forked from lijiext/lammps
509 lines
29 KiB
HTML
509 lines
29 KiB
HTML
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<title>restart command — LAMMPS 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_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_coeff.html">angle_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atom_modify.html">atom_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atom_style.html">atom_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="balance.html">balance command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_coeff.html">bond_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_style.html">bond_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="boundary.html">boundary command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="clear.html">clear command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_modify.html">comm_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_style.html">comm_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute.html">compute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_modify.html">compute_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_atoms.html">create_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_style.html">dihedral_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dimension.html">dimension command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="displace_atoms.html">displace_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-custom-vtk-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">custom/vtk</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-h5md-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">h5md</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-image-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">image</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-movie-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">movie</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-molfile-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">molfile</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_custom_vtk.html">dump custom/vtk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_image.html">dump image command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_image.html#dump-movie-command">dump movie command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_modify.html">dump_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_molfile.html">dump molfile command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="echo.html">echo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix.html">fix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_modify.html">fix_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_coeff.html">improper_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_style.html">improper_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="include.html">include command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="info.html">info command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="jump.html">jump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_modify.html">kspace_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_style.html">kspace_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="lattice.html">lattice command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="log.html">log command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="mass.html">mass command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_modify.html">min_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html">min_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="minimize.html">minimize command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="molecule.html">molecule command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_coeff.html">pair_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_modify.html">pair_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_style.html">pair_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_write.html">pair_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="partition.html">partition command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="prd.html">prd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="quit.html">quit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_data.html">read_data command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_dump.html">read_dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_restart.html">read_restart command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="region.html">region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="replicate.html">replicate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="rerun.html">rerun command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="reset_timestep.html">reset_timestep command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">restart command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
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</ul>
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<li class="toctree-l2"><a class="reference internal" href="run.html">run command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="run_style.html">run_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="set.html">set command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="shell.html">shell command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="special_bonds.html">special_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="suffix.html">suffix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="tad.html">tad command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="temper.html">temper command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo.html">thermo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_modify.html">thermo_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_style.html">thermo_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timer.html">timer command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timestep.html">timestep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="uncompute.html">uncompute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="undump.html">undump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="unfix.html">unfix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="units.html">units command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="variable.html">variable command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="velocity.html">velocity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_coeff.html">write_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_dump.html">write_dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_restart.html">write_restart command</a></li>
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</ul>
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<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
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<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
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<li>restart command</li>
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<div class="section" id="restart-command">
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<span id="index-0"></span><h1>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">restart</span> <span class="mi">0</span>
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<span class="n">restart</span> <span class="n">N</span> <span class="n">root</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
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<span class="n">restart</span> <span class="n">N</span> <span class="n">file1</span> <span class="n">file2</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
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</pre></div>
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</div>
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<ul>
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<li><p class="first">N = write a restart file every this many timesteps</p>
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</li>
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<li><p class="first">N can be a variable (see below)</p>
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</li>
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<li><p class="first">root = filename to which timestep # is appended</p>
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</li>
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<li><p class="first">file1,file2 = two full filenames, toggle between them when writing file</p>
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</li>
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<li><p class="first">zero or more keyword/value pairs may be appended</p>
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</li>
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<li><p class="first">keyword = <em>fileper</em> or <em>nfile</em></p>
|
|
<pre class="literal-block">
|
|
<em>fileper</em> arg = Np
|
|
Np = write one file for every this many processors
|
|
<em>nfile</em> arg = Nf
|
|
Nf = write this many files, one from each of Nf processors
|
|
</pre>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<pre class="literal-block">
|
|
restart 0
|
|
restart 1000 poly.restart
|
|
restart 1000 poly.restart.mpiio
|
|
restart 1000 restart.*.equil
|
|
restart 10000 poly.%.1 poly.%.2 nfile 10
|
|
restart v_mystep poly.restart
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Write out a binary restart file with the current state of the
|
|
simulation every so many timesteps, in either or both of two modes, as
|
|
a run proceeds. A value of 0 means do not write out any restart
|
|
files. The two modes are as follows. If one filename is specified, a
|
|
series of filenames will be created which include the timestep in the
|
|
filename. If two filenames are specified, only 2 restart files will
|
|
be created, with those names. LAMMPS will toggle between the 2 names
|
|
as it writes successive restart files.</p>
|
|
<p>Note that you can specify the restart command twice, once with a
|
|
single filename and once with two filenames. This would allow you,
|
|
for example, to write out archival restart files every 100000 steps
|
|
using a single filenname, and more frequent temporary restart files
|
|
every 1000 steps, using two filenames. Using restart 0 will turn off
|
|
both modes of output.</p>
|
|
<p>Similar to <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> files, the restart filename(s) can contain
|
|
two wild-card characters.</p>
|
|
<p>If a “*” appears in the single filename, it is replaced with the
|
|
current timestep value. This is only recognized when a single
|
|
filename is used (not when toggling back and forth). Thus, the 3rd
|
|
example above creates restart files as follows: restart.1000.equil,
|
|
restart.2000.equil, etc. If a single filename is used with no “*”,
|
|
then the timestep value is appended. E.g. the 2nd example above
|
|
creates restart files as follows: poly.restart.1000,
|
|
poly.restart.2000, etc.</p>
|
|
<p>If a “%” character appears in the restart filename(s), then one file
|
|
is written for each processor and the “%” character is replaced with
|
|
the processor ID from 0 to P-1. An additional file with the “%”
|
|
replaced by “base” is also written, which contains global information.
