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<li class="toctree-l2 current"><a class="current reference internal" href="#">dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#dump-vtk-command"><span class="xref std std-doc">dump vtk</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#dump-h5md-command"><span class="xref std std-doc">dump h5md</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#dump-molfile-command"><span class="xref std std-doc">dump molfile</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#dump-netcdf-command"><span class="xref std std-doc">dump netcdf</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#dump-movie-command"><span class="xref std std-doc">dump movie</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#dump-atom-adios-command"><span class="xref std std-doc">dump atom/adios</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#dump-custom-adios-command"><span class="xref std std-doc">dump custom/adios</span> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#dump-cfg-uef-command"><span class="xref std std-doc">dump cfg/uef</span> command</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="dump_adios.html">dump atom/adios command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_adios.html#dump-custom-adios-command">dump custom/adios command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_image.html#dump-modify-options-for-dump-image-movie">dump_modify options for dump image/movie</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_modify.html#dump-modify-command-for-image-movie-options"><span class="xref std std-doc">dump_modify</span> command for image/movie options</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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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="dump-command">
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<span id="index-20"></span><span id="index-19"></span><span id="index-18"></span><span id="index-17"></span><span id="index-16"></span><span id="index-15"></span><span id="index-14"></span><span id="index-13"></span><span id="index-12"></span><span id="index-11"></span><span id="index-10"></span><span id="index-9"></span><span id="index-8"></span><span id="index-7"></span><span id="index-6"></span><span id="index-5"></span><span id="index-4"></span><span id="index-3"></span><span id="index-2"></span><span id="index-1"></span><span id="index-0"></span><h1>dump command<a class="headerlink" href="#dump-command" title="Link to this heading"></a></h1>
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</section>
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<section id="dump-vtk-command">
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<h1><a class="reference internal" href="dump_vtk.html"><span class="doc">dump vtk</span></a> command<a class="headerlink" href="#dump-vtk-command" title="Link to this heading"></a></h1>
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</section>
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<section id="dump-h5md-command">
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<h1><a class="reference internal" href="dump_h5md.html"><span class="doc">dump h5md</span></a> command<a class="headerlink" href="#dump-h5md-command" title="Link to this heading"></a></h1>
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</section>
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<section id="dump-molfile-command">
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<h1><a class="reference internal" href="dump_molfile.html"><span class="doc">dump molfile</span></a> command<a class="headerlink" href="#dump-molfile-command" title="Link to this heading"></a></h1>
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</section>
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<section id="dump-netcdf-command">
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<h1><a class="reference internal" href="dump_netcdf.html"><span class="doc">dump netcdf</span></a> command<a class="headerlink" href="#dump-netcdf-command" title="Link to this heading"></a></h1>
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</section>
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<section id="dump-image-command">
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<h1><a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> command<a class="headerlink" href="#dump-image-command" title="Link to this heading"></a></h1>
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</section>
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<section id="dump-movie-command">
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<h1><a class="reference internal" href="dump_image.html"><span class="doc">dump movie</span></a> command<a class="headerlink" href="#dump-movie-command" title="Link to this heading"></a></h1>
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</section>
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<section id="dump-atom-adios-command">
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<h1><a class="reference internal" href="dump_adios.html"><span class="doc">dump atom/adios</span></a> command<a class="headerlink" href="#dump-atom-adios-command" title="Link to this heading"></a></h1>
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</section>
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<section id="dump-custom-adios-command">
|
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<h1><a class="reference internal" href="dump_adios.html"><span class="doc">dump custom/adios</span></a> command<a class="headerlink" href="#dump-custom-adios-command" title="Link to this heading"></a></h1>
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</section>
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<section id="dump-cfg-uef-command">
|
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<h1><a class="reference internal" href="dump_cfg_uef.html"><span class="doc">dump cfg/uef</span></a> command<a class="headerlink" href="#dump-cfg-uef-command" title="Link to this heading"></a></h1>
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<section id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">dump </span><span class="nv nv-Identifier">ID</span><span class="w"> </span><span class="nv nv-Identifier">group-ID</span><span class="w"> </span><span class="n">style</span><span class="w"> </span><span class="n">N</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="n">attribute1</span><span class="w"> </span><span class="n">attribute2</span><span class="w"> </span><span class="n">...</span>
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</pre></div>
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</div>
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<ul>
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<li><p>ID = user-assigned name for the dump</p></li>
