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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_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>rerun command</li>
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<div class="section" id="rerun-command">
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<span id="index-0"></span><h1>rerun 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">rerun</span> <span class="n">file1</span> <span class="n">file2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>file1,file2,... = dump file(s) to read</li>
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<li>one or more keywords may be appended, keyword <em>dump</em> must appear and be last</li>
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</ul>
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<pre class="literal-block">
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keyword = <em>first</em> or <em>last</em> or <em>every</em> or <em>skip</em> or <em>start</em> or <em>stop</em> or <em>dump</em>
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<em>first</em> args = Nfirts
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Nfirst = dump timestep to start on
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<em>last</em> args = Nlast
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Nlast = dumptimestep to stop on
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<em>every</em> args = Nevery
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Nevery = read snapshots matching every this many timesteps
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<em>skip</em> args = Nskip
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Nskip = read one out of every Nskip snapshots
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<em>start</em> args = Nstart
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Nstart = timestep on which pseudo run will start
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<em>stop</em> args = Nstop
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Nstop = timestep to which pseudo run will end
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<em>dump</em> args = same as <a class="reference internal" href="read_dump.html"><span class="doc">read_dump</span></a> command starting with its field arguments
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</pre>
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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">rerun</span> <span class="n">dump</span><span class="o">.</span><span class="n">file</span> <span class="n">dump</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span>
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<span class="n">rerun</span> <span class="n">dump1</span><span class="o">.</span><span class="n">txt</span> <span class="n">dump2</span><span class="o">.</span><span class="n">txt</span> <span class="n">first</span> <span class="mi">10000</span> <span class="n">every</span> <span class="mi">1000</span> <span class="n">dump</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span>
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<span class="n">rerun</span> <span class="n">dump</span><span class="o">.</span><span class="n">vels</span> <span class="n">dump</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span> <span class="n">box</span> <span class="n">yes</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">lammpstrj</span>
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<span class="n">rerun</span> <span class="n">dump</span><span class="o">.</span><span class="n">dcd</span> <span class="n">dump</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">box</span> <span class="n">no</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">dcd</span>
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<span class="n">rerun</span> <span class="o">../</span><span class="n">run7</span><span class="o">/</span><span class="n">dump</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">gz</span> <span class="n">skip</span> <span class="mi">2</span> <span class="n">dump</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">box</span> <span class="n">yes</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>Perform a psuedo simulation run where atom information is read one
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snapshot at a time from a dump file(s), and energies and forces are
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computed on the shapshot to produce thermodynamic or other output.</p>
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<p>This can be useful in the following kinds of scenarios, after an
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initial simulation produced the dump file:</p>
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<ul class="simple">
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<li>Compute the energy and forces of snaphots using a different potential.</li>
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<li>Calculate one or more diagnostic quantities on the snapshots that
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weren’t computed in the initial run. These can also be computed with
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settings not used in the initial run, e.g. computing an RDF via the
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<span class="xref doc">compute rdf</span> command with a longer cutoff than was
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used initially.</li>
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<li>Calculate the portion of per-atom forces resulting from a subset of
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the potential. E.g. compute only Coulombic forces. This can be done
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by only defining only a Coulombic pair style in the rerun script.
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Doing this in the original script would result in different (bad)
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dynamics.</li>
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</ul>
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<p>Conceptually, using the rerun command is like running an input script
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that has a loop in it (see the <a class="reference internal" href="next.html"><span class="doc">next</span></a> and <a class="reference internal" href="jump.html"><span class="doc">jump</span></a>
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commands). Each iteration of the loop reads one snapshot from the
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dump file via the <a class="reference internal" href="read_dump.html"><span class="doc">read_dump</span></a> command, sets the
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timestep to the appropriate value, and then invokes a <a class="reference internal" href="run.html"><span class="doc">run</span></a>
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command for zero timesteps to simply compute energy and forces, and
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any other <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a> or diagnostic info
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you have defined. This computation also invokes any fixes you have
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defined that apply constraints to the system, such as <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> or <a class="reference internal" href="fix_indent.html"><span class="doc">fix indent</span></a>.</p>
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<p>Note that a simulation box must already be defined before using the
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rerun command. This can be done by the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>,
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<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
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commands.</p>
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<p>Also note that reading per-atom information from dump snapshots is
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limited to the atom coordinates, velocities and image flags as
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explained in the <a class="reference internal" href="read_dump.html"><span class="doc">read_dump</span></a> command. Other atom
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properties, which may be necessary to compute energies and forces,
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such as atom charge, or bond topology information for a molecular
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system, are not read from (or even contained in) dump files. Thus
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this auxiliary information should be defined in the usual way, e.g. in
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a data file read in by a <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command, before
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using the rerun command.</p>
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<hr class="docutils" />
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<p>If more than one dump file is specified, the dump files are read one
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after the other. It is assumed that snapshot timesteps will be in
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ascending order. If a snapshot is encountered that is not in
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ascending order, it will cause the rerun command to complete.</p>
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<p>The <em>first</em>, <em>last</em>, <em>every</em>, <em>skip</em> keywords determine which
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snapshots are read from the dump file(s). Snapshots are skipped until
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they have a timestamp >= <em>Nfirst</em>. When a snapshot with a timestamp >
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<em>Nlast</em> is encountered, the rerun command finishes. Note below that
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the defaults for <em>first</em> and <em>last</em> are to read all snapshots. If the
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<em>every</em> keyword is set to a value > 0, then only snapshots with
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timestamps that are a multiple of <em>Nevery</em> are read (the first
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snapshot is always read). If <em>Nevery</em> = 0, then this criterion is
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ignored, i.e. every snapshot is read that meets the other criteria.
