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<title>run command — LAMMPS 15 May 2015 version documentation</title>
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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_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_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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<div class="section" id="run-command">
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<span id="index-0"></span><h1>run command<a class="headerlink" href="#run-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>run N keyword values ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>N = # of timesteps</li>
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>upto</em> or <em>start</em> or <em>stop</em> or <em>pre</em> or <em>post</em> or <em>every</em></li>
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</ul>
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<pre class="literal-block">
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<em>upto</em> value = none
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<em>start</em> value = N1
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N1 = timestep at which 1st run started
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<em>stop</em> value = N2
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N2 = timestep at which last run will end
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<em>pre</em> value = <em>no</em> or <em>yes</em>
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<em>post</em> value = <em>no</em> or <em>yes</em>
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<em>every</em> values = M c1 c2 ...
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M = break the run into M-timestep segments and invoke one or more commands between each segment
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c1,c2,...,cN = one or more LAMMPS commands, each enclosed in quotes
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c1 = NULL means no command will be invoked
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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<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>run 10000
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run 1000000 upto
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run 100 start 0 stop 1000
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run 1000 pre no post yes
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run 100000 start 0 stop 1000000 every 1000 "print 'Protein Rg = $r'"
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run 100000 every 1000 NULL
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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<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Run or continue dynamics for a specified number of timesteps.</p>
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<p>When the <a class="reference internal" href="run_style.html"><em>run style</em></a> is <em>respa</em>, N refers to outer
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loop (largest) timesteps.</p>
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<p>A value of N = 0 is acceptable; only the thermodynamics of the system
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are computed and printed without taking a timestep.</p>
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<p>The <em>upto</em> keyword means to perform a run starting at the current
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timestep up to the specified timestep. E.g. if the current timestep
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is 10,000 and “run 100000 upto” is used, then an additional 90,000
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timesteps will be run. This can be useful for very long runs on a
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machine that allocates chunks of time and terminate your job when time
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is exceeded. If you need to restart your script multiple times
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(reading in the last restart file), you can keep restarting your
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script with the same run command until the simulation finally
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completes.</p>
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<p>The <em>start</em> or <em>stop</em> keywords can be used if multiple runs are being
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performed and you want a <a class="reference internal" href="fix.html"><em>fix</em></a> command that changes some
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value over time (e.g. temperature) to make the change across the
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entire set of runs and not just a single run. See the doc page for
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individual fixes to see which ones can be used with the <em>start/stop</em>
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keywords.</p>
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<p>For example, consider this fix followed by 10 run commands:</p>
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<div class="highlight-python"><div class="highlight"><pre>fix 1 all nvt 200.0 300.0 1.0
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run 1000 start 0 stop 10000
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run 1000 start 0 stop 10000
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...
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run 1000 start 0 stop 10000
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</pre></div>
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</div>
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<p>The NVT fix ramps the target temperature from 200.0 to 300.0 during a
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run. If the run commands did not have the start/stop keywords (just
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“run 1000”), then the temperature would ramp from 200.0 to 300.0
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during the 1000 steps of each run. With the start/stop keywords, the
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ramping takes place over the 10000 steps of all runs together.</p>
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<p>The <em>pre</em> and <em>post</em> keywords can be used to streamline the setup,
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clean-up, and associated output to the screen that happens before and
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after a run. This can be useful if you wish to do many short runs in
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succession (e.g. LAMMPS is being called as a library which is doing
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other computations between successive short LAMMPS runs).</p>
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<p>By default (pre and post = yes), LAMMPS creates neighbor lists,
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computes forces, and imposes fix constraints before every run. And
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after every run it gathers and prints timings statistics. If a run is
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just a continuation of a previous run (i.e. no settings are changed),
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the initial computation is not necessary; the old neighbor list is
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still valid as are the forces. So if <em>pre</em> is specified as “no” then
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the initial setup is skipped, except for printing thermodynamic info.
