deploy: c8681b5

Author: simongravelle

sphinx/build/doctrees/environment.pickle

@@ -41,6 +41,18 @@ interactions :cite:`ewald1921berechnung`.  Finally, the
 :ref:`carbon-nanotube-label`, sets the LJ and Coulomb
 weighting factors for the interaction between neighboring atoms.
 
+.. admonition:: Note
+    :class: non-title-info
+
+    With Coulomb interactions, additional rules
+    apply to the ``pair_coeff`` command: (a) atom type values
+    only matter for assignment of LJ potential parameters; (b) for Coulomb interactions,
+    there are no parameters outside the cutoff, and when using a
+    ``coul/long`` pair style, that cutoff can only be set globally
+    for all atoms with the ``pair_style``  command;  (c) for
+    Coulomb interactions, only the per-atom charge and any
+    ``special_bonds`` exclusions are relevant.
+
 .. include:: ../shared/needhelp.rst
 
 Let us create a 3D simulation box of dimensions :math:`6 \times 3 \times 3 \; \text{nm}^3`,
@@ -518,3 +530,13 @@ named **pull.lammpstrj**, which can be opened in OVITO or VMD.
     only the trajectory dump needs to be added.  Alternatively, the
     ``dump custom`` command can be combined with ``dump`` command to
     include element names in the dump file and simplify visualization.
+
+.. admonition:: Note
+    :class: non-title-info
+
+    Microstates collected during a simulation in the form of a trajectory
+    can be analyzed within LAMMPS using the ``rerun`` command.  This is
+    particularly useful, for example, for computing properties not set up in
+    the original simulation without having to run it again.  A possible use of
+    the ``rerun`` command is estimating the self-diffusion coefficient
+    by using the ``compute msd`` command :cite:`frenkel2023understanding`.

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

@@ -353,6 +353,17 @@ <h2>Preparing the water reservoir<a class="headerlink" href="#preparing-the-wate
 <code class="docutils literal notranslate"><span class="pre">special_bonds</span></code> command, which was already seen in
 <a class="reference internal" href="../tutorial2/breaking-a-carbon-nanotube.html#carbon-nanotube-label"><span class="std std-ref">Pulling on a carbon nanotube</span></a>, sets the LJ and Coulomb
 weighting factors for the interaction between neighboring atoms.</p>
+<div class="non-title-info admonition">
+<p class="admonition-title">Note</p>
+<p>With Coulomb interactions, additional rules
+apply to the <code class="docutils literal notranslate"><span class="pre">pair_coeff</span></code> command: (a) atom type values
+only matter for assignment of LJ potential parameters; (b) for Coulomb interactions,
+there are no parameters outside the cutoff, and when using a
+<code class="docutils literal notranslate"><span class="pre">coul/long</span></code> pair style, that cutoff can only be set globally
+for all atoms with the <code class="docutils literal notranslate"><span class="pre">pair_style</span></code>  command;  (c) for
+Coulomb interactions, only the per-atom charge and any
+<code class="docutils literal notranslate"><span class="pre">special_bonds</span></code> exclusions are relevant.</p>
+</div>
 <div class="patreon admonition">
 <p class="admonition-title">Struggling with your molecular simulations project?</p>
 <p>Get guidance for your LAMMPS simulations and receive
@@ -729,6 +740,15 @@ <h3>Tip: using external visualization tools<a class="headerlink" href="#tip-usin
 include element names in the dump file and simplify visualization.</p>
 </div>
 <div class="non-title-info admonition">
+<p class="admonition-title">Note</p>
+<p>Microstates collected during a simulation in the form of a trajectory
+can be analyzed within LAMMPS using the <code class="docutils literal notranslate"><span class="pre">rerun</span></code> command.  This is
+particularly useful, for example, for computing properties not set up in
+the original simulation without having to run it again.  A possible use of
+the <code class="docutils literal notranslate"><span class="pre">rerun</span></code> command is estimating the self-diffusion coefficient
+by using the <code class="docutils literal notranslate"><span class="pre">compute</span> <span class="pre">msd</span></code> command <span id="id17">[<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>
+</div>
+<div class="non-title-info admonition">
 <p class="admonition-title">Cite</p>
 <p>You can access the input scripts and data files that
 are used in these tutorials from a dedicated <a href="https://github.com/lammpstutorials/lammpstutorials-inputs/" target="_blank">GitHub repository</a>.
@@ -757,7 +777,7 @@ <h3>Extract the radial distribution function<a class="headerlink" href="#extract
 </div>
 <p>Note the difference in the structure of the water before and after
 the PEG molecule is stretched. This effect is described in
-the 2017 publication by Liese et al. <span id="id17">[<a class="reference internal" href="../non-tutorials/bibliography.html#id52" title="Susanne Liese, Manuel Gensler, Stefanie Krysiak, Richard Schwarzl, Andreas Achazi, Beate Paulus, Thorsten Hugel, Jürgen P Rabe, and Roland R Netz. Hydration effects turn a highly stretched polymer from an entropic into an energetic spring. ACS nano, 11(1):702–712, 2017.">27</a>]</span>.</p>
+the 2017 publication by Liese et al. <span id="id18">[<a class="reference internal" href="../non-tutorials/bibliography.html#id52" title="Susanne Liese, Manuel Gensler, Stefanie Krysiak, Richard Schwarzl, Andreas Achazi, Beate Paulus, Thorsten Hugel, Jürgen P Rabe, and Roland R Netz. Hydration effects turn a highly stretched polymer from an entropic into an energetic spring. ACS nano, 11(1):702–712, 2017.">27</a>]</span>.</p>
 </section>
 <section id="add-salt-to-the-system">
 <h3>Add salt to the system<a class="headerlink" href="#add-salt-to-the-system" title="Link to this heading">¶</a></h3>