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If the <em>skip</em> keyword is used, then after the first snapshot is read,
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every Nth snapshot is read, where N = <em>Nskip</em>. E.g. if <em>Nskip</em> = 3,
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then only 1 out of every 3 snapshots is read, assuming the snapshot
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timestamp is also consistent with the other criteria.</p>
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<p>The <em>start</em> and <em>stop</em> keywords do not affect which snapshots are read
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from the dump file(s). Rather, they have the same meaning that they
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do for the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. They only need to be defined if
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(a) you are using a <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command that changes some value
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over time, and (b) you want the reference point for elapsed time (from
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start to stop) to be different than the <em>first</em> and <em>last</em> settings.
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See the doc page for individual fixes to see which ones can be used
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with the <em>start/stop</em> keywords. Note that if you define neither of
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the <em>start</em>/<em>stop</em> or <em>first</em>/<em>last</em> keywords, then LAMMPS treats the
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pseudo run as going from 0 to a huge value (effectively infinity).
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This means that any quantity that a fix scales as a fraction of
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elapsed time in the run, will essentially remain at its intiial value.
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Also note that an error will occur if you read a snapshot from the
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dump file with a timestep value larger than the <em>stop</em> setting you
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have specified.</p>
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<p>The <em>dump</em> keyword is required and must be the last keyword specified.
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Its arguments are passed internally to the <a class="reference internal" href="read_dump.html"><span class="doc">read_dump</span></a>
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command. The first argument following the <em>dump</em> keyword should be
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the <em>field1</em> argument of the <a class="reference internal" href="read_dump.html"><span class="doc">read_dump</span></a> command. See
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the <a class="reference internal" href="read_dump.html"><span class="doc">read_dump</span></a> doc page for details on the various
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options it allows for extracting information from the dump file
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snapshots, and for using that information to alter the LAMMPS
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simulation.</p>
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<hr class="docutils" />
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<p>In general, a LAMMPS input script that uses a rerun command can
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include and perform all the usual operations of an input script that
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uses the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. There are a few exceptions and
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points to consider, as discussed here.</p>
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<p>Fixes that perform time integration, such as <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or
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<a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a> are not invoked, since no time integration is
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performed. Fixes that perturb or constrain the forces on atoms will
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be invoked, just as they would during a normal run. Examples are <a class="reference internal" href="fix_indent.html"><span class="doc">fix indent</span></a> and <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>. So you
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should think carefully as to whether that makes sense for the manner
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in which you are reprocessing the dump snapshots.</p>
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<p>If you only want the rerun script to perform analyses that do not
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involve pair interactions, such as use compute msd to calculated
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displacements over time, you do not need to define a <a class="reference internal" href="pair_style.html"><span class="doc">pair style</span></a>, which may also mean neighbor lists will not
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need to be calculated which saves time. The <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify cutoff</span></a> command can also be used to insure ghost
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atoms are acquired from far enough away for operations like bond and
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angle evaluations, if no pair style is being used.</p>
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<p>Every time a snapshot is read, the timestep for the simulation is
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reset, as if the <a class="reference internal" href="reset_timestep.html"><span class="doc">reset_timestep</span></a> command were
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used. This command has some restrictions as to what fixes can be
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defined. See its doc page for details. For example, the <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a> and <a class="reference internal" href="fix_dt_reset.html"><span class="doc">fix dt/reset</span></a> fixes
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are in this category. They also make no sense to use with a rerun
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command.</p>
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<p>If time-averaging fixes like <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a> are
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used, they are invoked on timesteps that are a function of their
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<em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> settings. As an example, see the
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<a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a> doc page for details. You must
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insure those settings are consistent with the snapshot timestamps that
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are read from the dump file(s). If an averaging fix is not invoked on
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a timestep it expects to be, LAMMPS will flag an error.</p>
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<p>The various forms of LAMMPS output, as defined by the
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<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a>, <a class="reference internal" href="thermo.html"><span class="doc">thermo</span></a>,
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<a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, and <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> commands occur on
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specific timesteps. If successvive dump snapshots skip those
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timesteps, then no output will be produced. E.g. if you request
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thermodynamic output every 100 steps, but the dump file snapshots are
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every 1000 steps, then you will only see thermodynamic output every
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1000 steps.</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>To read gzipped dump files, you must compile LAMMPS with the
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-DLAMMPS_GZIP option - see the <a class="reference internal" href="Section_start.html#start-2"><span class="std std-ref">Making LAMMPS</span></a> section of the documentation.</p>
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</div>
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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="read_dump.html"><span class="doc">read_dump</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 option defaults are first = 0, last = a huge value (effectively
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infinity), start = same as first, stop = same as last, every = 0, skip
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= 1;</p>
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