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<li><p>group-ID = ID of the group of atoms to be dumped</p></li>
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<li><p>style = <em>atom</em> or <em>atom/adios</em> or <em>atom/gz</em> or <em>atom/zstd</em> or <em>cfg</em> or <em>cfg/gz</em> or <em>cfg/zstd</em> or <em>cfg/uef</em> or <em>custom</em> or <em>custom/gz</em> or <em>custom/zstd</em> or <em>custom/adios</em> or <em>dcd</em> or <em>grid</em> or <em>grid/vtk</em> or <em>h5md</em> or <em>image</em> or <em>local</em> or <em>local/gz</em> or <em>local/zstd</em> or <em>molfile</em> or <em>movie</em> or <em>netcdf</em> or <em>netcdf/mpiio</em> or <em>vtk</em> or <em>xtc</em> or <em>xyz</em> or <em>xyz/gz</em> or <em>xyz/zstd</em> or <em>yaml</em></p></li>
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<li><p>N = dump on timesteps which are multiples of N</p></li>
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<li><p>file = name of file to write dump info to</p></li>
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<li><p>attribute1,attribute2,… = list of attributes for a particular style</p>
|
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<pre class="literal-block"><em>atom</em> attributes = none
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<em>atom/adios</em> attributes = none, discussed on <a class="reference internal" href="dump_adios.html"><span class="doc">dump atom/adios</span></a> page
|
||
<em>atom/gz</em> attributes = none
|
||
<em>atom/zstd</em> attributes = none
|
||
<em>cfg</em> attributes = same as <em>custom</em> attributes, see below
|
||
<em>cfg/gz</em> attributes = same as <em>custom</em> attributes, see below
|
||
<em>cfg/zstd</em> attributes = same as <em>custom</em> attributes, see below
|
||
<em>cfg/uef</em> attributes = same as <em>custom</em> attributes, discussed on <a class="reference internal" href="dump_cfg_uef.html"><span class="doc">dump cfg/uef</span></a> page
|
||
<em>custom</em>, <em>custom/gz</em>, <em>custom/zstd</em> attributes = see below
|
||
<em>custom/adios</em> attributes = same as <em>custom</em> attributes, discussed on <a class="reference internal" href="dump_adios.html"><span class="doc">dump custom/adios</span></a> page
|
||
<em>dcd</em> attributes = none
|
||
<em>h5md</em> attributes = discussed on <a class="reference internal" href="dump_h5md.html"><span class="doc">dump h5md</span></a> page
|
||
<em>grid</em> attributes = see below
|
||
<em>grid/vtk</em> attributes = see below
|
||
<em>image</em> attributes = discussed on <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> page
|
||
<em>local</em>, <em>local/gz</em>, <em>local/zstd</em> attributes = see below
|
||
<em>molfile</em> attributes = discussed on <a class="reference internal" href="dump_molfile.html"><span class="doc">dump molfile</span></a> page
|
||
<em>movie</em> attributes = discussed on <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> page
|
||
<em>netcdf</em> attributes = discussed on <a class="reference internal" href="dump_netcdf.html"><span class="doc">dump netcdf</span></a> page
|
||
<em>netcdf/mpiio</em> attributes = discussed on <a class="reference internal" href="dump_netcdf.html"><span class="doc">dump netcdf</span></a> page
|
||
<em>vtk</em> attributes = same as <em>custom</em> attributes, see below, also <a class="reference internal" href="dump_vtk.html"><span class="doc">dump vtk</span></a> page
|
||
<em>xtc</em> attributes = none
|
||
<em>xyz</em> attributes = none
|
||
<em>xyz/gz</em> attributes = none
|
||
<em>xyz/zstd</em> attributes = none
|
||
<em>yaml</em> attributes = same as <em>custom</em> attributes, see below</pre>
|
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</li>
|
||
<li><p><em>custom</em> or <em>custom/gz</em> or <em>custom/zstd</em> or <em>cfg</em> or <em>cfg/gz</em> or <em>cfg/zstd</em> or <em>cfg/uef</em> or <em>netcdf</em> or <em>netcdf/mpiio</em> or <em>yaml</em> attributes:</p>
|
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<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>possible attributes = id, mol, proc, procp1, type, element, mass,
|
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x, y, z, xs, ys, zs, xu, yu, zu,
|
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xsu, ysu, zsu, ix, iy, iz,
|
||
vx, vy, vz, fx, fy, fz,
|
||
q, mux, muy, muz, mu,
|
||
radius, diameter, omegax, omegay, omegaz,
|
||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||
c_ID, c_ID[I], f_ID, f_ID[I], v_name,
|
||
i_name, d_name, i2_name[I], d2_name[I]
|
||
</pre></div>
|
||
</div>
|
||
<pre class="literal-block">id = atom ID
|
||
mol = molecule ID
|
||
proc = ID of processor that owns atom
|
||
procp1 = ID+1 of processor that owns atom
|
||
type = atom type
|
||
typelabel = atom <a class="reference internal" href="Howto_type_labels.html"><span class="doc">type label</span></a>
|
||
element = name of atom element, as defined by <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command
|
||
mass = atom mass
|
||
x,y,z = unscaled atom coordinates
|
||
xs,ys,zs = scaled atom coordinates
|
||
xu,yu,zu = unwrapped atom coordinates
|
||
xsu,ysu,zsu = scaled unwrapped atom coordinates
|
||
ix,iy,iz = box image that the atom is in
|
||
vx,vy,vz = atom velocities
|
||
fx,fy,fz = forces on atoms
|
||
q = atom charge
|
||
mux,muy,muz = orientation of dipole moment of atom
|
||
mu = magnitude of dipole moment of atom
|
||
radius,diameter = radius, diameter of spherical particle
|
||
omegax,omegay,omegaz = angular velocity of spherical particle
|
||
angmomx,angmomy,angmomz = angular momentum of aspherical particle
|
||
tqx,tqy,tqz = torque on finite-size particles
|
||
c_ID = per-atom vector calculated by a compute with ID
|
||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
|
||
f_ID = per-atom vector calculated by a fix with ID
|
||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
|
||
v_name = per-atom vector calculated by an atom-style variable with name
|
||
i_name = custom integer vector with name
|
||
d_name = custom floating point vector with name
|
||
i2_name[I] = Ith column of custom integer array with name, I can include wildcard (see below)
|
||
d2_name[I] = Ith column of custom floating point vector with name, I can include wildcard (see below)</pre>
|
||
</li>
|
||
<li><p><em>local</em> or <em>local/gz</em> or <em>local/zstd</em> attributes:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>possible attributes = index, c_ID, c_ID[I], f_ID, f_ID[I]
|
||
index = enumeration of local values
|
||
c_ID = local vector calculated by a compute with ID
|
||
c_ID[I] = Ith column of local array calculated by a compute with ID, I can include wildcard (see below)
|
||
f_ID = local vector calculated by a fix with ID
|
||
f_ID[I] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below)
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p><em>grid</em> or <em>grid/vtk</em> attributes:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>possible attributes = c_ID:gname:dname, c_ID:gname:dname[I], f_ID:gname:dname, f_ID:gname:dname[I]
