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so on. By excluding the non-bonded (Lennard-Jones) interactions for
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these pairs, those interactions do not need to be considered when determining
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the force constants.</p>
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<p>The <codeclass="docutils literal notranslate"><spanclass="pre">read_data</span></code> command imports the <ahref="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/unbreakable.data" target="_blank">unbreakable.data</a>
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<p>The <codeclass="docutils literal notranslate"><spanclass="pre">read_data</span></code> command imports the <ahref="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/unbreakable.data" target="_blank">unbreakable.data</a>
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file that should be downloaded next to <strong>unbreakable.lmp</strong>. This file contains information about the box size, atom positions,
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as well as the identity of the atoms that are linked by <codeclass="docutils literal notranslate"><spanclass="pre">bonds</span></code>, <codeclass="docutils literal notranslate"><spanclass="pre">angles</span></code>,
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<codeclass="docutils literal notranslate"><spanclass="pre">dihedrals</span></code>, and <codeclass="docutils literal notranslate"><spanclass="pre">impropers</span></code> interactions. It was created using VMD and TopoTools
as <spanclass="math notranslate nohighlight">\((L_\text{cnt}-L_\text{cnt-0})/L_\text{cnt-0}\)</span>, where <spanclass="math notranslate nohighlight">\(L_\text{cnt-0}\)</span> is the initial CNT length.</p>
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<p>Right-click inside the <codeclass="docutils literal notranslate"><spanclass="pre">Output</span></code> window, and select
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<codeclass="docutils literal notranslate"><spanclass="pre">Export</span><spanclass="pre">YAML</span><spanclass="pre">data</span><spanclass="pre">to</span><spanclass="pre">file</span></code>. Call the output <strong>unbreakable.yaml</strong>, and save
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it within the same folder as the input files, where a Python script named <ahref="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/unbreakable-yaml-reader.py" target="_blank">unbreakable-yaml-reader.py</a> should also
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it within the same folder as the input files, where a Python script named <ahref="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/unbreakable-yaml-reader.py" target="_blank">unbreakable-yaml-reader.py</a> should also
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be located. When executed using Python, this .py file first imports
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the <strong>unbreakable.yaml</strong> file. Then, a certain pattern is
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identified and stored as a string character named <codeclass="docutils literal notranslate"><spanclass="pre">docs</span></code>. The string is
@@ -649,7 +649,7 @@ <h2>Breakable bonds<a class="headerlink" href="#breakable-bonds" title="Link to
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large enough.</p>
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<sectionid="input-file-initialization">
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<h3>Input file initialization<aclass="headerlink" href="#input-file-initialization" title="Link to this heading">¶</a></h3>
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<p>Open the input named <ahref="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/breakable.lmp" target="_blank">breakable.lmp</a>
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<p>Open the input named <ahref="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/breakable.lmp" target="_blank">breakable.lmp</a>
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that should have been downloaded next to <strong>unbreakable.lmp</strong> during
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the tutorial setup. There are only a few differences with the previous
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input. First, the AIREBO force field requires the <codeclass="docutils literal notranslate"><spanclass="pre">metal</span></code> units
<p>Here, <ahref="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/CH.airebo" target="_blank">CH.airebo</a> is the file containing the parameters for AIREBO,
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<p>Here, <ahref="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/CH.airebo" target="_blank">CH.airebo</a> is the file containing the parameters for AIREBO,
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and must be placed next to <strong>breakable.lmp</strong>.</p>
<p>Since bonds, angles, and dihedrals do not need to be explicitly set when
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using AIREBO, some simplification must be made to the <strong>.data</strong>
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file. The new <strong>.data</strong> file is named <ahref="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/breakable.data" target="_blank">breakable.data</a>
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file. The new <strong>.data</strong> file is named <ahref="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/breakable.data" target="_blank">breakable.data</a>
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and must be placed within the same folder as the input file. Just like
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<strong>unbreakable.data</strong>, the <strong>breakable.data</strong> contains the
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information required for placing the atoms in the box, but no
@@ -748,7 +748,7 @@ <h3>Launch the deformation<a class="headerlink" href="#launch-the-deformation" t
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energy <spanclass="math notranslate nohighlight">\(E\)</span> is initially increasing with the deformation. When bonds
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break, the energy relaxes abruptly, as can be seen near <spanclass="math notranslate nohighlight">\(t=32~\text{ps}\)</span>.
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Using a similar script as previously,
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i.e., <ahref="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/unbreakable-yaml-reader.py" target="_blank">unbreakable-yaml-reader.py</a>, import the data into Python and generate
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i.e., <ahref="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/unbreakable-yaml-reader.py" target="_blank">unbreakable-yaml-reader.py</a>, import the data into Python and generate
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the stress-strain curve. The stress-strain
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curve reveals a linear (elastic) regime where
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<spanclass="math notranslate nohighlight">\(F_\text{cnt} \propto \Delta L_\text{cnt}\)</span> for
@@ -771,7 +771,7 @@ <h3>Launch the deformation<a class="headerlink" href="#launch-the-deformation" t
<h3>Tip: bonds representation with AIREBO<aclass="headerlink" href="#tip-bonds-representation-with-airebo" title="Link to this heading">¶</a></h3>
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<p>In the input file named <ahref="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/breakable-with-tip.lmp" target="_blank">breakable-with-tip.lmp</a>,,
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<p>In the input file named <ahref="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/breakable-with-tip.lmp" target="_blank">breakable-with-tip.lmp</a>,,
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which is an alternate solution for <strong>breakable.lmp</strong>, a trick is
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used to represent bonds while using AIREBO. A detailed explanation of
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the script is beyond the scope of the present tutorial. In short, the
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