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<li class="toctree-l3"><a class="reference internal" href="Howto_cmake.html">8.6.1. Using CMake with LAMMPS</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_moltemplate.html">8.6.4. Moltemplate Tutorial</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_pylammps.html">8.6.5. PyLammps Tutorial</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Howto_wsl.html">8.6.6. Using LAMMPS on Windows 10 with WSL</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</a></li>
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<a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="using-lammps-gui">
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<h1><span class="section-number">8.6.3. </span>Using LAMMPS-GUI<a class="headerlink" href="#using-lammps-gui" title="Link to this heading"></a></h1>
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<p>This document describes <strong>LAMMPS-GUI version 1.6</strong>.</p>
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<hr class="docutils" />
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<p>LAMMPS-GUI is a graphical text editor customized for editing LAMMPS
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input files that is linked to the <a class="reference internal" href="Library.html#lammps-c-api"><span class="std std-ref">LAMMPS library</span></a>
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and thus can run LAMMPS directly using the contents of the editor’s text
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buffer as input. It can retrieve and display information from LAMMPS
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while it is running, display visualizations created with the <a class="reference internal" href="dump_image.html"><span class="doc">dump
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image command</span></a>, and is adapted specifically for editing
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LAMMPS input files through text completion and reformatting, and linking
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to the online LAMMPS documentation for known LAMMPS commands and styles.</p>
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<div class="admonition note">
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<p class="admonition-title">Note</p>
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<p>Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux x86_64
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(Ubuntu 20.04LTS or later and compatible), macOS (version 11 aka Big
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Sur or later), and Windows (version 10 or later) <a class="reference internal" href="Tools.html#lammps-gui-install"><span class="std std-ref">are available</span></a> for download. Non-MPI LAMMPS executables (as
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<code class="docutils literal notranslate"><span class="pre">lmp</span></code>) for running LAMMPS from the command-line and <a class="reference internal" href="Tools.html"><span class="doc">some
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LAMMPS tools</span></a> compiled executables are also included.
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Also, the pre-compiled LAMMPS-GUI packages include the WHAM executables
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from <a class="reference external" href="http://membrane.urmc.rochester.edu/content/wham/">http://membrane.urmc.rochester.edu/content/wham/</a> for use with
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LAMMPS tutorials.</p>
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<p>The source code for LAMMPS-GUI is included in the LAMMPS source code
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distribution and can be found in the <code class="docutils literal notranslate"><span class="pre">tools/lammps-gui</span></code> folder. It
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can be compiled alongside LAMMPS when <a class="reference internal" href="Build_cmake.html"><span class="doc">compiling with CMake</span></a>.</p>
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</div>
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<p>LAMMPS-GUI tries to provide an experience similar to what people
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traditionally would have running LAMMPS using a command-line window and
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the console LAMMPS executable but just rolled into a single executable:</p>
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<ul class="simple">
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<li><p>writing & editing LAMMPS input files with a text editor</p></li>
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<li><p>run LAMMPS on those input file with selected command-line flags</p></li>
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<li><p>extract data from the created files and visualize it with and
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external software</p></li>
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</ul>
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<p>That procedure is quite effective for people proficient in using the
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command-line, as that allows them to use tools for the individual steps
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that they are most comfortable with. In fact, it is often <em>required</em> to
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adopt this workflow when running LAMMPS simulations on high-performance
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computing facilities.</p>
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<p>The main benefit of using LAMMPS-GUI is that many basic tasks can be
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done directly from the GUI <strong>without</strong> switching to a text console
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window or using external programs, let alone writing scripts to extract
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data from the generated output. It also integrates well with graphical
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desktop environments where the <cite>.lmp</cite> filename extension can be
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registered with LAMMPS-GUI as the executable to launch when double
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clicking on such files. Also, LAMMPS-GUI has support for drag-n-drop,
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i.e. an input file can be selected and then moved and dropped on the
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LAMMPS-GUI executable, and LAMMPS-GUI will launch and read the file into
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its buffer. In many cases LAMMPS-GUI will be integrated into the
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graphical desktop environment and can be launched like other
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applications.</p>
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<p>LAMMPS-GUI thus makes it easier for beginners to get started running
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simple LAMMPS simulations. It is very suitable for tutorials on LAMMPS
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since you only need to learn how to use a single program for most tasks
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and thus time can be saved and people can focus on learning LAMMPS.
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The tutorials at <a class="reference external" href="https://lammpstutorials.github.io/">https://lammpstutorials.github.io/</a> are specifically
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updated for use with LAMMPS-GUI.</p>
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<p>Another design goal is to keep the barrier low when replacing part of
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the functionality of LAMMPS-GUI with external tools. That said, LAMMPS-GUI
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has some unique functionality that is not found elsewhere:</p>
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<ul class="simple">
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<li><p>auto-adapting to features available in the integrated LAMMPS library</p></li>
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<li><p>interactive visualization using the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a>
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command with the option to copy-paste the resulting settings</p></li>
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<li><p>automatic slide show generation from dump image out at runtime</p></li>
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<li><p>automatic plotting of thermodynamics data at runtime</p></li>
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<li><p>inspection of binary restart files</p></li>
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</ul>
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<p>The following text provides a detailed tour of the features and
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functionality of LAMMPS-GUI. Suggestions for new features and
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reports of bugs are always welcome. You can use the <a class="reference internal" href="Errors_bugs.html"><span class="doc">the same
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channels as for LAMMPS itself</span></a> for that purpose.</p>
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<hr class="docutils" />
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<section id="installing-pre-compiled-lammps-gui-packages">
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<h2>Installing Pre-compiled LAMMPS-GUI Packages<a class="headerlink" href="#installing-pre-compiled-lammps-gui-packages" title="Link to this heading"></a></h2>
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<p>LAMMPS-GUI is available as pre-compiled binary packages for Linux
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x86_64, macOS 11 and later, and Windows 10 and later. Alternately, it
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can be compiled from source.</p>
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<section id="windows-10-and-later">
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<h3>Windows 10 and later<a class="headerlink" href="#windows-10-and-later" title="Link to this heading"></a></h3>
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<p>After downloading the <code class="docutils literal notranslate"><span class="pre">LAMMPS-Win10-64bit-GUI-<version>.exe</span></code> installer
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package, you need to execute it, and start the installation process.
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Since those packages are currently unsigned, you have to enable “Developer Mode”
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in the Windows System Settings to run the installer.</p>
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</section>
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<section id="macos-11-and-later">
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<h3>MacOS 11 and later<a class="headerlink" href="#macos-11-and-later" title="Link to this heading"></a></h3>
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<p>After downloading the <code class="docutils literal notranslate"><span class="pre">LAMMPS-macOS-multiarch-GUI-<version>.dmg</span></code>
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application bundle disk image, you need to double-click it and then, in
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the window that opens, drag the app bundle as indicated into the
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“Applications” folder. Afterwards, the disk image can be unmounted.
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Then follow the instructions in the “README.txt” file to get access to
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the other included command-line executables.</p>
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</section>
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<section id="linux-on-x86-64">
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<h3>Linux on x86_64<a class="headerlink" href="#linux-on-x86-64" title="Link to this heading"></a></h3>
|
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<p>For Linux with x86_64 CPU there are currently two variants. The first
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is compiled on Ubuntu 20.04LTS, is using some wrapper scripts, and
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should be compatible with more recent Linux distributions. After
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downloading and unpacking the
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<code class="docutils literal notranslate"><span class="pre">LAMMPS-Linux-x86_64-GUI-<version>.tar.gz</span></code> package. You can switch
|
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into the “LAMMPS_GUI” folder and execute “./lammps-gui” directly.</p>
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<p>The second variant uses <a class="reference external" href="https://www.flatpak.org">flatpak</a> and
|
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requires the flatpak management and runtime software to be installed.