|
||
gname = name of grid defined by compute or fix
|
||
dname = name of data field defined by compute or fix
|
||
c_ID = per-grid vector calculated by a compute with ID
|
||
c_ID[I] = Ith column of per-grid array calculated by a compute with ID, I can include wildcard (see below)
|
||
f_ID = per-grid vector calculated by a fix with ID
|
||
f_ID[I] = Ith column of per-grid array calculated by a fix with ID, I can include wildcard (see below)
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
</section>
|
||
<section id="examples">
|
||
<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">dump </span><span class="nv nv-Identifier">myDump</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">atom</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">dump.lammpstrj</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">myDump</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">atom</span><span class="o">/</span><span class="n">gz</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">dump.atom.gz</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">myDump</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">atom</span><span class="o">/</span><span class="n">zstd</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">dump.atom.zst</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">2</span><span class="w"> </span><span class="nv nv-Identifier">subgroup</span><span class="w"> </span><span class="n">atom</span><span class="w"> </span><span class="m">50</span><span class="w"> </span><span class="n">dump.run.bin</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">4a</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">custom</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">dump.myforce.</span><span class="o">*</span><span class="w"> </span><span class="n">id</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="n">vx</span><span class="w"> </span><span class="n">fx</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">4a</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">custom</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">dump.myvel.lammpsbin</span><span class="w"> </span><span class="n">id</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="n">z</span><span class="w"> </span><span class="n">vx</span><span class="w"> </span><span class="n">vy</span><span class="w"> </span><span class="n">vz</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">4b</span><span class="w"> </span><span class="nv nv-Identifier">flow</span><span class="w"> </span><span class="n">custom</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">dump.</span><span class="o">%</span><span class="n">.myforce</span><span class="w"> </span><span class="n">id</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="n">c_myF[3]</span><span class="w"> </span><span class="n">v_ke</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">4b</span><span class="w"> </span><span class="nv nv-Identifier">flow</span><span class="w"> </span><span class="n">custom</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">dump.</span><span class="o">%</span><span class="n">.myforce</span><span class="w"> </span><span class="n">id</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="n">c_myF[</span><span class="o">*</span><span class="n">]</span><span class="w"> </span><span class="n">v_ke</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">2</span><span class="w"> </span><span class="nv nv-Identifier">inner</span><span class="w"> </span><span class="n">cfg</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="n">dump.snap.</span><span class="o">*</span><span class="n">.cfg</span><span class="w"> </span><span class="n">mass</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="n">xs</span><span class="w"> </span><span class="n">ys</span><span class="w"> </span><span class="n">zs</span><span class="w"> </span><span class="n">vx</span><span class="w"> </span><span class="n">vy</span><span class="w"> </span><span class="n">vz</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">snap</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">cfg</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">dump.config.</span><span class="o">*</span><span class="n">.cfg</span><span class="w"> </span><span class="n">mass</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="n">xs</span><span class="w"> </span><span class="n">ys</span><span class="w"> </span><span class="n">zs</span><span class="w"> </span><span class="n">id</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="n">c_Stress[2]</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">xtc</span><span class="w"> </span><span class="m">1000</span><span class="w"> </span><span class="n">file.xtc</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Dump a snapshot of quantities to one or more files once every
|
||
<span class="math notranslate nohighlight">\(N\)</span> timesteps in one of several styles. The timesteps on which
|
||
dump output is written can also be controlled by a variable. See the
|
||
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command.</p>
|
||
<p>Almost all the styles output per-atom data, i.e. one or more values
|
||
per atom. The exceptions are as follows. The <em>local</em> styles output
|
||
one or more values per bond (angle, dihedral, improper) or per pair of
|
||
interacting atoms (force or neighbor interactions). The <em>grid</em> styles
|
||
output one or more values per grid cell, which are produced by other
|
||
commands which overlay the simulation domain with a regular grid. See
|
||
the <a class="reference internal" href="Howto_grid.html"><span class="doc">Howto grid</span></a> doc page for details. The <em>image</em>
|
||
style renders a JPG, PNG, or PPM image file of the system for each
|
||
snapshot, while the <em>movie</em> style combines and compresses the series
|
||
of images into a movie file; both styles are discussed in detail on
|
||
the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> page.</p>
|
||
<p>Only information for atoms in the specified group is dumped. The
|
||
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify thresh and region and refresh</span></a>
|
||
commands can also alter what atoms are included. Not all styles
|
||
support these options; see details on the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> doc page.</p>
|
||
<p>As described below, the filename determines the kind of output: text
|
||
or binary or gzipped, one big file or one per timestep, one file for
|
||
all the processors or multiple smaller files.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Because periodic boundary conditions are enforced only on timesteps
|
||
when neighbor lists are rebuilt, the coordinates of an atom written
|
||
to a dump file may be slightly outside the simulation box.