sphinx/build/doctrees/tutorial3/tutorial.doctree

@@ -305,6 +305,17 @@ <h1>Preparing the water reservoir<a class="headerlink" href="#preparing-the-wate
 <code class="docutils literal notranslate"><span class="pre">special_bonds</span></code> command, which was already seen in
 <a class="reference internal" href="../tutorial2/breaking-a-carbon-nanotube.html#carbon-nanotube-label"><span class="std std-ref">Pulling on a carbon nanotube</span></a>, sets the LJ and Coulomb
 weighting factors for the interaction between neighboring atoms.</p>
+<div class="non-title-info admonition">
+<p class="admonition-title">Note</p>
+<p>With Coulomb interactions, additional rules
+apply to the <code class="docutils literal notranslate"><span class="pre">pair_coeff</span></code> command: (a) atom type values
+only matter for assignment of LJ potential parameters; (b) for Coulomb interactions,
+there are no parameters outside the cutoff, and when using a
+<code class="docutils literal notranslate"><span class="pre">coul/long</span></code> pair style, that cutoff can only be set globally
+for all atoms with the <code class="docutils literal notranslate"><span class="pre">pair_style</span></code>  command;  (c) for
+Coulomb interactions, only the per-atom charge and any
+<code class="docutils literal notranslate"><span class="pre">special_bonds</span></code> exclusions are relevant.</p>
+</div>
 <div class="patreon admonition">
 <p class="admonition-title">Struggling with your molecular simulations project?</p>
 <p>Get guidance for your LAMMPS simulations and receive
@@ -680,6 +691,15 @@ <h2>Tip: using external visualization tools<a class="headerlink" href="#tip-usin
 <code class="docutils literal notranslate"><span class="pre">dump</span> <span class="pre">custom</span></code> command can be combined with <code class="docutils literal notranslate"><span class="pre">dump</span></code> command to
 include element names in the dump file and simplify visualization.</p>
 </div>
+<div class="non-title-info admonition">
+<p class="admonition-title">Note</p>
+<p>Microstates collected during a simulation in the form of a trajectory
+can be analyzed within LAMMPS using the <code class="docutils literal notranslate"><span class="pre">rerun</span></code> command.  This is
+particularly useful, for example, for computing properties not set up in
+the original simulation without having to run it again.  A possible use of
+the <code class="docutils literal notranslate"><span class="pre">rerun</span></code> command is estimating the self-diffusion coefficient
+by using the <code class="docutils literal notranslate"><span class="pre">compute</span> <span class="pre">msd</span></code> command <span id="id11">[<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>
+</div>
 </section>
 </section>
 

sphinx/build/html/_sources/tutorial3/tutorial.rst.txt

@@ -41,6 +41,18 @@ interactions :cite:`ewald1921berechnung`.  Finally, the
 :ref:`carbon-nanotube-label`, sets the LJ and Coulomb
 weighting factors for the interaction between neighboring atoms.
 
+.. admonition:: Note
+    :class: non-title-info
+
+    With Coulomb interactions, additional rules
+    apply to the ``pair_coeff`` command: (a) atom type values
+    only matter for assignment of LJ potential parameters; (b) for Coulomb interactions,
+    there are no parameters outside the cutoff, and when using a
+    ``coul/long`` pair style, that cutoff can only be set globally
+    for all atoms with the ``pair_style``  command;  (c) for
+    Coulomb interactions, only the per-atom charge and any
+    ``special_bonds`` exclusions are relevant.
+
 .. include:: ../shared/needhelp.rst
 
 Let us create a 3D simulation box of dimensions :math:`6 \times 3 \times 3 \; \text{nm}^3`,
@@ -518,3 +530,13 @@ named **pull.lammpstrj**, which can be opened in OVITO or VMD.
     only the trajectory dump needs to be added.  Alternatively, the
     ``dump custom`` command can be combined with ``dump`` command to
     include element names in the dump file and simplify visualization.
+
+.. admonition:: Note
+    :class: non-title-info
+
+    Microstates collected during a simulation in the form of a trajectory
+    can be analyzed within LAMMPS using the ``rerun`` command.  This is
+    particularly useful, for example, for computing properties not set up in
+    the original simulation without having to run it again.  A possible use of
+    the ``rerun`` command is estimating the self-diffusion coefficient
+    by using the ``compute msd`` command :cite:`frenkel2023understanding`.