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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_accelerate.html">5. Accelerating LAMMPS performance</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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<li>read_restart command</li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div class="section" id="read-restart-command">
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<span id="index-0"></span><h1>read_restart 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">read_restart</span> <span class="n">file</span> <span class="n">flag</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>file = name of binary restart file to read in</li>
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<li>flag = remap (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">read_restart</span> <span class="n">save</span><span class="o">.</span><span class="mi">10000</span>
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<span class="n">read_restart</span> <span class="n">save</span><span class="o">.</span><span class="mi">10000</span> <span class="n">remap</span>
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<span class="n">read_restart</span> <span class="n">restart</span><span class="o">.*</span>
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<span class="n">read_restart</span> <span class="n">restart</span><span class="o">.*.</span><span class="n">mpiio</span>
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<span class="n">read_restart</span> <span class="n">poly</span><span class="o">.*.%</span> <span class="n">remap</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>Read in a previously saved system configuration from a restart file.
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This allows continuation of a previous run. Details about what
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information is stored (and not stored) in a restart file is given
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below. Basically this operation will re-create the simulation box
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with all its atoms and their attributes as well as some related global
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settings, at the point in time it was written to the restart file by a
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previous simluation. The simulation box will be partitioned into a
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regular 3d grid of rectangular bricks, one per processor, based on the
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number of processors in the current simulation and the settings of the
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<a class="reference internal" href="processors.html"><span class="doc">processors</span></a> command. The partitioning can later be
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changed by the <a class="reference internal" href="balance.html"><span class="doc">balance</span></a> or <a class="reference internal" href="fix_balance.html"><span class="doc">fix balance</span></a> commands.</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">Normally, restart files are written by the
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<a class="reference internal" href="restart.html"><span class="doc">restart</span></a> or <a class="reference internal" href="write_restart.html"><span class="doc">write_restart</span></a> commands
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so that all atoms in the restart file are inside the simulation box.
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If this is not the case, the read_restart command will print an error
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that atoms were “lost” when the file is read. This error should be
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reported to the LAMMPS developers so the invalid writing of the
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restart file can be fixed. If you still wish to use the restart file,
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the optional <em>remap</em> flag can be appended to the read_restart command.
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This should avoid the error, by explicitly remapping each atom back
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into the simulation box, updating image flags for the atom
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appropriately.</p>
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</div>
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<p>Restart files are saved in binary format to enable exact restarts,
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meaning that the trajectories of a restarted run will precisely match
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those produced by the original run had it continued on.</p>
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<p>Several things can prevent exact restarts due to round-off effects, in
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which case the trajectories in the 2 runs will slowly diverge. These
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include running on a different number of processors or changing
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certain settings such as those set by the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> or
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<a class="reference internal" href="processors.html"><span class="doc">processors</span></a> commands. LAMMPS will issue a warning in
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these cases.</p>
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<p>Certain fixes will not restart exactly, though they should provide
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statistically similar results. These include <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> and <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>.</p>
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<p>Certain pair styles will not restart exactly, though they should
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provide statistically similar results. This is because the forces
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they compute depend on atom velocities, which are used at half-step
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values every timestep when forces are computed. When a run restarts,
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forces are initially evaluated with a full-step velocity, which is
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different than if the run had continued. These pair styles include
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<a class="reference internal" href="pair_gran.html"><span class="doc">granular pair styles</span></a>, <a class="reference internal" href="pair_dpd.html"><span class="doc">pair dpd</span></a>, and
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<a class="reference internal" href="pair_lubricate.html"><span class="doc">pair lubricate</span></a>.</p>
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<p>If a restarted run is immediately different than the run which
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produced the restart file, it could be a LAMMPS bug, so consider
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<a class="reference internal" href="Section_errors.html#err-2"><span class="std std-ref">reporting it</span></a> if you think the behavior is
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wrong.</p>
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<p>Because restart files are binary, they may not be portable to other
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machines. In this case, you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-restart command-line switch</span></a> to convert a restart file to a data
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file.</p>
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<p>Similar to how restart files are written (see the
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<a class="reference internal" href="write_restart.html"><span class="doc">write_restart</span></a> and <a class="reference internal" href="restart.html"><span class="doc">restart</span></a>
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commands), the restart filename can contain two wild-card characters.