|
||
Re-neighbor timesteps will not typically coincide with the
|
||
timesteps dump snapshots are written. See the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify
|
||
pbc</span></a> command if you wish to force coordinates to be
|
||
strictly inside the simulation box.</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Unless the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify sort</span></a> option is invoked,
|
||
the lines of atom or grid information written to dump files
|
||
(typically one line per atom or grid cell) will be in an
|
||
indeterminate order for each snapshot. This is even true when
|
||
running on a single processor, if the <a class="reference internal" href="atom_modify.html"><span class="doc">atom_modify sort</span></a> option is on, which it is by default. In this case
|
||
atoms are re-ordered periodically during a simulation, due to
|
||
spatial sorting. It is also true when running in parallel, because
|
||
data for a single snapshot is collected from multiple processors,
|
||
each of which owns a subset of the atoms.</p>
|
||
</div>
|
||
<div class="admonition warning">
|
||
<p class="admonition-title">Warning</p>
|
||
<p>Without either including atom IDs or using the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify sort</span></a> option, it is impossible for visualization programs
|
||
(e.g. OVITO or VMD) or analysis tools to assign data in different
|
||
frames consistently to the same atom. This can lead to incorrect
|
||
visualizations or results. LAMMPS will print a warning in such cases.</p>
|
||
</div>
|
||
<p>For the <em>atom</em>, <em>custom</em>, <em>cfg</em>, <em>grid</em>, and <em>local</em> styles, sorting
|
||
is off by default. For the <em>dcd</em>, <em>grid/vtk</em>, <em>xtc</em>, <em>xyz</em>, and
|
||
<em>molfile</em> styles, sorting by atom ID or grid ID is on by default. See
|
||
the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> page for details.</p>
|
||
<p>The <em>style</em> keyword determines what kind of data is written to the
|
||
dump file(s) and in what format.</p>
|
||
<p>Note that <em>atom</em>, <em>custom</em>, <em>dcd</em>, <em>xtc</em>, <em>xyz</em>, and <em>yaml</em> style dump
|
||
files can be read directly by <a class="reference external" href="https://www.ks.uiuc.edu/Research/vmd">VMD</a>,
|
||
a popular tool for visualizing and analyzing trajectories from atomic
|
||
and molecular systems. For reading <em>netcdf</em> style dump files, the
|
||
netcdf plugin needs to be recompiled from source using a NetCDF version
|
||
compatible with the one used by LAMMPS. The bundled plugin binary
|
||
uses a very old version of NetCDF that is not compatible with LAMMPS.</p>
|
||
<p>Likewise the <a class="reference external" href="https://www.ovito.org">OVITO visualization package</a>,
|
||
popular for materials modeling, can read the <em>atom</em>, <em>custom</em>,
|
||
<em>local</em>, <em>xtc</em>, <em>cfg</em>, <em>netcdf</em>, and <em>xyz</em> style atom dump files
|
||
directly. With version 3.8 and above, OVITO can also read and
|
||
visualize <em>grid</em> style dump files with grid cell data, including
|
||
iso-surface images of the grid cell values.</p>
|
||
<p>Note that settings made via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a>
|
||
command can also alter the format of individual values and content of
|
||
the dump file itself. This includes the precision of values output to
|
||
text-based dump files which is controlled by the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify
|
||
format</span></a> command and its options.</p>
|
||
<hr class="docutils" />
|
||
<p>Format of native LAMMPS format dump files:</p>
|
||
<p>The <em>atom</em>, <em>custom</em>, <em>grid</em>, and <em>local</em> styles create files in a
|
||
simple LAMMPS-specific text format that is mostly self-explanatory
|
||
when viewing a dump file. Many post-processing tools either included
|
||
with LAMMPS or third-party tools can read this format, as does the
|
||
<a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command. See tools described on the <a class="reference internal" href="Tools.html"><span class="doc">Tools</span></a> doc page for examples, including <a class="reference external" href="https://lammps.github.io/pizza">Pizza.py</a>.</p>
|
||
<p>For all these styles, the dimensions of the simulation box are
|
||
included in each snapshot. The simulation box in LAMMPS can be
|
||
defined in one of 3 ways: orthogonal, restricted triclinic, and
|
||
general triclinic. See the <a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto triclinic</span></a>
|
||
doc page for a detailed description of all 3 options.</p>
|
||
<p>For an orthogonal simulation box the box information is formatted as:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ITEM: BOX BOUNDS xx yy zz
|
||
xlo xhi
|
||
ylo yhi
|
||
zlo zhi
|
||
</pre></div>
|
||
</div>
|
||
<p>where xlo,xhi are the maximum extents of the simulation box in the
|
||
<span class="math notranslate nohighlight">\(x\)</span>-dimension, and similarly for <span class="math notranslate nohighlight">\(y\)</span> and <span class="math notranslate nohighlight">\(z\)</span>. The
|
||
“xx yy zz” terms are six characters that encode the style of boundary for each
|
||
of the six simulation box boundaries (xlo,xhi; ylo,yhi; and zlo,zhi). Each of
|
||
the six characters is one of <em>p</em> (periodic), <em>f</em> (fixed), <em>s</em> (shrink wrap),
|
||
or <em>m</em> (shrink wrapped with a minimum value). See the
|
||
<a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command for details.</p>
|
||
<p>For a restricted triclinic simulation box, an orthogonal bounding box
|
||
which encloses the restricted triclinic simulation box is output,