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After downloading the <code class="docutils literal notranslate"><span class="pre">LAMMPS-GUI-Linux-x86_64-GUI-<version>.flatpak</span></code>
|
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flatpak bundle, you can install it with <code class="docutils literal notranslate"><span class="pre">flatpak</span> <span class="pre">install</span> <span class="pre">--user</span>
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<span class="pre">LAMMPS-GUI-Linux-x86_64-GUI-<version>.flatpak</span></code>. After installation,
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LAMMPS-GUI should be integrated into your desktop environment under
|
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“Applications > Science” but also can be launched from the console with
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<code class="docutils literal notranslate"><span class="pre">flatpak</span> <span class="pre">run</span> <span class="pre">org.lammps.lammps-gui</span></code>. The flatpak bundle also includes
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||
the console LAMMPS executable <code class="docutils literal notranslate"><span class="pre">lmp</span></code> which can be launched to run
|
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simulations with, for example with:</p>
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<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>flatpak<span class="w"> </span>run<span class="w"> </span>--command<span class="o">=</span>lmp<span class="w"> </span>org.lammps.lammps-gui<span class="w"> </span>-in<span class="w"> </span><span class="k">in</span>.melt
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</pre></div>
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</div>
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<p>Other bundled command-line executables are run the same way and can be
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listed with:</p>
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<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>ls<span class="w"> </span><span class="k">$(</span>flatpak<span class="w"> </span>info<span class="w"> </span>--show-location<span class="w"> </span>org.lammps.lammps-gui<span class="w"> </span><span class="k">)</span>/files/bin
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</pre></div>
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</div>
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</section>
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<section id="compiling-from-source">
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||
<h3>Compiling from Source<a class="headerlink" href="#compiling-from-source" title="Link to this heading"></a></h3>
|
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<p>There also are instructions for <a class="reference internal" href="Tools.html#lammps-gui-compilation"><span class="std std-ref">compiling LAMMPS-GUI from source
|
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code</span></a> available elsewhere in the manual.
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Compilation from source <em>requires</em> using CMake.</p>
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</section>
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</section>
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<hr class="docutils" />
|
||
<section id="starting-lammps-gui">
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<h2>Starting LAMMPS-GUI<a class="headerlink" href="#starting-lammps-gui" title="Link to this heading"></a></h2>
|
||
<p>When LAMMPS-GUI starts, it shows the main window, labeled <em>Editor</em>, with
|
||
either an empty buffer or the contents of the file used as argument. In
|
||
the latter case it may look like the following:</p>
|
||
<p><a class="reference internal" href="_images/lammps-gui-main.png"><img alt="gui-main1" src="_images/lammps-gui-main.png" style="width: 48%;" /></a> <a class="reference internal" href="_images/lammps-gui-dark.png"><img alt="gui-main2" src="_images/lammps-gui-dark.png" style="width: 48%;" /></a></p>
|
||
<p>There is the typical menu bar at the top, then the main editor buffer,
|
||
and a status bar at the bottom. The input file contents are shown
|
||
with line numbers on the left and the input is colored according to
|
||
the LAMMPS input file syntax. The status bar shows the status of
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||
LAMMPS execution on the left (e.g. “Ready.” when idle) and the current
|
||
working directory on the right. The name of the current file in the
|
||
buffer is shown in the window title; the word <cite>*modified*</cite> is added if
|
||
the buffer edits have not yet saved to a file. The geometry of the main
|
||
window is stored when exiting and restored when starting again.</p>
|
||
<section id="opening-files">
|
||
<h3>Opening Files<a class="headerlink" href="#opening-files" title="Link to this heading"></a></h3>
|
||
<p>The LAMMPS-GUI application can be launched without command-line arguments
|
||
and then starts with an empty buffer in the <em>Editor</em> window. If arguments
|
||
are given LAMMPS will use first command-line argument as the file name for
|
||
the <em>Editor</em> buffer and reads its contents into the buffer, if the file
|
||
exists. All further arguments are ignored. Files can also be opened via
|
||
the <em>File</em> menu, the <cite>Ctrl-O</cite> (<cite>Command-O</cite> on macOS) keyboard shortcut
|
||
or by drag-and-drop of a file from a graphical file manager into the editor
|
||
window. If a file extension (e.g. <code class="docutils literal notranslate"><span class="pre">.lmp</span></code>) has been registered with the
|
||
graphical environment to launch LAMMPS-GUI, an existing input file can
|
||
be launched with LAMMPS-GUI through double clicking.</p>
|
||
<p>Only one file can be edited at a time, so opening a new file with a
|
||
filled buffer closes that buffer. If the buffer has unsaved
|
||
modifications, you are asked to either cancel the operation, discard the
|
||
changes, or save them. A buffer with modifications can be saved any
|
||
time from the “File” menu, by the keyboard shortcut <cite>Ctrl-S</cite>
|
||
(<cite>Command-S</cite> on macOS), or by clicking on the “Save” button at the very
|
||
left in the status bar.</p>
|
||
</section>
|
||
<section id="running-lammps">
|
||
<h3>Running LAMMPS<a class="headerlink" href="#running-lammps" title="Link to this heading"></a></h3>
|
||
<p>From within the LAMMPS-GUI main window LAMMPS can be started either from
|
||
the <em>Run</em> menu using the <em>Run LAMMPS from Editor Buffer</em> entry, by
|
||
the keyboard shortcut <cite>Ctrl-Enter</cite> (<cite>Command-Enter</cite> on macOS), or by
|
||
clicking on the green “Run” button in the status bar. All of these
|
||
operations causes LAMMPS to process the entire input script in the
|
||
editor buffer, which may contain multiple <a class="reference internal" href="run.html"><span class="doc">run</span></a> or
|
||
<a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> commands.</p>
|
||
<p>LAMMPS runs in a separate thread, so the GUI stays responsive and is
|
||
able to interact with the running calculation and access data it
|
||
produces. It is important to note that running LAMMPS this way is
|
||
using the contents of the input buffer for the run (via the
|
||
<a class="reference internal" href="Library_execute.html#_CPPv422lammps_commands_stringPvPKc" title="lammps_commands_string"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_commands_string()</span></code></a> function of the LAMMPS C-library
|
||
interface), and <strong>not</strong> the original file it was read from. Thus, if
|
||
there are unsaved changes in the buffer, they <em>will</em> be used. As an
|
||
alternative, it is also possible to run LAMMPS by reading the contents
|
||
of a file from the <em>Run LAMMPS from File</em> menu entry or with
|
||
<cite>Ctrl-Shift-Enter</cite>. This option may be required in some rare cases
|
||
where the input uses some functionality that is not compatible with
|
||
running LAMMPS from a string buffer. For consistency, any unsaved
|
||
changes in the buffer must be either saved to the file or undone
|
||
before LAMMPS can be run from a file.</p>
|
||
<a class="reference internal image-reference" href="_images/lammps-gui-running.png"><img alt="_images/lammps-gui-running.png" class="align-center" src="_images/lammps-gui-running.png" style="width: 679.5px; height: 117.0px;" />
|
||
</a>
|
||
<p>While LAMMPS is running, the contents of the status bar change. On
|
||
the left side there is a text indicating that LAMMPS is running, which
|
||
also indicates the number of active threads, when thread-parallel
|
||
acceleration was selected in the <em>Preferences</em> dialog. On the right
|
||
side, a progress bar is shown that displays the estimated progress for
|
||
the current <a class="reference internal" href="run.html"><span class="doc">run</span></a> or <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command.</p>
|
||
<p>Also, the line number of the currently executed command is highlighted
|
||
in green.</p>
|
||
<p>If an error occurs (in the example below the command <a class="reference internal" href="label.html"><span class="doc">label</span></a> was incorrectly capitalized as “Label”), an error message
|
||
dialog is shown and the line of the input which triggered the error is
|
||
highlighted. The state of LAMMPS in the status bar is set to “Failed.”
