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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>temper command</li>
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<div class="section" id="temper-command">
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<span id="index-0"></span><h1>temper command<a class="headerlink" href="#temper-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>temper N M temp fix-ID seed1 seed2 index
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</pre></div>
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</div>
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<ul class="simple">
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<li>N = total # of timesteps to run</li>
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<li>M = attempt a tempering swap every this many steps</li>
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<li>temp = initial temperature for this ensemble</li>
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<li>fix-ID = ID of the fix that will control temperature during the run</li>
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<li>seed1 = random # seed used to decide on adjacent temperature to partner with</li>
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<li>seed2 = random # seed for Boltzmann factor in Metropolis swap</li>
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<li>index = which temperature (0 to N-1) I am simulating (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<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>temper 100000 100 $t tempfix 0 58728
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temper 40000 100 $t tempfix 0 32285 $w
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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 a parallel tempering or replica exchange simulation using multiple
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replicas (ensembles) of a system. Two or more replicas must be used.</p>
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<p>Each replica runs on a partition of one or more processors. Processor
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partitions are defined at run-time using the -partition command-line
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switch; see <a class="reference internal" href="Section_start.html#start-7"><span>Section_start 6</span></a> of the
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manual. Note that if you have MPI installed, you can run a
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multi-replica simulation with more replicas (partitions) than you have
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physical processors, e.g you can run a 10-replica simulation on one or
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two processors. You will simply not get the performance speed-up you
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would see with one or more physical processors per replica. See <a class="reference internal" href="Section_howto.html#howto-5"><span>this section</span></a> of the manual for further
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discussion.</p>
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<p>Each replica’s temperature is controlled at a different value by a fix
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with <em>fix-ID</em> that controls temperature. Possible fix styles are
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<a class="reference internal" href="fix_nh.html"><em>nvt</em></a>, <a class="reference internal" href="fix_nh.html"><em>temp/berendsen</em></a>,
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<a class="reference internal" href="fix_langevin.html"><em>langevin</em></a> and <a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale</em></a>.
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The desired temperature is specified by <em>temp</em>, which is typically a
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variable previously set in the input script, so that each partition is
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assigned a different temperature. See the <a class="reference internal" href="variable.html"><em>variable</em></a>
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command for more details. For example:</p>
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<div class="highlight-python"><div class="highlight"><pre>variable t world 300.0 310.0 320.0 330.0
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fix myfix all nvt temp $t $t 100.0
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temper 100000 100 $t myfix 3847 58382
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</pre></div>
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</div>
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<p>would define 4 temperatures, and assign one of them to the thermostat
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used by each replica, and to the temper command.</p>
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<p>As the tempering simulation runs for <em>N</em> timesteps, a temperature swap
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between adjacent ensembles will be attempted every <em>M</em> timesteps. If
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<em>seed1</em> is 0, then the swap attempts will alternate between odd and
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even pairings. If <em>seed1</em> is non-zero then it is used as a seed in a
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random number generator to randomly choose an odd or even pairing each
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time. Each attempted swap of temperatures is either accepted or
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rejected based on a Boltzmann-weighted Metropolis criterion which uses
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<em>seed2</em> in the random number generator.</p>
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<p>As a tempering run proceeds, multiple log files and screen output
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files are created, one per replica. By default these files are named
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log.lammps.M and screen.M where M is the replica number from 0 to N-1,
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with N = # of replicas. See the <a class="reference internal" href="Section_start.html#start-7"><span>section on command-line switches</span></a> for info on how to change these
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names.</p>
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<p>The main screen and log file (log.lammps) will list information about
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which temperature is assigned to each replica at each thermodynamic
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output timestep. E.g. for a simulation with 16 replicas:</p>
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<div class="highlight-python"><div class="highlight"><pre>Running on 16 partitions of processors
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Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
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0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
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500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
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1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
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1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
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2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
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2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
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...
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</pre></div>
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</div>
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<p>The column headings T0 to TN-1 mean which temperature is currently
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assigned to the replica 0 to N-1. Thus the columns represent replicas
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and the value in each column is its temperature (also numbered 0 to
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N-1). For example, a 0 in the 4th column (column T3, step 2500) means
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that the 4th replica is assigned temperature 0, i.e. the lowest
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temperature. You can verify this time sequence of temperature
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assignments for the Nth replica by comparing the Nth column of screen
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output to the thermodynamic data in the corresponding log.lammps.N or
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screen.N files as time proceeds.</p>
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<p>You can have each replica create its own dump file in the following
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manner:</p>
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<div class="highlight-python"><div class="highlight"><pre>variable rep world 0 1 2 3 4 5 6 7
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dump 1 all atom 1000 dump.temper.$*rep*
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</pre></div>
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</div>
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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">Each replica’s dump file will contain a continuous trajectory
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for its atoms where the temperature varies over time as swaps take
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place involving that replica. If you want a series of dump files,
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each with snapshots (from all replicas) that are all at a single
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temperature, then you will need to post-process the dump files using
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the information from the log.lammps file. E.g. you could produce one
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dump file with snapshots at 300K (from all replicas), another with
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snapshots at 310K, etc. Note that these new dump files will not
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contain “continuous trajectories” for individual atoms, because two
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successive snapshots (in time) may be from different replicas.</p>
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</div>
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<p>The last argument <em>index</em> in the temper command is optional and is
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used when restarting a tempering run from a set of restart files (one
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for each replica) which had previously swapped to new temperatures.
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The <em>index</em> value (from 0 to N-1, where N is the # of replicas)
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identifies which temperature the replica was simulating on the
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timestep the restart files were written. Obviously, this argument
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must be a variable so that each partition has the correct value. Set
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the variable to the <em>N</em> values listed in the log file for the previous
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run for the replica temperatures at that timestep. For example if the
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log file listed the following for a simulation with 5 replicas:</p>
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<div class="highlight-python"><div class="highlight"><pre>500000 2 4 0 1 3
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</pre></div>
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</div>
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<p>then a setting of</p>
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<div class="highlight-python"><div class="highlight"><pre>variable w world 2 4 0 1 3
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</pre></div>
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</div>
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<p>would be used to restart the run with a tempering command like the
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example above with $w as the last argument.</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<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>This command can only be used if LAMMPS was built with the REPLICA
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package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
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for more info on packages.</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="variable.html"><em>variable</em></a>, <a class="reference internal" href="prd.html"><em>prd</em></a>, <a class="reference internal" href="neb.html"><em>neb</em></a></p>
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<p><strong>Default:</strong> none</p>
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