|
||
along with the three tilt factors (<em>xy</em>, <em>xz</em>, <em>yz</em>) of the triclinic
|
||
box, formatted as follows:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ITEM: BOX BOUNDS xy xz yz xx yy zz
|
||
xlo_bound xhi_bound xy
|
||
ylo_bound yhi_bound xz
|
||
zlo_bound zhi_bound yz
|
||
</pre></div>
|
||
</div>
|
||
<p>The presence of the text “xy xz yz” in the ITEM line indicates that
|
||
the three tilt factors will be included on each of the three following lines.
|
||
This bounding box is convenient for many visualization programs. The
|
||
meaning of the six character flags for “xx yy zz” is the same as above.</p>
|
||
<p>Note that the first two numbers on each line are now xlo_bound instead
|
||
of xlo, etc. because they represent a bounding box. See the <a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto
|
||
triclinic</span></a> page for a geometric description of
|
||
triclinic boxes, as defined by LAMMPS, simple formulas for how the six
|
||
bounding box extents (xlo_bound, xhi_bound, etc.) are calculated from the
|
||
triclinic parameters, and how to transform those parameters to and
|
||
from other commonly used triclinic representations.</p>
|
||
<p>For a general triclinic simulation box, see the “General triclinic”
|
||
section below for a description of the ITEM: BOX BOUNDS format as well
|
||
as how per-atom coordinates and per-atom vector quantities are output.</p>
|
||
<p>The <em>atom</em> and <em>custom</em> styles output a “ITEM: NUMBER OF ATOMS” line
|
||
with the count of atoms in the snapshot. Likewise they output an
|
||
“ITEM: ATOMS” line which includes column descriptors for the per-atom
|
||
lines that follow. For example, the descriptors would be “id type xs
|
||
ys zs” for the default <em>atom</em> style, and would be the atom attributes
|
||
you specify in the dump command for the <em>custom</em> style. Each
|
||
subsequent line will list the data for a single atom.</p>
|
||
<p>For style <em>atom</em>, atom coordinates are written to the file, along with
|
||
the atom ID and atom type. By default, atom coords are written in a
|
||
scaled format (from 0 to 1). That is, an <span class="math notranslate nohighlight">\(x\)</span> value of 0.25 means the
|
||
atom is at a location 1/4 of the distance from <em>xlo</em> to <em>xhi</em> of the box
|
||
boundaries. The format can be changed to unscaled coords via the
|
||
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> settings. Image flags can also be
|
||
added for each atom via dump_modify.</p>
|
||
<p>Style <em>custom</em> allows you to specify a list of atom attributes to be
|
||
written to the dump file for each atom. Possible attributes are
|
||
listed above and will appear in the order specified. You cannot
|
||
specify a quantity that is not defined for a particular
|
||
simulation—such as <em>q</em> for atom style <em>bond</em>, since that atom style
|
||
does not assign charges. Dumps occur at the very end of a timestep,
|
||
so atom attributes will include effects due to fixes that are applied
|
||
during the timestep. An explanation of the possible dump custom
|
||
attributes is given below.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 22Dec2022.</span></p>
|
||
</div>
|
||
<p>For style <em>grid</em> the dimension of the simulation domain and size of
|
||
the Nx by Ny by Nz grid that overlays the simulation domain are also
|
||
output with each snapshot:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ITEM: DIMENSION
|
||
dim
|
||
ITEM: GRID SIZE
|
||
nx ny nz
|
||
</pre></div>
|
||
</div>
|
||
<p>The value dim will be 2 or 3 for 2d or 3d simulations. It is included
|
||
so that post-processing tools like <a class="reference external" href="https://www.ovito.org">OVITO</a>,
|
||
which can visualize grid-based quantities know how to draw each grid
|
||
cell. The grid size will match the input script parameters for
|
||
grid(s) created by the computes or fixes which are referenced by the
|
||
the dump command. For 2d simulations (and grids), nz will always
|
||
be 1.</p>
|
||
<p>There will also be an “ITEM: GRID DATA” line which includes column
|
||
descriptors for the per grid cell data. Each subsequent line (Nx *
|
||
Ny * Nz lines) will list the data for a single grid cell. If grid
|
||
cell IDs are included in the output via the <a class="reference internal" href="compute_property_grid.html"><span class="doc">compute
|
||
property/grid</span></a> command, then the IDs will
|
||
range from 1 to N = Nx*Ny*Nz. The ordering of IDs is with the x index
|
||
varying fastest, then the y index, and the z index varying slowest.</p>
|
||
<p>For style <em>local</em>, local output generated by <a class="reference internal" href="compute.html"><span class="doc">computes</span></a>
|
||
and <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a> is used to generate lines of output that is
|
||
written to the dump file. This local data is typically calculated by
|
||
each processor based on the atoms it owns, but there may be zero or
|
||
more entities per atom (e.g., a list of bond distances). An explanation
|
||
of the possible dump local attributes is given below. Note that by
|
||
using input from the <a class="reference internal" href="compute_property_local.html"><span class="doc">compute property/local</span></a> command with dump local, it is possible to
|
||
generate information on bonds, angles, etc. that can be cut and pasted
|
||
directly into a data file read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>
|
||
command.</p>
|
||
<hr class="docutils" />
|
||
<p>Dump files in other popular formats:</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>This section only discusses file formats relevant to this doc page.