|
||
instead of “Ready.”</p>
|
||
<a class="reference internal image-reference" href="_images/lammps-gui-run-error.png"><img alt="_images/lammps-gui-run-error.png" class="align-center" src="_images/lammps-gui-run-error.png" style="width: 649.5px; height: 214.5px;" />
|
||
</a>
|
||
<p>Up to three additional windows may open during a run:</p>
|
||
<ul class="simple">
|
||
<li><p>an <em>Output</em> window with the captured screen output from LAMMPS</p></li>
|
||
<li><p>a <em>Charts</em> window with a line graph created from thermodynamic output of the run</p></li>
|
||
<li><p>a <em>Slide Show</em> window with images created by a <a class="reference internal" href="dump_image.html"><span class="doc">dump image command</span></a>
|
||
in the input</p></li>
|
||
</ul>
|
||
<p>More information on those windows and how to adjust their behavior and
|
||
contents is given below.</p>
|
||
<p>An active LAMMPS run can be stopped cleanly by using either the <em>Stop
|
||
LAMMPS</em> entry in the <em>Run</em> menu, the keyboard shortcut <cite>Ctrl-/</cite>
|
||
(<cite>Command-/</cite> on macOS), or by clicking on the red button in the status
|
||
bar. This will cause the running LAMMPS process to complete the current
|
||
timestep (or iteration for energy minimization) and then complete the
|
||
processing of the buffer while skipping all run or minimize commands.
|
||
This is equivalent to the input script command <a class="reference internal" href="timer.html"><span class="doc">timer timeout 0</span></a> and is implemented by calling the
|
||
<a class="reference internal" href="Library_utility.html#_CPPv420lammps_force_timeoutPv" title="lammps_force_timeout"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_force_timeout()</span></code></a> function of the LAMMPS C-library
|
||
interface. Please see the corresponding documentation pages to
|
||
understand the implications of this operation.</p>
|
||
</section>
|
||
</section>
|
||
<section id="output-window">
|
||
<h2>Output Window<a class="headerlink" href="#output-window" title="Link to this heading"></a></h2>
|
||
<p>By default, when starting a run, an <em>Output</em> window opens that displays
|
||
the screen output of the running LAMMPS calculation, as shown below.
|
||
This text would normally be seen in the command-line window.</p>
|
||
<a class="reference internal image-reference" href="_images/lammps-gui-log.png"><img alt="_images/lammps-gui-log.png" class="align-center" src="_images/lammps-gui-log.png" style="width: 404.0px; height: 169.0px;" />
|
||
</a>
|
||
<p>LAMMPS-GUI captures the screen output from LAMMPS as it is generated and
|
||
updates the <em>Output</em> window regularly during a run. If there are any
|
||
warnings or errors in the LAMMPS output, they are highlighted by using
|
||
bold text colored in red. There is a small panel at the bottom center
|
||
of the <em>Output</em> window showing how many warnings and errors were
|
||
detected and how many lines the entire output has. By clicking on the
|
||
button on the right with the warning symbol or by using the keyboard
|
||
shortcut <cite>Ctrl-N</cite> (<cite>Command-N</cite> on macOS), you can jump to the next
|
||
line with a warning or error.</p>
|
||
<p>By default, the <em>Output</em> window is replaced each time a run is started.
|
||
The runs are counted and the run number for the current run is displayed
|
||
in the window title. It is possible to change the behavior of
|
||
LAMMPS-GUI in the preferences dialog to create a <em>new</em> <em>Output</em> window
|
||
for every run or to not show the current <em>Output</em> window. It is also
|
||
possible to show or hide the <em>current</em> <em>Output</em> window from the <em>View</em>
|
||
menu.</p>
|
||
<p>The text in the <em>Output</em> window is read-only and cannot be modified, but
|
||
keyboard shortcuts to select and copy all or parts of the text can be
|
||
used to transfer text to another program. Also, the keyboard shortcut
|
||
<cite>Ctrl-S</cite> (<cite>Command-S</cite> on macOS) is available to save the <em>Output</em> buffer to a
|
||
file. The “Select All” and “Copy” functions, as well as a “Save Log to
|
||
File” option are also available from a context menu by clicking with the
|
||
right mouse button into the <em>Output</em> window text area.</p>
|
||
<a class="reference internal image-reference" href="_images/lammps-gui-yaml.png"><img alt="_images/lammps-gui-yaml.png" class="align-center" src="_images/lammps-gui-yaml.png" style="width: 673.5px; height: 220.5px;" />
|
||
</a>
|
||
<p>Should the <em>Output</em> window contain embedded YAML format text (see above for a
|
||
demonstration), for example from using <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style yaml</span></a> or <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify line yaml</span></a>, the
|
||
keyboard shortcut <cite>Ctrl-Y</cite> (<cite>Command-Y</cite> on macOS) is available to save
|
||
only the YAML parts to a file. This option is also available from a
|
||
context menu by clicking with the right mouse button into the <em>Output</em> window
|
||
text area.</p>
|
||
</section>
|
||
<section id="charts-window">
|
||
<h2>Charts Window<a class="headerlink" href="#charts-window" title="Link to this heading"></a></h2>
|
||
<p>By default, when starting a run, a <em>Charts</em> window opens that displays a
|
||
plot of thermodynamic output of the LAMMPS calculation as shown below.</p>
|
||
<a class="reference internal image-reference" href="_images/lammps-gui-chart.png"><img alt="_images/lammps-gui-chart.png" class="align-center" src="_images/lammps-gui-chart.png" style="width: 317.46000000000004px; height: 247.83px;" />
|
||
</a>
|
||
<p>The drop down menu on the top right allows selection of different
|
||
properties that are computed and written to thermo output. Only one
|
||
property can be shown at a time. The plots are updated regularly with
|
||
new data as the run progresses, so they can be used to visually monitor
|
||
the evolution of available properties. The update interval can be set
|
||
in the <em>Preferences</em> dialog. By default, the raw data for the selected
|
||
property is plotted as a blue graph. As soon as there are a sufficient
|
||
number of data points, there will be a second graph shown in red with a
|
||
smoothed version of the data. From the drop down menu on the top left,
|
||
you can select whether to plot only the raw data, only the smoothed
|
||
data or both. The smoothing uses a <a class="reference external" href="https://en.wikipedia.org/wiki/Savitzky%E2%80%93Golay_filter">Savitzky-Golay convolution filter</a> The
|
||
window width (left) and order (right) parameters can be set in the boxes
|
||
next to the drop down menu. Default settings are 10 and 4 which means
|
||
that the smoothing window includes 10 points each to the left and the
|
||
right of the current data point and a fourth order polynomial is fit to
|
||
the data in the window.</p>
|
||
<p>You can use the mouse to zoom into the graph (hold the left button and
|
||
drag to mark an area) or zoom out (right click) and you can reset the
|
||
view with a click to the “lens” button next to the data drop down menu.</p>
|
||
<p>The window title shows the current run number that this chart window
|
||
corresponds to. Same as for the <em>Output</em> window, the chart window is
