresponding to the atoms located in each of the three regions,
 respectively, by adding to <em>input.lammps</em>:</p>
 </div>
 <div class="highlight-lammps notranslate"><div class="highlight"><pre><span></span><span class="k">group </span><span class="nv nv-Identifier">carbon_top</span><span class="w"> </span><span class="k">region </span><span class="nv nv-Identifier">rtop</span>
@@ -641,7 +643,8 @@ <h3>Prepare initial state<a class="headerlink" href="#prepare-initial-state" tit
 </pre></div>
 </div>
 <div class="justify docutils container">
-<p>Finally, let us randomly delete some of the carbon atoms.
+<p>Finally, to start from a less ideal state and create a system with some defects,
+let us randomly delete some of the carbon atoms.
 In order to avoid deleting atoms that are too close to the edges,
 let us define a new region name <em>rdel</em> that
 starts <span class="math notranslate nohighlight">\(2\,Å\)</span>
@@ -814,7 +817,9 @@ <h3>Data extraction<a class="headerlink" href="#data-extraction" title="Link to
 </pre></div>
 </div>
 <div class="justify docutils container">
-<p>The chosen velocity for the deformation is <span class="math notranslate nohighlight">\(100\,\text{m/s}\)</span>.</p>
+<p>The chosen velocity for the deformation is <span class="math notranslate nohighlight">\(100\,\text{m/s}\)</span>.
+The length <span class="math notranslate nohighlight">\(L\)</span> of the CNT increase linearly over
+time for <span class="math notranslate nohighlight">\(t &gt; 5\,\text{ps}\)</span>, as expected from the imposed constant velocity.</p>
 </div>
 <figure class="align-default">
 <img alt="length of the CNT with time - lammps molecular dynamics" class="only-dark" src="../../_images/length-unbreakable-dark.png" />
@@ -823,7 +828,7 @@ <h3>Data extraction<a class="headerlink" href="#data-extraction" title="Link to
 <img alt="length of the CNT with time - lammps molecular dynamics" class="only-light" src="../../_images/length-unbreakable-light.png" />
 </figure>
 <div class="figurelegend docutils container">
-<p>Figure: Evolution of the length of the CNT with time.
+<p>Figure: Evolution of the length <span class="math notranslate nohighlight">\(L\)</span> of the CNT with time.
 The CNT starts deforming at <span class="math notranslate nohighlight">\(t = 5\,\text{ps}\)</span>.</p>
 </div>
 <div class="justify docutils container">
@@ -860,9 +865,9 @@ <h3>Data extraction<a class="headerlink" href="#data-extraction" title="Link to
 <section id="breakable-bonds">
 <h2>Breakable bonds<a class="headerlink" href="#breakable-bonds" title="Link to this heading">¶</a></h2>
 <div class="justify docutils container">
-<p>When using a classical force field, as we just did, the bonds between atoms
-are non-breakable. Let us perform a similar simulation,
-but this time using a reactive force field instead, allowing for the bonds to break
+<p>When using a classical force field, as we just did, the bonds between the atoms
+are non-breakable. Let us perform a similar simulation and deform a small CNT again,
+but this time using a reactive force field that allows for the bonds to break
 if the applied deformation is large enough.</p>
 </div>
 <section id="input-file-initialization">
@@ -1280,7 +1285,7 @@ <h3>Make a membrane of CNTs<a class="headerlink" href="#make-a-membrane-of-cnts"
 <li><a class="reference internal" href="#unbreakable-bonds">Unbreakable bonds</a><ul>
 <li><a class="reference internal" href="#create-topology-with-vmd">Create topology with VMD</a></li>
 <li><a class="reference internal" href="#the-lammps-input">The LAMMPS input</a></li>
-<li><a class="reference internal" href="#prepare-initial-state">Prepare initial state</a></li>
+<li><a class="reference internal" href="#prepare-the-initial-state">Prepare the initial state</a></li>
 <li><a class="reference internal" href="#the-molecular-dynamics">The molecular dynamics</a></li>
 <li><a class="reference internal" href="#data-extraction">Data extraction</a></li>
 </ul>