|
||
The top of this page has links to other dump commands (with their
|
||
own pages) which write files in additional popular formats.</p>
|
||
</div>
|
||
<p>Style <em>cfg</em> has the same command syntax as style <em>custom</em> and writes
|
||
extended CFG format files, as used by the <a class="reference external" href="http://li.mit.edu/Archive/Graphics/A/">AtomEye</a> visualization package.
|
||
Since the extended CFG format uses a single snapshot of the system per
|
||
file, a wildcard “*” must be included in the filename, as discussed
|
||
below. The list of atom attributes for style <em>cfg</em> must begin with
|
||
either “mass type xs ys zs” or “mass type xsu ysu zsu” since these
|
||
quantities are needed to write the CFG files in the appropriate format
|
||
(though the “mass” and “type” fields do not appear explicitly in the
|
||
file). Any remaining attributes will be stored as “auxiliary
|
||
properties” in the CFG files. Note that you will typically want to
|
||
use the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify element</span></a> command with
|
||
CFG-formatted files, to associate element names with atom types, so
|
||
that AtomEye can render atoms appropriately. When unwrapped
|
||
coordinates <em>xsu</em>, <em>ysu</em>, and <em>zsu</em> are requested, the nominal AtomEye
|
||
periodic cell dimensions are expanded by a large factor UNWRAPEXPAND =
|
||
10.0, which ensures atoms that are displayed correctly for up to
|
||
UNWRAPEXPAND/2 periodic boundary crossings in any direction. Beyond
|
||
this, AtomEye will rewrap the unwrapped coordinates. The expansion
|
||
causes the atoms to be drawn farther away from the viewer, but it is
|
||
easy to zoom the atoms closer, and the interatomic distances are
|
||
unaffected.</p>
|
||
<p>The <em>dcd</em> style writes DCD files, a standard atomic trajectory format
|
||
used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
|
||
files are binary and thus may not be portable to different machines.
|
||
The number of atoms per snapshot cannot change with the <em>dcd</em> style.
|
||
The <em>unwrap</em> option of the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command
|
||
allows DCD coordinates to be written “unwrapped” by the image flags
|
||
for each atom. Unwrapped means that if the atom has passed through
|
||
a periodic boundary one or more times, the value is printed for what
|
||
the coordinate would be if it had not been wrapped back into the
|
||
periodic box. Note that these coordinates may thus be far outside
|
||
the box size stored with the snapshot.</p>
|
||
<p>The <em>xtc</em> style writes XTC files, a compressed trajectory format used
|
||
by the GROMACS molecular dynamics package, and described <a class="reference external" href="https://manual.gromacs.org/current/reference-manual/file-formats.html#xtc">here</a>.
|
||
The precision used in XTC files can be adjusted via the
|
||
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command. The default value of 1000
|
||
means that coordinates are stored to 1/1000 nanometer accuracy. XTC
|
||
files are portable binary files written in the NFS XDR data format, so
|
||
that any machine which supports XDR should be able to read them. The
|
||
number of atoms per snapshot cannot change with the <em>xtc</em> style. The
|
||
<em>unwrap</em> option of the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command allows
|
||
XTC coordinates to be written “unwrapped” by the image flags for each
|
||
atom. Unwrapped means that if the atom has passed through a periodic
|
||
boundary one or more times, the value is printed for what the
|
||
coordinate would be if it had not been wrapped back into the periodic
|
||
box. Note that these coordinates may thus be far outside the box size
|
||
stored with the snapshot.</p>
|
||
<p>The <em>xyz</em> style writes XYZ files, which is a simple text-based
|
||
coordinate format that many codes can read. Specifically it has a line
|
||
with the number of atoms, then a comment line that is usually ignored
|
||
followed by one line per atom with the atom type and the <span class="math notranslate nohighlight">\(x\)</span>-,
|
||
<span class="math notranslate nohighlight">\(y\)</span>-, and <span class="math notranslate nohighlight">\(z\)</span>-coordinate of that atom. You can use the
|
||
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify element</span></a> option to change the output
|
||
from using the (numerical) atom type to an element name (or some other
|
||
label). This option will help many visualization programs to guess bonds
|
||
and colors. You can use the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify types labels</span></a>
|
||
option to replace numeric atom types with <a class="reference internal" href="Howto_type_labels.html"><span class="doc">type labels</span></a>.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 22Dec2022.</span></p>
|
||
</div>
|
||
<p>The <em>grid/vtk</em> style writes VTK files for grid data on a regular
|
||
rectilinear grid. Its content is conceptually similar to that of the
|
||
text file produced by the <em>grid</em> style, except that it in an XML-based
|
||
format which visualization programs which support the VTK format can
|
||
read, e.g. the <a class="reference external" href="https://www.paraview.org">ParaView tool</a>. For this
|
||
style, there can only be 1 or 3 per grid cell attributes specified.