|
||
replaced on each new run, but the behavior can be changed in the
|
||
<em>Preferences</em> dialog.</p>
|
||
<p>From the <em>File</em> menu on the top left, it is possible to save an image
|
||
of the currently displayed plot or export the data in either plain text
|
||
columns (for use by plotting tools like <a class="reference external" href="http://www.gnuplot.info/">gnuplot</a> or <a class="reference external" href="https://plasma-gate.weizmann.ac.il/Grace/">grace</a>), as CSV data which can be
|
||
imported for further processing with Microsoft Excel <a class="reference external" href="https://www.libreoffice.org/">LibreOffice Calc</a> or with Python via <a class="reference external" href="https://pandas.pydata.org/">pandas</a>, or as YAML which can be imported into
|
||
Python with <a class="reference external" href="https://pyyaml.org/">PyYAML</a> or pandas.</p>
|
||
<p>Thermo output data from successive run commands in the input script is
|
||
combined into a single data set unless the format, number, or names of
|
||
output columns are changed with a <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> or
|
||
a <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command, or the current time step
|
||
is reset with <a class="reference internal" href="reset_timestep.html"><span class="doc">reset_timestep</span></a>, or if a
|
||
<a class="reference internal" href="clear.html"><span class="doc">clear</span></a> command is issued. This is where the YAML export
|
||
from the <em>Charts</em> window differs from that of the <em>Output</em> window:
|
||
here you get the compounded data set starting with the last change of
|
||
output fields or timestep setting, while the export from the log will
|
||
contain <em>all</em> YAML output but <em>segmented</em> into individual runs.</p>
|
||
</section>
|
||
<section id="image-slide-show">
|
||
<h2>Image Slide Show<a class="headerlink" href="#image-slide-show" title="Link to this heading"></a></h2>
|
||
<p>By default, if the LAMMPS input contains a <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> command, a “Slide Show” window opens which loads and
|
||
displays the images created by LAMMPS as they are written. This is a
|
||
convenient way to visually monitor the progress of the simulation.</p>
|
||
<a class="reference internal image-reference" href="_images/lammps-gui-slideshow.png"><img alt="_images/lammps-gui-slideshow.png" class="align-center" src="_images/lammps-gui-slideshow.png" style="width: 272.0px; height: 315.5px;" />
|
||
</a>
|
||
<p>The various buttons at the bottom right of the window allow single
|
||
stepping through the sequence of images or playing an animation (as a
|
||
continuous loop or once from first to last). It is also possible to
|
||
zoom in or zoom out of the displayed images. The button on the very
|
||
left triggers an export of the slide show animation to a movie file,
|
||
provided the <a class="reference external" href="https://ffmpeg.org/">FFmpeg program</a> is installed.</p>
|
||
<p>When clicking on the “garbage can” icon, all image files of the slide
|
||
show will be deleted. Since their number can be large for long
|
||
simulations, this option enables to safely and quickly clean up the
|
||
clutter caused in the working directory by those image files without
|
||
risk of deleting other files by accident when using wildcards.</p>
|
||
</section>
|
||
<section id="variable-info">
|
||
<h2>Variable Info<a class="headerlink" href="#variable-info" title="Link to this heading"></a></h2>
|
||
<p>During a run, it may be of interest to monitor the value of input script
|
||
variables, for example to monitor the progress of loops. This can be
|
||
done by enabling the “Variables Window” in the <em>View</em> menu or by using
|
||
the <cite>Ctrl-Shift-W</cite> keyboard shortcut. This shows info similar to the
|
||
<a class="reference internal" href="info.html"><span class="doc">info variables</span></a> command in a separate window as shown
|
||
below.</p>
|
||
<a class="reference internal image-reference" href="_images/lammps-gui-variable-info.png"><img alt="_images/lammps-gui-variable-info.png" class="align-center" src="_images/lammps-gui-variable-info.png" style="width: 333.0px; height: 67.0px;" />
|
||
</a>
|
||
<p>Like for the <em>Output</em> and <em>Charts</em> windows, its content is continuously
|
||
updated during a run. It will show “(none)” if there are no variables
|
||
defined. Note that it is also possible to <em>set</em> <a class="reference internal" href="variable.html"><span class="doc">index style
|
||
variables</span></a>, that would normally be set via command-line
|
||
flags, via the “Set Variables…” dialog from the <em>Run</em> menu.
|
||
LAMMPS-GUI automatically defines the variable “gui_run” to the current
|
||
value of the run counter. That way it is possible to automatically
|
||
record a separate log for each run attempt by using the command</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">log</span><span class="w"> </span><span class="n">logfile</span><span class="o">-</span><span class="nv">${gui_run}</span><span class="n">.txt</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>at the beginning of an input file. That would record logs to files
|
||
<code class="docutils literal notranslate"><span class="pre">logfile-1.txt</span></code>, <code class="docutils literal notranslate"><span class="pre">logfile-2.txt</span></code>, and so on for successive runs.</p>
|
||
</section>
|
||
<section id="snapshot-image-viewer">
|
||
<span id="snapshot-viewer"></span><h2>Snapshot Image Viewer<a class="headerlink" href="#snapshot-image-viewer" title="Link to this heading"></a></h2>
|
||
<p>By selecting the <em>Create Image</em> entry in the <em>Run</em> menu, or by
|
||
hitting the <cite>Ctrl-I</cite> (<cite>Command-I</cite> on macOS) keyboard shortcut, or by
|
||
clicking on the “palette” button in the status bar of the <em>Editor</em>
|
||
window, LAMMPS-GUI sends a custom <a class="reference internal" href="dump_image.html"><span class="doc">write_dump image</span></a>
|
||
command to LAMMPS and reads back the resulting snapshot image with the
|
||
current state of the system into an image viewer. This functionality is
|
||
<em>not</em> available <em>during</em> an ongoing run. In case LAMMPS is not yet
|
||
initialized, LAMMPS-GUI tries to identify the line with the first run or
|
||
minimize command and execute all commands from the input buffer up to
|
||
that line, and then executes a “run 0” command. This initializes the
|
||
system so an image of the initial state of the system can be rendered.
|
||
If there was an error in that process, the snapshot image viewer does
|
||
not appear.</p>
|
||
<p>When possible, LAMMPS-GUI tries to detect which elements the atoms
|
||
correspond to (via their mass) and then colorize them in the image and
|
||
set their atom diameters accordingly. If this is not possible, for
|
||
instance when using reduced (= ‘lj’) <a class="reference internal" href="units.html"><span class="doc">units</span></a>, then
|
||
LAMMPS-GUI will check the current pair style and if it is a
|
||
Lennard-Jones type potential, it will extract the <em>sigma</em> parameter
|
||
for each atom type and assign atom diameters from those numbers.