|
|
For example, the files written on step 1000 for filename restart.%
|
|
would be restart.base.1000, restart.0.1000, restart.1.1000, ...,
|
|
restart.P-1.1000. This creates smaller files and can be a fast mode
|
|
of output and subsequent input on parallel machines that support
|
|
parallel I/O. The optional <em>fileper</em> and <em>nfile</em> keywords discussed
|
|
below can alter the number of files written.</p>
|
|
<p>The restart file can also be written in parallel as one large binary
|
|
file via the MPI-IO library, which is part of the MPI standard for
|
|
versions 2.0 and above. Using MPI-IO requires two steps. First,
|
|
build LAMMPS with its MPIIO package installed, e.g.</p>
|
|
<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>
|
|
<span class="n">make</span> <span class="n">g</span><span class="o">++</span> <span class="c1"># build LAMMPS for your platform</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>Second, use a restart filename which contains ”.mpiio”. Note that it
|
|
does not have to end in ”.mpiio”, just contain those characters.
|
|
Unlike MPI-IO dump files, a particular restart file must be both
|
|
written and read using MPI-IO.</p>
|
|
<p>Restart files are written on timesteps that are a multiple of N but
|
|
not on the first timestep of a run or minimization. You can use the
|
|
<a class="reference internal" href="write_restart.html"><span class="doc">write_restart</span></a> command to write a restart file
|
|
before a run begins. A restart file is not written on the last
|
|
timestep of a run unless it is a multiple of N. A restart file is
|
|
written on the last timestep of a minimization if N > 0 and the
|
|
minimization converges.</p>
|
|
<p>Instead of a numeric value, N can be specifed as an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>, which should be specified as v_name, where
|
|
name is the variable name. In this case, the variable is evaluated at
|
|
the beginning of a run to determine the next timestep at which a
|
|
restart file will be written out. On that timestep, the variable will
|
|
be evaluated again to determine the next timestep, etc. Thus the
|
|
variable should return timestep values. See the stagger() and
|
|
logfreq() and stride() math functions for <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a>, as examples of useful functions to use in
|
|
this context. Other similar math functions could easily be added as
|
|
options for <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a>.</p>
|
|
<p>For example, the following commands will write restart files
|
|
every step from 1100 to 1200, and could be useful for debugging
|
|
a simulation where something goes wrong at step 1163:</p>
|
|
<pre class="literal-block">
|
|
variable s equal stride(1100,1200,1)
|
|
restart v_s tmp.restart
|
|
</pre>
|
|
<hr class="docutils" />
|
|
<p>See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for information about
|
|
what is stored in a restart file.</p>
|
|
<p>Restart files can be read by a <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
|
|
command to restart a simulation from a particular state. Because the
|
|
file is binary (to enable exact restarts), it may not be readable on
|
|
another machine. In this case, you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-r command-line switch</span></a> to convert a restart file to a data
|
|
file.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">Although the purpose of restart files is to enable restarting a
|
|
simulation from where it left off, not all information about a
|
|
simulation is stored in the file. For example, the list of fixes that
|
|
were specified during the initial run is not stored, which means the
|
|
new input script must specify any fixes you want to use. Even when
|
|
restart information is stored in the file, as it is for some fixes,
|
|
commands may need to be re-specified in the new input script, in order
|
|
to re-use that information. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
|
|
command for information about what is stored in a restart file.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>The optional <em>nfile</em> or <em>fileper</em> keywords can be used in conjunction
|
|
with the “%” wildcard character in the specified restart file name(s).
|
|
As explained above, the “%” character causes the restart file to be
|
|
written in pieces, one piece for each of P processors. By default P =
|
|
the number of processors the simulation is running on. The <em>nfile</em> or
|
|
<em>fileper</em> keyword can be used to set P to a smaller value, which can
|
|
be more efficient when running on a large number of processors.</p>
|
|
<p>The <em>nfile</em> keyword sets P to the specified Nf value. For example, if
|
|
Nf = 4, and the simulation is running on 100 processors, 4 files will
|
|
be written, by processors 0,25,50,75. Each will collect information
|
|
from itself and the next 24 processors and write it to a restart file.</p>
|
|
<p>For the <em>fileper</em> keyword, the specified value of Np means write one
|
|
file for every Np processors. For example, if Np = 4, every 4th
|
|
processor (0,4,8,12,etc) will collect information from itself and the
|
|
next 3 processors and write it to a restart file.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<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="write_restart.html"><span class="doc">write_restart</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">restart</span> <span class="mi">0</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
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</div>
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<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
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<a href="run.html" class="btn btn-neutral float-right" title="run command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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<a href="reset_timestep.html" class="btn btn-neutral" title="reset_timestep command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
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