|
||
If it is a single value, it is a scalar quantity. If 3 values are
|
||
specified it is encoded in the VTK file as a vector quantity (for each
|
||
grid cell). The filename for this style must include a “*” wildcard
|
||
character to produce one file per snapshot; see details below.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 4May2022.</span></p>
|
||
</div>
|
||
<p>Dump style <em>yaml</em> has the same command syntax as style <em>custom</em> and
|
||
writes YAML format files that can be easily parsed by a variety of
|
||
data processing tools and programming languages. Each timestep will
|
||
be written as a YAML “document” (i.e., starts with “—” and ends with
|
||
“…”). The style supports writing one file per timestep through the
|
||
“*” wildcard but not multi-processor outputs with the “%” token in
|
||
the filename. In addition to per-atom data, <a class="reference internal" href="thermo.html"><span class="doc">thermo</span></a>
|
||
data can be included in the <em>yaml</em> style dump file using the
|
||
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify thermo yes</span></a>. The data included in the
|
||
dump file uses the “thermo” tag and is otherwise identical to data
|
||
specified by the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command.</p>
|
||
<p>Below is an example for a YAML format dump created by the following commands.</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">dump </span><span class="nv nv-Identifier">out</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">yaml</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">dump.yaml</span><span class="w"> </span><span class="n">id</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="n">z</span><span class="w"> </span><span class="n">vx</span><span class="w"> </span><span class="n">vy</span><span class="w"> </span><span class="n">vz</span><span class="w"> </span><span class="n">ix</span><span class="w"> </span><span class="n">iy</span><span class="w"> </span><span class="n">iz</span>
|
||
<span class="k">dump_modify </span><span class="nv nv-Identifier">out</span><span class="w"> </span><span class="n">time</span><span class="w"> </span><span class="n">yes</span><span class="w"> </span><span class="n">units</span><span class="w"> </span><span class="n">yes</span><span class="w"> </span><span class="n">thermo</span><span class="w"> </span><span class="n">yes</span><span class="w"> </span><span class="n">format</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="o">%</span><span class="m">5</span><span class="n">d</span><span class="w"> </span><span class="n">format</span><span class="w"> </span><span class="s">"% 10.6e"</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>The tags “time”, “units”, and “thermo” are optional and enabled by the
|
||
dump_modify command. The list under the “box” tag has three lines for
|
||
orthogonal boxes and four lines for triclinic boxes, where the first
|
||
three are the box boundaries and the fourth the three tilt factors
|
||
(<span class="math notranslate nohighlight">\(xy\)</span>, <span class="math notranslate nohighlight">\(xz\)</span>, <span class="math notranslate nohighlight">\(yz\)</span>). The “thermo” data follows the
|
||
format of the <em>yaml</em> thermo style. The “keywords” tag lists the
|
||
per-atom properties contained in the “data” columns, which contain a
|
||
list with one line per atom. The keywords may be renamed using the
|
||
dump_modify command same as for the <em>custom</em> dump style.</p>
|
||
<div class="highlight-yaml notranslate"><div class="highlight"><pre><span></span><span class="nn">---</span>
|
||
<span class="nt">creator</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">LAMMPS</span>
|
||
<span class="nt">timestep</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0</span>
|
||
<span class="nt">units</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">lj</span>
|
||
<span class="nt">time</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0</span>
|
||
<span class="nt">natoms</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">4000</span>
|
||
<span class="nt">boundary</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="w"> </span><span class="nv">p</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">p</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">p</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">p</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">p</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">p</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="p p-Indicator">]</span>
|
||
<span class="nt">thermo</span><span class="p">:</span>
|
||
<span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="nt">keywords</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="w"> </span><span class="nv">Step</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">Temp</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">E_pair</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">E_mol</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">TotEng</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">Press</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="p p-Indicator">]</span>
|
||
<span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="nt">data</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="w"> </span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">-27093.472213010766</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="p p-Indicator">]</span>
|
||
<span class="nt">box</span><span class="p">:</span>
|
||
<span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="w"> </span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">16.795961913825074</span><span class="w"> </span><span class="p p-Indicator">]</span>
|
||
<span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="w"> </span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">16.795961913825074</span><span class="w"> </span><span class="p p-Indicator">]</span>
|
||
<span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="w"> </span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">16.795961913825074</span><span class="w"> </span><span class="p p-Indicator">]</span>
|
||
<span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="w"> </span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="w"> </span><span class="p p-Indicator">]</span>
|
||
