forked from lijiext/lammps
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HTML
304 lines
13 KiB
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<a href="Manual.html" class="icon icon-home"> LAMMPS
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li><a href="Manual.html">Docs</a> »</li>
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<li>dump molfile command</li>
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<a href="http://lammps.sandia.gov">Website</a>
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<a href="Section_commands.html#comm">Commands</a>
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<div itemprop="articleBody">
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<div class="section" id="dump-molfile-command">
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<span id="index-0"></span><h1>dump molfile command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">molfile</span> <span class="n">N</span> <span class="n">file</span> <span class="nb">format</span> <span class="n">path</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID = user-assigned name for the dump</li>
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<li>group-ID = ID of the group of atoms to be imaged</li>
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<li>molfile = style of dump command (other styles <em>atom</em> or <em>cfg</em> or <em>dcd</em> or <em>xtc</em> or <em>xyz</em> or <em>local</em> or <em>custom</em> are discussed on the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> doc page)</li>
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<li>N = dump every this many timesteps</li>
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<li>file = name of file to write to</li>
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<li>format = file format to be used</li>
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<li>path = file path with plugins (optional)</li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">mf1</span> <span class="nb">all</span> <span class="n">molfile</span> <span class="mi">10</span> <span class="n">melt1</span><span class="o">.</span><span class="n">xml</span> <span class="n">hoomd</span>
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<span class="n">dump</span> <span class="n">mf2</span> <span class="nb">all</span> <span class="n">molfile</span> <span class="mi">10</span> <span class="n">melt2</span><span class="o">-*.</span><span class="n">pdb</span> <span class="n">pdb</span> <span class="o">.</span>
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<span class="n">dump</span> <span class="n">mf3</span> <span class="nb">all</span> <span class="n">molfile</span> <span class="mi">50</span> <span class="n">melt3</span><span class="o">.</span><span class="n">xyz</span> <span class="n">xyz</span> <span class="o">.</span><span class="p">:</span><span class="o">/</span><span class="n">home</span><span class="o">/</span><span class="n">akohlmey</span><span class="o">/</span><span class="n">vmd</span><span class="o">/</span><span class="n">plugins</span><span class="o">/</span><span class="n">LINUX</span><span class="o">/</span><span class="n">molfile</span>
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description</h2>
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<p>Dump a snapshot of atom coordinates and selected additional quantities
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to one or more files every N timesteps in one of several formats.
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Only information for atoms in the specified group is dumped. This
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specific dump style uses molfile plugins that are bundled with the
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<a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> molecular visualization and
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analysis program. See <a class="reference internal" href="Section_tools.html#vmd"><span class="std std-ref">Section tools</span></a> of the
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manual and the tools/lmp2vmd/README.txt file for more information
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about support in VMD for reading and visualizing native LAMMPS dump
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files.</p>
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<p>Unless the filename contains a * character, the output will be written
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to one single file with the specified format. Otherwise there will be
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one file per snapshot and the * will be replaced by the time step number
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when the snapshot is written.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Because periodic boundary conditions are enforced only on
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timesteps when neighbor lists are rebuilt, the coordinates of an atom
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written to a dump file may be slightly outside the simulation box.</p>
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</div>
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<p>The molfile plugin API has a few restrictions that have to be honored
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by this dump style: the number of atoms must not change, the atoms
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must be sorted, outside of the coordinates no change in atom properties
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(like type, mass, charge) will be recorded.</p>
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<hr class="docutils" />
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<p>The <em>format</em> keyword determines what format is used to write out the
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dump. For this to work, LAMMPS must be able to find and load a
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compatible molfile plugin that supports this format. Settings made via
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the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command can alter per atom properties
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like element names.</p>
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<p>The <em>path</em> keyword determines which in directories. This is a “path”
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like other search paths, i.e. it can contain multiple directories
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separated by a colon (or semi-colon on windows). This keyword is
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optional and default to ”.”, the current directory.</p>
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<p>The <em>unwrap</em> option of the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command allows
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coordinates to be written “unwrapped” by the image flags for each atom.
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Unwrapped means that if the atom has passed through a periodic boundary
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one or more times, the value is printed for what the coordinate would be
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if it had not been wrapped back into the periodic box. Note that these
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coordinates may thus be far outside the box size stored with the
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snapshot.</p>
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<hr class="docutils" />
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<p>Dumps are performed on timesteps that are a multiple of N (including
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timestep 0) and on the last timestep of a minimization if the
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minimization converges. Note that this means a dump will not be
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performed on the initial timestep after the dump command is invoked,
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if the current timestep is not a multiple of N. This behavior can be
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changed via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify first</span></a> command, which can
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be useful if the dump command is invoked after a minimization ended on
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an arbitrary timestep. N can be changed between runs by using the
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<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command. The <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command also allows a variable to be used to
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determine the sequence of timesteps on which dump files are written.</p>
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</div>
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<hr class="docutils" />
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<p>The <em>molfile</em> dump style is part of the USER-MOLFILE package. It is
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only enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
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<p>Molfile plugins provide a consistent programming interface to read and
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write file formats commonly used in molecular simulations. The
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USER-MOLFILE package only provides the interface code, not the plugins.
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These can be obtained from a VMD installation which has to match the
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platform that you are using to compile LAMMPS for. By adding plugins
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to VMD, support for new file formats can be added to LAMMPS (or VMD
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or other programs that use them) without having to recompile the
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application itself. The plugins are installed in the directory:
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<VMDHOME>/plugins/<VMDARCH>/molfile</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">while the programming interface (API) to the plugins is backward
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compatible, the binary interface (ABI) has been changing over time, so
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it is necessary to compile this package with the plugin header files
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from VMD that match the binary plugins. These header files in the
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directory: <VMDHOME>/plugins/include For convenience, the package ships
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with a set of header files that are compatible with VMD 1.9 and 1.9.1
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(June 2012)</p>
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</div>
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</div>
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<hr class="docutils" />
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a>, <a class="reference internal" href="undump.html"><span class="doc">undump</span></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default</h2>
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<p>The default path is ”.”. All other properties have to be specified.</p>
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</div>
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<p>
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</p>
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