|
||
For cases where atom diameters are not auto-detected, the <em>Atom size</em> field
|
||
can be edited and a suitable value set manually. The default value
|
||
is inferred from the x-direction lattice spacing.</p>
|
||
<p>If elements cannot be detected the default sequence of colors of the
|
||
<a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> command is assigned to the different atom
|
||
types.</p>
|
||
<p><a class="reference internal" href="_images/lammps-gui-image.png"><img alt="gui-image1" src="_images/lammps-gui-image.png" style="width: 48%;" /></a> <a class="reference internal" href="_images/lammps-gui-funnel.png"><img alt="gui-image2" src="_images/lammps-gui-funnel.png" style="width: 48%;" /></a></p>
|
||
<p>The default image size, some default image quality settings, the view
|
||
style and some colors can be changed in the <em>Preferences</em> dialog
|
||
window. From the image viewer window further adjustments can be made:
|
||
actual image size, high-quality (SSAO) rendering, anti-aliasing, view
|
||
style, display of box or axes, zoom factor. The view of the system can
|
||
be rotated horizontally and vertically. It is also possible to only
|
||
display the atoms within a group defined in the input script (default is
|
||
“all”). The image can also be re-centered on the center of mass of the
|
||
selected group. After each change, the image is rendered again and the
|
||
display updated. The small palette icon on the top left is colored
|
||
while LAMMPS is running to render the new image; it is grayed out when
|
||
LAMMPS is finished. When there are many atoms to render and high
|
||
quality images with anti-aliasing are requested, re-rendering may take
|
||
several seconds. From the <em>File</em> menu of the image window, the
|
||
current image can be saved to a file (keyboard shortcut <cite>Ctrl-S</cite>) or
|
||
copied to the clipboard (keyboard shortcut <cite>Ctrl-C</cite>) for pasting the
|
||
image into another application.</p>
|
||
<p>From the <em>File</em> menu it is also possible to copy the current
|
||
<a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> and <a class="reference internal" href="dump_image.html"><span class="doc">dump_modify</span></a>
|
||
commands to the clipboard so they can be pasted into a LAMMPS input file
|
||
so that the visualization settings of the snapshot image can be repeated
|
||
for the entire simulation (and thus be repeated in the slide show
|
||
viewer). This feature has the keyboard shortcut <cite>Ctrl-D</cite>.</p>
|
||
</section>
|
||
<section id="editor-window">
|
||
<h2>Editor Window<a class="headerlink" href="#editor-window" title="Link to this heading"></a></h2>
|
||
<p>The <em>Editor</em> window of LAMMPS-GUI has most of the usual functionality
|
||
that similar programs have: text selection via mouse or with cursor
|
||
moves while holding the Shift key, Cut (<cite>Ctrl-X</cite>), Copy (<cite>Ctrl-C</cite>),
|
||
Paste (<cite>Ctrl-V</cite>), Undo (<cite>Ctrl-Z</cite>), Redo (<cite>Ctrl-Shift-Z</cite>), Select All
|
||
(<cite>Ctrl-A</cite>). When trying to exit the editor with a modified buffer, a
|
||
dialog will pop up asking whether to cancel the exit operation, or to
|
||
save or not save the buffer contents to a file.</p>
|
||
<p>The editor has an auto-save mode that can be enabled or disabled in the
|
||
<em>Preferences</em> dialog. In auto-save mode, the editor buffer is
|
||
automatically saved before running LAMMPS or before exiting LAMMPS-GUI.</p>
|
||
<section id="context-specific-word-completion">
|
||
<h3>Context Specific Word Completion<a class="headerlink" href="#context-specific-word-completion" title="Link to this heading"></a></h3>
|
||
<p>By default, LAMMPS-GUI displays a small pop-up frame with possible
|
||
choices for LAMMPS input script commands or styles after 2 characters of
|
||
a word have been typed.</p>
|
||
<a class="reference internal image-reference" href="_images/lammps-gui-complete.png"><img alt="_images/lammps-gui-complete.png" class="align-center" src="_images/lammps-gui-complete.png" style="width: 407.25px; height: 170.25px;" />
|
||
</a>
|
||
<p>The word can then be completed through selecting an entry by scrolling
|
||
up and down with the cursor keys and selecting with the ‘Enter’ key or
|
||
by clicking on the entry with the mouse. The automatic completion
|
||
pop-up can be disabled in the <em>Preferences</em> dialog, but the completion
|
||
can still be requested manually by either hitting the ‘Shift-TAB’ key or
|
||
by right-clicking with the mouse and selecting the option from the
|
||
context menu. Most of the completion information is retrieved from the
|
||
active LAMMPS instance and thus it shows only available options that
|
||
have been enabled when compiling LAMMPS. That list, however, excludes
|
||
accelerated styles and commands; for improved clarity, only the
|
||
non-suffix version of styles are shown.</p>
|
||
</section>
|
||
<section id="line-reformatting">
|
||
<h3>Line Reformatting<a class="headerlink" href="#line-reformatting" title="Link to this heading"></a></h3>
|
||
<p>The editor supports reformatting lines according to the syntax in order
|
||
to have consistently aligned lines. This primarily means adding
|
||
whitespace padding to commands, type specifiers, IDs and names. This
|
||
reformatting is performed manually by hitting the ‘Tab’ key. It is
|
||
also possible to have this done automatically when hitting the ‘Enter’
|
||
key to start a new line. This feature can be turned on or off in the
|
||
<em>Preferences</em> dialog for <em>Editor Settings</em> with the
|
||
“Reformat with ‘Enter’” checkbox. The amount of padding for multiple
|
||
categories can be adjusted in the same dialog.</p>
|
||
<p>Internally this functionality is achieved by splitting the line into
|
||
“words” and then putting it back together with padding added where the
|
||
context can be detected; otherwise a single space is used between words.</p>
|
||
</section>
|
||
<section id="context-specific-help">
|
||
<h3>Context Specific Help<a class="headerlink" href="#context-specific-help" title="Link to this heading"></a></h3>
|
||
<p><a class="reference internal" href="_images/lammps-gui-popup-help.png"><img alt="gui-popup1" src="_images/lammps-gui-popup-help.png" style="width: 48%;" /></a> <a class="reference internal" href="_images/lammps-gui-popup-view.png"><img alt="gui-popup2" src="_images/lammps-gui-popup-view.png" style="width: 48%;" /></a></p>
|
||
<p>A unique feature of LAMMPS-GUI is the option to look up the LAMMPS
|
||
documentation for the command in the current line. This can be done by
|
||
either clicking the right mouse button or by using the <cite>Ctrl-?</cite> keyboard
|
||
shortcut. When using the mouse, there are additional entries in the
|
||
context menu that open the corresponding documentation page in the
|
||
online LAMMPS documentation in a web browser window. When using the
|
||
keyboard, the first of those entries is chosen.</p>
|
||
<p>If the word under the cursor is a file, then additionally the context
|
||
menu has an entry to open the file in a read-only text viewer window.