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Note that if <em>pre</em> is set to “no” for the very 1st run LAMMPS
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performs, then it is overridden, since the initial setup computations
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must be done.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">If your input script changes the system between 2
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runs, then the initial setup must be performed to insure the change is
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recognized by all parts of the code that are affected. Examples are
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adding a <a class="reference internal" href="fix.html"><em>fix</em></a> or <a class="reference internal" href="dump.html"><em>dump</em></a> or <a class="reference internal" href="compute.html"><em>compute</em></a>,
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changing a <a class="reference internal" href="neigh_modify.html"><em>neighbor</em></a> list parameter, or writing
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restart file which can migrate atoms between processors. LAMMPS has
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no easy way to check if this has happened, but it is an error to use
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the <em>pre no</em> option in this case.</p>
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</div>
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<p>If <em>post</em> is specified as “no”, the full timing summary is skipped;
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only a one-line summary timing is printed.</p>
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<p>The <em>every</em> keyword provides a means of breaking a LAMMPS run into a
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series of shorter runs. Optionally, one or more LAMMPS commands (c1,
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c2, ..., cN) will be executed in between the short runs. If used, the
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<em>every</em> keyword must be the last keyword, since it has a variable
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number of arguments. Each of the trailing arguments is a single
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LAMMPS command, and each command should be enclosed in quotes, so that
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the entire command will be treated as a single argument. This will
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also prevent any variables in the command from being evaluated until
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it is executed multiple times during the run. Note that if a command
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itself needs one of its arguments quoted (e.g. the <a class="reference internal" href="print.html"><em>print</em></a>
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command), then you can use a combination of single and double quotes,
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as in the example above or below.</p>
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<p>The <em>every</em> keyword is a means to avoid listing a long series of runs
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and interleaving commands in your input script. For example, a
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<a class="reference internal" href="print.html"><em>print</em></a> command could be invoked or a <a class="reference internal" href="fix.html"><em>fix</em></a> could
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be redefined, e.g. to reset a thermostat temperature. Or this could
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be useful for invoking a command you have added to LAMMPS that wraps
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some other code (e.g. as a library) to perform a computation
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periodically during a long LAMMPS run. See <a class="reference internal" href="Section_modify.html"><em>this section</em></a> of the documentation for info about how
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to add new commands to LAMMPS. See <a class="reference internal" href="Section_howto.html#howto-10"><span>this section</span></a> of the documentation for ideas
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about how to couple LAMMPS to other codes.</p>
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<p>With the <em>every</em> option, N total steps are simulated, in shorter runs
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of M steps each. After each M-length run, the specified commands are
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invoked. If only a single command is specified as NULL, then no
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command is invoked. Thus these lines:</p>
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<div class="highlight-python"><div class="highlight"><pre>variable q equal x[100]
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run 6000 every 2000 "print 'Coord = $q'"
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</pre></div>
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</div>
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<p>are the equivalent of:</p>
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<div class="highlight-python"><div class="highlight"><pre>variable q equal x[100]
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run 2000
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print "Coord = $q"
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run 2000
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print "Coord = $q"
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run 2000
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print "Coord = $q"
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</pre></div>
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</div>
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<p>which does 3 runs of 2000 steps and prints the x-coordinate of a
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particular atom between runs. Note that the variable “$q” will
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be evaluated afresh each time the print command is executed.</p>
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<p>Note that by using the line continuation character “&”, the run every
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command can be spread across many lines, though it is still a single
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command:</p>
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<div class="highlight-python"><div class="highlight"><pre>run 100000 every 1000 &
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"print 'Minimum value = $a'" &
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"print 'Maximum value = $b'" &
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"print 'Temp = $c'" &
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"print 'Press = $d'"
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</pre></div>
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</div>
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<p>If the <em>pre</em> and <em>post</em> options are set to “no” when used with the
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<em>every</em> keyword, then the 1st run will do the full setup and the last
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run will print the full timing summary, but these operations will be
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skipped for intermediate runs.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">You might hope to specify a command that exits the run
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by jumping out of the loop, e.g.</p>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>variable t equal temp
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run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'"
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</pre></div>
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</div>
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<p>Unfortunately this will not currently work. The run command simply
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executes each command one at a time each time it pauses, then
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continues the run. You can replace the jump command with a simple
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<a class="reference internal" href="quit.html"><em>quit</em></a> command and cause LAMMPS to exit during the
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middle of a run when the condition is met.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>When not using the <em>upto</em> keyword, the number of specified timesteps N
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must fit in a signed 32-bit integer, so you are limited to slightly
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more than 2 billion steps (2^31) in a single run. When using <em>upto</em>,
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N can be larger than a signed 32-bit integer, however the difference
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between N and the current timestep must still be no larger than
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2^31 steps.</p>
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<p>However, with or without the <em>upto</em> keyword, you can perform
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successive runs to run a simulation for any number of steps (ok, up to
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2^63 total steps). I.e. the timestep counter within LAMMPS is a
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64-bit signed integer.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="minimize.html"><em>minimize</em></a>, <a class="reference internal" href="run_style.html"><em>run_style</em></a>,
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<a class="reference internal" href="temper.html"><em>temper</em></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
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<p>The option defaults are start = the current timestep, stop = current
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timestep + N, pre = yes, and post = yes.</p>
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