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If a “*” appears in the filename, the directory is searched for all
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filenames that match the pattern where “*” is replaced with a timestep
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value. The file with the largest timestep value is read in. Thus,
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this effectively means, read the latest restart file. It’s useful if
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you want your script to continue a run from where it left off. See
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the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command and its “upto” option for how to specify
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the run command so it doesn’t need to be changed either.</p>
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<p>If a “%” character appears in the restart filename, LAMMPS expects a
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set of multiple files to exist. The <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> and
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<a class="reference internal" href="write_restart.html"><span class="doc">write_restart</span></a> commands explain how such sets are
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created. Read_restart will first read a filename where “%” is
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replaced by “base”. This file tells LAMMPS how many processors
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created the set and how many files are in it. Read_restart then reads
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the additional files. For example, if the restart file was specified
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as save.% when it was written, then read_restart reads the files
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save.base, save.0, save.1, ... save.P-1, where P is the number of
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processors that created the restart file.</p>
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<p>Note that P could be the total number of processors in the previous
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simulation, or some subset of those processors, if the <em>fileper</em> or
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<em>nfile</em> options were used when the restart file was written; see the
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<a class="reference internal" href="restart.html"><span class="doc">restart</span></a> and <a class="reference internal" href="write_restart.html"><span class="doc">write_restart</span></a> commands
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for details. The processors in the current LAMMPS simulation share
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the work of reading these files; each reads a roughly equal subset of
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the files. The number of processors which created the set can be
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different the number of processors in the current LAMMPS simulation.
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This can be a fast mode of input on parallel machines that support
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parallel I/O.</p>
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<p>A restart file can also be read in parallel as one large binary file
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via the MPI-IO library, assuming it was also written with MPI-IO.
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MPI-IO is part of the MPI standard for versions 2.0 and above. Using
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MPI-IO requires two steps. First, build LAMMPS with its MPIIO package
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installed, e.g.</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">mpiio</span> <span class="c1"># installs the MPIIO package</span>
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<span class="n">make</span> <span class="n">g</span><span class="o">++</span> <span class="c1"># build LAMMPS for your platform</span>
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</pre></div>
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</div>
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<p>Second, use a restart filename which contains ”.mpiio”. Note that it
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does not have to end in ”.mpiio”, just contain those characters.
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Unlike MPI-IO dump files, a particular restart file must be both
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written and read using MPI-IO.</p>
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<hr class="docutils" />
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<p>Here is the list of information included in a restart file, which
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means these quantities do not need to be re-specified in the input
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script that reads the restart file, though you can redefine many of
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these settings after the restart file is read.</p>
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<ul class="simple">
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<li><a class="reference internal" href="units.html"><span class="doc">units</span></a></li>
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<li><a class="reference internal" href="newton.html"><span class="doc">newton bond</span></a> (see discussion of newton command below)</li>
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<li><a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a> and <a class="reference internal" href="atom_modify.html"><span class="doc">atom_modify</span></a> settings id, map, sort</li>
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<li><a class="reference internal" href="comm_style.html"><span class="doc">comm style</span></a> and <a class="reference external" href="comm_modify">comm_modify</a> settings mode, cutoff, vel</li>
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<li><a class="reference internal" href="timestep.html"><span class="doc">timestep</span></a></li>
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<li>simulation box size and shape and <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> settings</li>
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<li>atom <a class="reference internal" href="group.html"><span class="doc">group</span></a> definitions</li>
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<li>per-type atom settings such as <a class="reference external" href="mass.thml">mass</a></li>
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<li>per-atom attributes including their group assignments and molecular topology attributes (bonds, angles, etc)</li>
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<li>force field styles (<a class="reference internal" href="pair_style.html"><span class="doc">pair</span></a>, <a class="reference internal" href="bond_style.html"><span class="doc">bond</span></a>, <a class="reference internal" href="angle_style.html"><span class="doc">angle</span></a>, etc)</li>
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<li>force field coefficients (<a class="reference internal" href="pair_coeff.html"><span class="doc">pair</span></a>, <a class="reference internal" href="bond_coeff.html"><span class="doc">bond</span></a>, <a class="reference internal" href="angle_coeff.html"><span class="doc">angle</span></a>, etc) in some cases (see below)</li>
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<li><a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> settings, except the compute option</li>
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<li><a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> settings</li>
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</ul>
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<p>Here is a list of information not stored in a restart file, which
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means you must re-issue these commands in your input script, after
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reading the restart file.</p>
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<ul class="simple">
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<li><a class="reference internal" href="newton.html"><span class="doc">newton pair</span></a> (see discussion of newton command below)</li>
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<li><a class="reference internal" href="fix.html"><span class="doc">fix</span></a> commands (see below)</li>
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<li><a class="reference internal" href="compute.html"><span class="doc">compute</span></a> commands (see below)</li>