|
||
If the file is a LAMMPS restart file, instead the menu entry offers to
|
||
<a class="reference internal" href="#inspect-restart"><span class="std std-ref">inspect the restart</span></a>.</p>
|
||
<p>The text viewer is a convenient way to view the contents of files that
|
||
are referenced in the input. The file viewer also supports on-the-fly
|
||
decompression based on the file name suffix in a <a class="reference internal" href="Build_settings.html#gzip"><span class="std std-ref">similar fashion
|
||
as available with LAMMPS</span></a>. If the necessary decompression
|
||
program is missing or the file cannot be decompressed, the viewer window
|
||
will contain a corresponding message.</p>
|
||
</section>
|
||
<section id="inspecting-a-restart-file">
|
||
<span id="inspect-restart"></span><h3>Inspecting a Restart file<a class="headerlink" href="#inspecting-a-restart-file" title="Link to this heading"></a></h3>
|
||
<p>When LAMMPS-GUI is asked to “Inspect a Restart”, it will read the
|
||
restart file into a LAMMPS instance and then open three different
|
||
windows. The first window is a text viewer with the output of an
|
||
<a class="reference internal" href="info.html"><span class="doc">info command</span></a> with system information stored in the
|
||
restart. The second window is text viewer containing a data file
|
||
generated with a <a class="reference internal" href="write_data.html"><span class="doc">write_data command</span></a>. The third
|
||
window is a <a class="reference internal" href="#snapshot-viewer"><span class="std std-ref">Snapshot Image Viewer</span></a> containing a
|
||
visualization of the system in the restart.</p>
|
||
<p>If the restart file is larger than 250 MBytes, a dialog will ask
|
||
for confirmation before continuing, since large restart files
|
||
may require large amounts of RAM since the entire system must
|
||
be read into RAM. Thus restart file for large simulations that
|
||
have been run on an HPC cluster may overload a laptop or local
|
||
workstation. The <em>Show Details…</em> button will display a rough
|
||
estimate of the additional memory required.</p>
|
||
</section>
|
||
</section>
|
||
<section id="menu">
|
||
<h2>Menu<a class="headerlink" href="#menu" title="Link to this heading"></a></h2>
|
||
<p>The menu bar has entries <em>File</em>, <em>Edit</em>, <em>Run</em>, <em>View</em>, and
|
||
<em>About</em>. Instead of using the mouse to click on them, the individual
|
||
menus can also be activated by hitting the <cite>Alt</cite> key together with the
|
||
corresponding underlined letter, that is <cite>Alt-F</cite> activates the
|
||
<em>File</em> menu. For the corresponding activated sub-menus, the key
|
||
corresponding the underlined letters can be used to select entries
|
||
instead of using the mouse.</p>
|
||
<section id="file">
|
||
<h3>File<a class="headerlink" href="#file" title="Link to this heading"></a></h3>
|
||
<p>The <em>File</em> menu offers the usual options:</p>
|
||
<ul class="simple">
|
||
<li><p><em>New</em> clears the current buffer and resets the file name to <code class="docutils literal notranslate"><span class="pre">*unknown*</span></code></p></li>
|
||
<li><p><em>Open</em> opens a dialog to select a new file for editing in the <em>Editor</em></p></li>
|
||
<li><p><em>View</em> opens a dialog to select a file for viewing in a <em>separate</em> window (read-only) with support for on-the-fly decompression as explained above.</p></li>
|
||
<li><p><em>Inspect restart</em> opens a dialog to select a file. If that file is a <a class="reference internal" href="write_restart.html"><span class="doc">LAMMPS restart</span></a> three windows with <a class="reference internal" href="#inspect-restart"><span class="std std-ref">information about the file are opened</span></a>.</p></li>
|
||
<li><p><em>Save</em> saves the current file; if the file name is <code class="docutils literal notranslate"><span class="pre">*unknown*</span></code>
|
||
a dialog will open to select a new file name</p></li>
|
||
<li><p><em>Save As</em> opens a dialog to select and new file name (and folder, if
|
||
desired) and saves the buffer to it. Writing the buffer to a
|
||
different folder will also switch the current working directory to
|
||
that folder.</p></li>
|
||
<li><p><em>Quit</em> exits LAMMPS-GUI. If there are unsaved changes, a dialog will
|
||
appear to either cancel the operation, or to save, or to not save the
|
||
modified buffer.</p></li>
|
||
</ul>
|
||
<p>In addition, up to 5 recent file names will be listed after the <em>Open</em>
|
||
entry that allows re-opening recently opened files. This list is stored
|
||
when quitting and recovered when starting again.</p>
|
||
</section>
|
||
<section id="edit">
|
||
<h3>Edit<a class="headerlink" href="#edit" title="Link to this heading"></a></h3>
|
||
<p>The <em>Edit</em> menu offers the usual editor functions like <em>Undo</em>, <em>Redo</em>,
|
||
<em>Cut</em>, <em>Copy</em>, <em>Paste</em>, and a <em>Find and Replace</em> dialog (keyboard
|
||
shortcut <cite>Ctrl-F</cite>). It can also open a <em>Preferences</em> dialog (keyboard
|
||
shortcut <cite>Ctrl-P</cite>) and allows deleting all stored preferences and
|
||
settings, so they are reset to their default values.</p>
|
||
</section>
|
||
<section id="run">
|
||
<h3>Run<a class="headerlink" href="#run" title="Link to this heading"></a></h3>
|
||
<p>The <em>Run</em> menu has options to start and stop a LAMMPS process. Rather
|
||
than calling the LAMMPS executable as a separate executable, the
|
||
LAMMPS-GUI is linked to the LAMMPS library and thus can run LAMMPS
|
||
internally through the <a class="reference internal" href="Library.html#lammps-c-api"><span class="std std-ref">LAMMPS C-library interface</span></a>
|
||
in a separate thread.</p>
|
||
<p>Specifically, a LAMMPS instance will be created by calling
|
||
<a class="reference internal" href="Library_create.html#_CPPv418lammps_open_no_mpiiPPcPPv" title="lammps_open_no_mpi"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_open_no_mpi()</span></code></a>. The buffer contents are then executed by
|
||
calling <a class="reference internal" href="Library_execute.html#_CPPv422lammps_commands_stringPvPKc" title="lammps_commands_string"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_commands_string()</span></code></a>. Certain commands and
|
||
features are only available after a LAMMPS instance is created. Its
|
||
presence is indicated by a small LAMMPS <code class="docutils literal notranslate"><span class="pre">L</span></code> logo in the status bar
|
||
at the bottom left of the main window. As an alternative, it is also
|
||
possible to run LAMMPS using the contents of the edited file by
|
||
reading the file. This is mainly provided as a fallback option in
|
||
case the input uses some feature that is not available when running
|
||
from a string buffer.</p>
|
||
<p>The LAMMPS calculations are run in a concurrent thread so that the GUI
|
||
can stay responsive and be updated during the run. The GUI can retrieve
|
||
data from the running LAMMPS instance and tell it to stop at the next
|
||
timestep. The <em>Stop LAMMPS</em> entry will do this by calling the
|
||
<a class="reference internal" href="Library_utility.html#_CPPv420lammps_force_timeoutPv" title="lammps_force_timeout"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_force_timeout()</span></code></a> library function, which is equivalent
|
||
to a <a class="reference internal" href="timer.html"><span class="doc">timer timeout 0</span></a> command.</p>
|
||
<p>The <em>Set Variables…</em> entry opens a dialog box where
|
||
<a class="reference internal" href="variable.html"><span class="doc">index style variables</span></a> can be set. Those variables
|
||
are passed to the LAMMPS instance when it is created and are thus
|
||
set <em>before</em> a run is started.</p>
|
||
<a class="reference internal image-reference" href="_images/lammps-gui-variables.png"><img alt="_images/lammps-gui-variables.png" class="align-center" src="_images/lammps-gui-variables.png" style="width: 155.0px; height: 117.0px;" />
|
||
</a>
|
||
<p>The <em>Set Variables</em> dialog will be pre-populated with entries that
|
||
are set as index variables in the input and any variables that are
|
||
used but not defined, if the built-in parser can detect them. New
|
||
rows for additional variables can be added through the <em>Add Row</em>
|
||
button and existing rows can be deleted by clicking on the <em>X</em> icons
|
||
on the right.</p>
|
||
<p>The <em>Create Image</em> entry will send a <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a>
|
||
command to the LAMMPS instance, read the resulting file, and show it
|
||
in an <em>Image Viewer</em> window.</p>
|
||
<p>The <em>View in OVITO</em> entry will launch <a class="reference external" href="https://ovito.org">OVITO</a>
|
||
with a <a class="reference internal" href="write_data.html"><span class="doc">data file</span></a> containing the current state of
|
||
the system. This option is only available if LAMMPS-GUI can find
|
||
the OVITO executable in the system path.</p>
|
||
<p>The <em>View in VMD</em> entry will launch VMD with a <a class="reference internal" href="write_data.html"><span class="doc">data file</span></a> containing the current state of the system. This option
|
||
is only available if LAMMPS-GUI can find the VMD executable in the
|
||
system path.</p>
|
||
</section>
|
||
<section id="view">
|
||
<h3>View<a class="headerlink" href="#view" title="Link to this heading"></a></h3>
|
||
<p>The <em>View</em> menu offers to show or hide additional windows with log
|
||
output, charts, slide show, variables, or snapshot images. The
|
||
default settings for their visibility can be changed in the
|
||
<em>Preferences</em> dialog.</p>
|
||
</section>
|
||
<section id="about">
|
||
<h3>About<a class="headerlink" href="#about" title="Link to this heading"></a></h3>
|
||
<p>The <em>About</em> menu finally offers a couple of dialog windows and an
|
||
option to launch the LAMMPS online documentation in a web browser. The
|
||
<em>About LAMMPS-GUI</em> entry displays a dialog with a summary of the
|
||
configuration settings of the LAMMPS library in use and the version
|
||
number of LAMMPS-GUI itself. The <em>Quick Help</em> displays a dialog with
|
||
a minimal description of LAMMPS-GUI. The <em>LAMMPS-GUI Howto</em> entry
|
||
will open this documentation page from the online documentation in a web
|
||
browser window. The <em>LAMMPS Manual</em> entry will open the main page of
|
||
the LAMMPS online documentation in a web browser window.
|
||
The <em>LAMMPS Tutorial</em> entry will open the main page of the set of
|
||
LAMMPS tutorials authored and maintained by Simon Gravelle at
|
||
<a class="reference external" href="https://lammpstutorials.github.io/">https://lammpstutorials.github.io/</a> in a web browser window.</p>
|
||
</section>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="find-and-replace">
|
||
<h2>Find and Replace<a class="headerlink" href="#find-and-replace" title="Link to this heading"></a></h2>
|
||
<a class="reference internal image-reference" href="_images/lammps-gui-find.png"><img alt="_images/lammps-gui-find.png" class="align-center" src="_images/lammps-gui-find.png" style="width: 299.64px; height: 159.72px;" />
|
||
</a>
|
||
<p>The <em>Find and Replace</em> dialog allows searching for and replacing
|
||
text in the <em>Editor</em> window.</p>
|
||
<p>The dialog can be opened either from the <em>Edit</em> menu or with the
|
||
keyboard shortcut <cite>Ctrl-F</cite>. You can enter the text to search for.
|
||
Through three check-boxes the search behavior can be adjusted:</p>
|
||
<ul class="simple">
|
||
<li><p>If checked, “Match case” does a case sensitive search; otherwise
|
||
the search is case insensitive.</p></li>
|
||
<li><p>If checked, “Wrap around” starts searching from the start of the
|
||
document, if there is no match found from the current cursor position
|
||
until the end of the document; otherwise the search will stop.</p></li>
|
||
<li><p>If checked, the “Whole word” setting only finds full word matches
|
||
(white space and special characters are word boundaries).</p></li>
|
||
</ul>
|
||
<p>Clicking on the <em>Next</em> button will search for the next occurrence of the
|
||
search text and select / highlight it. Clicking on the <em>Replace</em> button
|
||
will replace an already highlighted search text and find the next one.
|
||
If no text is selected, or the selected text does not match the
|
||
selection string, then the first click on the <em>Replace</em> button will
|
||
only search and highlight the next occurrence of the search string.
|
||
Clicking on the <em>Replace All</em> button will replace all occurrences from
|
||
the cursor position to the end of the file; if the <em>Wrap around</em> box is
|
||
checked, then it will replace <strong>all</strong> occurrences in the <strong>entire</strong>
|
||
document. Clicking on the <em>Done</em> button will dismiss the dialog.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="preferences">
|
||
<h2>Preferences<a class="headerlink" href="#preferences" title="Link to this heading"></a></h2>
|
||
<p>The <em>Preferences</em> dialog allows customization of the behavior and
|
||
look of LAMMPS-GUI. The settings are grouped and each group is
|
||
displayed within a tab.</p>
|
||
<p><a class="reference internal" href="_images/lammps-gui-prefs-general.png"><img alt="guiprefs1" src="_images/lammps-gui-prefs-general.png" style="width: 24%;" /></a> <a class="reference internal" href="_images/lammps-gui-prefs-accel.png"><img alt="guiprefs2" src="_images/lammps-gui-prefs-accel.png" style="width: 24%;" /></a> <a class="reference internal" href="_images/lammps-gui-prefs-image.png"><img alt="guiprefs3" src="_images/lammps-gui-prefs-image.png" style="width: 24%;" /></a> <a class="reference internal" href="_images/lammps-gui-prefs-editor.png"><img alt="guiprefs4" src="_images/lammps-gui-prefs-editor.png" style="width: 24%;" /></a></p>
|
||
<section id="general-settings">
|
||
<h3>General Settings:<a class="headerlink" href="#general-settings" title="Link to this heading"></a></h3>
|
||
<ul class="simple">
|
||
<li><p><em>Echo input to log:</em> when checked, all input commands, including
|
||
variable expansions, are echoed to the <em>Output</em> window. This is
|
||
equivalent to using <cite>-echo screen</cite> at the command-line. There is no
|
||
log <em>file</em> produced by default, since LAMMPS-GUI uses <cite>-log none</cite>.</p></li>
|
||
<li><p><em>Include citation details:</em> when checked full citation info will be
|
||
included to the log window. This is equivalent to using <cite>-cite
|
||
screen</cite> on the command-line.</p></li>
|
||
<li><p><em>Show log window by default:</em> when checked, the screen output of a
|
||
LAMMPS run will be collected in a log window during the run</p></li>
|
||
<li><p><em>Show chart window by default:</em> when checked, the thermodynamic
|
||
output of a LAMMPS run will be collected and displayed in a chart
|
||
window as line graphs.</p></li>
|
||
<li><p><em>Show slide show window by default:</em> when checked, a slide show
|
||
window will be shown with images from a dump image command, if
|
||
present, in the LAMMPS input.</p></li>
|
||
<li><p><em>Replace log window on new run:</em> when checked, an existing log
|
||
window will be replaced on a new LAMMPS run, otherwise each run will
|
||
create a new log window.</p></li>
|
||
<li><p><em>Replace chart window on new run:</em> when checked, an existing chart
|
||
window will be replaced on a new LAMMPS run, otherwise each run will
|
||
create a new chart window.</p></li>
|
||
<li><p><em>Replace image window on new render:</em> when checked, an existing
|
||
chart window will be replaced when a new snapshot image is requested,
|
||
otherwise each command will create a new image window.</p></li>
|
||
<li><p><em>Path to LAMMPS Shared Library File:</em> this option is only visible
|
||
when LAMMPS-GUI was compiled to load the LAMMPS library at run time
|
||
instead of being linked to it directly. With the <em>Browse..</em> button
|
||
or by changing the text, a different shared library file with a
|
||
different compilation of LAMMPS with different settings or from a
|
||
different version can be loaded. After this setting was changed,
|
||
LAMMPS-GUI needs to be re-launched.</p></li>
|
||
<li><p><em>Select Default Font:</em> Opens a font selection dialog where the type
|
||
and size for the default font (used for everything but the editor and
|
||
log) of the application can be set.</p></li>
|
||
<li><p><em>Select Text Font:</em> Opens a font selection dialog where the type and
|
||
size for the text editor and log font of the application can be set.</p></li>
|
||
<li><p><em>Data update interval:</em> Allows to set the time interval between data
|
||
updates during a LAMMPS run in milliseconds. The default is to update
|
||
the data (for charts and output window) every 10 milliseconds. This
|
||
is good for many cases. Set this to 100 milliseconds or more if
|
||
LAMMPS-GUI consumes too many resources during a run. For LAMMPS runs
|
||
that run <em>very</em> fast (for example in tutorial examples), however, data
|
||
may be missed and through lowering this interval, this can be
|
||
corrected. However, this will make the GUI use more resources. This
|
||
setting may be changed to a value between 1 and 1000 milliseconds.</p></li>
|
||
<li><p><em>Charts update interval:</em> Allows to set the time interval between redrawing
|
||
the plots in the <em>Charts</em> window in milliseconds. The default is to
|
||
redraw the plots every 500 milliseconds. This is just for the drawing,
|
||
data collection is managed with the previous setting.</p></li>
|
||
</ul>
|
||
</section>
|
||
<section id="accelerators">
|
||