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<li><a class="reference internal" href="variable.html"><span class="doc">variable</span></a> commands</li>
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<li><a class="reference internal" href="region.html"><span class="doc">region</span></a> commands</li>
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<li><a class="reference internal" href="neighbor.html"><span class="doc">neighbor list</span></a> criteria including <a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify</span></a> settings</li>
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<li><a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> and <a class="reference internal" href="kspace_modify.html"><span class="doc">kspace_modify</span></a> settings</li>
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<li>info for <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, or <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> output</li>
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</ul>
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<p>The <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> command has two settings, one for pairwise
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interactions, the other for bonded. Both settings are stored in the
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restart file. For the bond setting, the value in the file will
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overwrite the current value (at the time the read_restart command is
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issued) and warn if the two values are not the same and the current
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value is not the default. For the pair setting, the value in the file
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will not overwrite the current value (so that you can override the
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previous run’s value), but a warning is issued if the two values are
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not the same and the current value is not the default.</p>
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<p>Note that some force field styles (pair, bond, angle, etc) do not
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store their coefficient info in restart files. Typically these are
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many-body or tabulated potentials which read their parameters from
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separate files. In these cases you will need to re-specify the “pair
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<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>, <a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, etc
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commands in your restart input script. The doc pages for individual
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force field styles mention if this is the case. This is also true of
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<a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid</span></a> (bond hybrid, angle hybrid, etc)
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commands; they do not store coefficient info.</p>
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<p>As indicated in the above list, the <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a> used for a
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simulation are not stored in the restart file. This means the new
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input script should specify all fixes it will use. However, note that
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some fixes store an internal “state” which is written to the restart
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file. This allows the fix to continue on with its calculations in a
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restarted simulation. To re-enable such a fix, the fix command in the
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new input script must use the same fix-ID and group-ID as was used in
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the input script that wrote the restart file. If a match is found,
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LAMMPS prints a message indicating that the fix is being re-enabled.
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If no match is found before the first run or minimization is performed
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by the new script, the “state” information for the saved fix is
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discarded. See the doc pages for individual fixes for info on which
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ones can be restarted in this manner.</p>
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<p>Likewise, the <a class="reference internal" href="fix.html"><span class="doc">computes</span></a> used for a simulation are not stored
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in the restart file. This means the new input script should specify
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all computes it will use. However, some computes create a fix
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internally to store “state” information that persists from timestep to
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timestep. An example is the <a class="reference internal" href="compute_msd.html"><span class="doc">compute msd</span></a> command
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which uses a fix to store a reference coordinate for each atom, so
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that a displacement can be calculated at any later time. If the
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compute command in the new input script uses the same compute-ID and
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group-ID as was used in the input script that wrote the restart file,
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then it will create the same fix in the restarted run. This means the
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re-created fix will be re-enabled with the stored state information as
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described in the previous paragraph, so that the compute can continue
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its calculations in a consistent manner.</p>
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<p>Some pair styles, like the <a class="reference internal" href="pair_gran.html"><span class="doc">granular pair styles</span></a>, also
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use a fix to store “state” information that persists from timestep to
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timestep. In the case of granular potentials, it is contact
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information between pairs of touching particles. This info will also
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be re-enabled in the restart script, assuming you re-use the same
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granular pair style.</p>
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<p>LAMMPS allows bond interactions (angle, etc) to be turned off or
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deleted in various ways, which can affect how their info is stored in
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a restart file.</p>
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<p>If bonds (angles, etc) have been turned off by the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> or <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a> command,
|
|
their info will be written to a restart file as if they are turned on.
|
|
This means they will need to be turned off again in a new run after
|
|
the restart file is read.</p>
|
|
<p>Bonds that are broken (e.g. by a bond-breaking potential) are written
|
|
to the restart file as broken bonds with a type of 0. Thus these
|
|
bonds will still be broken when the restart file is read.</p>
|
|
<p>Bonds that have been broken by the <a class="reference internal" href="fix_bond_break.html"><span class="doc">fix bond/break</span></a> command have disappeared from the
|
|
system. No information about these bonds is written to the restart
|
|
file.</p>
|
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</div>
|
|
<hr class="docutils" />
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|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>To write and read restart files in parallel with MPI-IO, the MPIIO
|
|
package must be installed.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="read_dump.html"><span class="doc">read_dump</span></a>,
|
|
<a class="reference internal" href="write_restart.html"><span class="doc">write_restart</span></a>, <a class="reference internal" href="restart.html"><span class="doc">restart</span></a></p>
|
|
<p><strong>Default:</strong> none</p>
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