<h3>Accelerators:<a class="headerlink" href="#accelerators" title="Link to this heading"></a></h3>
|
||
<p>This tab enables selection of an accelerator package for LAMMPS to use
|
||
and is equivalent to using the <cite>-suffix</cite> and <cite>-package</cite> flags on the
|
||
command-line. Only settings supported by the LAMMPS library and local
|
||
hardware are available. The <cite>Number of threads</cite> field allows setting
|
||
the maximum number of threads for the accelerator packages that use
|
||
threads.</p>
|
||
</section>
|
||
<section id="snapshot-image">
|
||
<h3>Snapshot Image:<a class="headerlink" href="#snapshot-image" title="Link to this heading"></a></h3>
|
||
<p>This tab allows setting defaults for the snapshot images displayed in
|
||
the <em>Image Viewer</em> window, such as its dimensions and the zoom factor
|
||
applied. The <em>Antialias</em> switch will render images with twice the
|
||
number of pixels for width and height and then smoothly scale the image
|
||
back to the requested size. This produces higher quality images with
|
||
smoother edges at the expense of requiring more CPU time to render the
|
||
image. The <em>HQ Image mode</em> option turns on screen space ambient
|
||
occlusion (SSAO) mode when rendering images. This is also more time
|
||
consuming, but produces a more ‘spatial’ representation of the system
|
||
shading of atoms by their depth. The <em>Shiny Image mode</em> option will
|
||
render objects with a shiny surface when enabled. Otherwise the
|
||
surfaces will be matted. The <em>Show Box</em> option selects whether the
|
||
system box is drawn as a colored set of sticks. Similarly, the <em>Show
|
||
Axes</em> option selects whether a representation of the three system axes
|
||
will be drawn as colored sticks. The <em>VDW Style</em> checkbox selects
|
||
whether atoms are represented by space filling spheres when checked or
|
||
by smaller spheres and sticks. Finally there are a couple of drop down
|
||
lists to select the background and box colors.</p>
|
||
</section>
|
||
<section id="editor-settings">
|
||
<h3>Editor Settings:<a class="headerlink" href="#editor-settings" title="Link to this heading"></a></h3>
|
||
<p>This tab allows tweaking settings of the editor window. Specifically
|
||
the amount of padding to be added to LAMMPS commands, types or type
|
||
ranges, IDs (e.g. for fixes), and names (e.g. for groups). The value
|
||
set is the minimum width for the text element and it can be chosen in
|
||
the range between 1 and 32.</p>
|
||
<p>The three settings which follow enable or disable the automatic
|
||
reformatting when hitting the ‘Enter’ key, the automatic display of
|
||
the completion pop-up window, and whether auto-save mode is enabled.
|
||
In auto-save mode the editor buffer is saved before a run or before
|
||
exiting LAMMPS-GUI.</p>
|
||
</section>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="keyboard-shortcuts">
|
||
<h2>Keyboard Shortcuts<a class="headerlink" href="#keyboard-shortcuts" title="Link to this heading"></a></h2>
|
||
<p>Almost all functionality is accessible from the menu of the editor
|
||
window or through keyboard shortcuts. The following shortcuts are
|
||
available (On macOS use the Command key instead of Ctrl/Control).</p>
|
||
<table class="docutils align-default">
|
||
<colgroup>
|
||
<col style="width: 16.2%" />
|
||
<col style="width: 19.2%" />
|
||
<col style="width: 13.1%" />
|
||
<col style="width: 16.2%" />
|
||
<col style="width: 13.1%" />
|
||
<col style="width: 22.2%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="row-odd"><th class="head"><p>Shortcut</p></th>
|
||
<th class="head"><p>Function</p></th>
|
||
<th class="head"><p>Shortcut</p></th>
|
||
<th class="head"><p>Function</p></th>
|
||
<th class="head"><p>Shortcut</p></th>
|
||
<th class="head"><p>Function</p></th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="row-even"><td><p>Ctrl+N</p></td>
|
||
<td><p>New File</p></td>
|
||
<td><p>Ctrl+Z</p></td>
|
||
<td><p>Undo edit</p></td>
|
||
<td><p>Ctrl+Enter</p></td>
|
||
<td><p>Run Input</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>Ctrl+O</p></td>
|
||
<td><p>Open File</p></td>
|
||
<td><p>Ctrl+Shift+Z</p></td>
|
||
<td><p>Redo edit</p></td>
|
||
<td><p>Ctrl+/</p></td>
|
||
<td><p>Stop Active Run</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>Ctrl+Shift+F</p></td>
|
||
<td><p>View File</p></td>
|
||
<td><p>Ctrl+C</p></td>
|
||
<td><p>Copy text</p></td>
|
||
<td><p>Ctrl+Shift+V</p></td>
|
||
<td><p>Set Variables</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>Ctrl+S</p></td>
|
||
<td><p>Save File</p></td>
|
||
<td><p>Ctrl+X</p></td>
|
||
<td><p>Cut text</p></td>
|
||
<td><p>Ctrl+I</p></td>
|
||
<td><p>Snapshot Image</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>Ctrl+Shift+S</p></td>
|
||
<td><p>Save File As</p></td>
|
||
<td><p>Ctrl+V</p></td>
|
||
<td><p>Paste text</p></td>
|
||
<td><p>Ctrl+L</p></td>
|
||
<td><p>Slide Show</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>Ctrl+Q</p></td>
|
||
<td><p>Quit Application</p></td>
|
||
<td><p>Ctrl+A</p></td>
|
||
<td><p>Select All</p></td>
|
||
<td><p>Ctrl+F</p></td>
|
||
<td><p>Find and Replace</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>Ctrl+W</p></td>
|
||
<td><p>Close Window</p></td>
|
||
<td><p>TAB</p></td>
|
||
<td><p>Reformat line</p></td>
|
||
<td><p>Shift+TAB</p></td>
|
||
<td><p>Show Completions</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>Ctrl+Shift+Enter</p></td>
|
||
<td><p>Run File</p></td>
|
||
<td><p>Ctrl+Shift+W</p></td>
|
||
<td><p>Show Variables</p></td>
|
||
<td><p>Ctrl+P</p></td>
|
||
<td><p>Preferences</p></td>
|
||
</tr>
|
||
<tr class="row-even"><td><p>Ctrl+Shift+A</p></td>
|
||
<td><p>About LAMMPS</p></td>
|
||
<td><p>Ctrl+Shift+H</p></td>
|
||
<td><p>Quick Help</p></td>
|
||
<td><p>Ctrl+Shift+G</p></td>
|
||
<td><p>LAMMPS-GUI Howto</p></td>
|
||
</tr>
|
||
<tr class="row-odd"><td><p>Ctrl+Shift+M</p></td>
|
||
<td><p>LAMMPS Manual</p></td>
|
||
<td><p>Ctrl+?</p></td>
|
||
<td><p>Context Help</p></td>
|
||
<td><p>Ctrl+Shift+T</p></td>
|
||
<td><p>LAMMPS Tutorial</p></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>Further editing keybindings <a class="reference external" href="https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings">are documented with the Qt documentation</a>. In
|
||
case of conflicts the list above takes precedence.</p>
|
||
<p>All other windows only support a subset of keyboard shortcuts listed
|
||
above. Typically, the shortcuts <cite>Ctrl-/</cite> (Stop Run), <cite>Ctrl-W</cite> (Close
|
||
Window), and <cite>Ctrl-Q</cite> (Quit Application) are supported.</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
|
||
<a href="Howto_github.html" class="btn btn-neutral float-left" title="8.6.2. LAMMPS GitHub tutorial" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
|
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<a href="Howto_moltemplate.html" class="btn btn-neutral float-right" title="8.6.4. Moltemplate Tutorial" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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||
|
||
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|
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<p>© Copyright 2003-2025 Sandia Corporation.</p>
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