<span class="nt">keywords</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="w"> </span><span class="nv">id</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">type</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">x</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">y</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">z</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">vx</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">vy</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">vz</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">ix</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">iy</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">iz</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="p p-Indicator">]</span>
|
||
<span class="nt">data</span><span class="p">:</span>
|
||
<span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="w"> </span><span class="nv">1</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">1</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0.000000e+00</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0.000000e+00</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0.000000e+00</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">-1.841579e-01</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">-9.710036e-01</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">-2.934617e+00</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="p p-Indicator">]</span>
|
||
<span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="w"> </span><span class="nv">2</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">1</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">8.397981e-01</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">8.397981e-01</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0.000000e+00</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">-1.799591e+00</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">2.127197e+00</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">2.298572e+00</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="p p-Indicator">]</span>
|
||
<span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="w"> </span><span class="nv">3</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">1</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">8.397981e-01</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0.000000e+00</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">8.397981e-01</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">-1.807682e+00</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">-9.585130e-01</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">1.605884e+00</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="w"> </span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="p p-Indicator">]</span>
|
||
|
||
<span class="w"> </span><span class="p p-Indicator">[</span><span class="nv">...</span><span class="p p-Indicator">]</span>
|
||
<span class="nn">...</span>
|
||
<span class="nn">---</span>
|
||
<span class="nt">timestep</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">100</span>
|
||
<span class="nt">units</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">lj</span>
|
||
<span class="nt">time</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.5</span>
|
||
|
||
<span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">[...]</span>
|
||
|
||
<span class="nn">...</span>
|
||
</pre></div>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>Frequency of dump output:</p>
|
||
<p>Dumps are performed on timesteps that are a multiple of <span class="math notranslate nohighlight">\(N\)</span>
|
||
(including timestep 0) and on the last timestep of a minimization if
|
||
the minimization converges. Note that this means a dump will not be
|
||
performed on the initial timestep after the dump command is invoked,
|
||
if the current timestep is not a multiple of <span class="math notranslate nohighlight">\(N\)</span>. This behavior
|
||
can be changed via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify first</span></a> command,
|
||
which can also be useful if the dump command is invoked after a
|
||
minimization ended on an arbitrary timestep.</p>
|
||
<p>The value of <span class="math notranslate nohighlight">\(N\)</span> can be changed between runs by using the
|
||
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command (not allowed for <em>dcd</em>
|
||
style). The <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command also
|
||
allows a variable to be used to determine the sequence of timesteps on
|
||
which dump files are written. In this mode a dump on the first
|
||
timestep of a run will also not be written unless the
|
||
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify first</span></a> command is used.</p>
|
||
<p>If you instead want to dump snapshots based on simulation time (in
|
||
time units of the <a class="reference internal" href="units.html"><span class="doc">units command</span></a> command), the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify
|
||
every/time</span></a> command can be used. This can be useful
|
||
when the timestep size varies during a simulation run, e.g. by use of
|
||
the <a class="reference internal" href="fix_dt_reset.html"><span class="doc">fix dt/reset</span></a> command.</p>
|
||
<hr class="docutils" />
|
||
<p>Dump filenames:</p>
|
||
<p>The specified dump filename determines how the dump file(s) is
|
||
written. The default is to write one large text file, which is opened
|
||
when the dump command is invoked and closed when an <a class="reference internal" href="undump.html"><span class="doc">undump</span></a> command is used or when LAMMPS exits. For the <em>dcd</em> and
|
||
<em>xtc</em> styles, this is a single large binary file.</p>
|
||
<p>Many of the styles allow dump filenames to contain either or both of
|
||
two wildcard characters. If a “*” character appears in the filename,
|
||
then one file per snapshot is written and the “*” character is
|
||
replaced with the timestep value. For example, tmp.dump.* becomes
|
||
tmp.dump.0, tmp.dump.10000, tmp.dump.20000, etc. This option is not
|
||
available for the <em>dcd</em> and <em>xtc</em> styles. Note that the
|
||
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify pad</span></a> command can be used to ensure all
|
||
timestep numbers are the same length (e.g., 00010), which can make it
|
||
easier to read a series of dump files in order with some
|
||
post-processing tools.</p>
|
||
<p>If a “%” character appears in the filename, then each of P processors
|
||
writes a portion of the dump file, and the “%” character is replaced
|
||
with the processor ID from <span class="math notranslate nohighlight">\(0\)</span> to <span class="math notranslate nohighlight">\(P-1\)</span>. For example,
|
||
tmp.dump.% becomes tmp.dump.0, tmp.dump.1, … tmp.dump.:math:<cite>P-1</cite>,
|
||
etc. This creates smaller files and can be a fast mode of output on
|
||
parallel machines that support parallel I/O for output. This option is
|
||
<strong>not</strong> available for the <em>dcd</em>, <em>xtc</em>, <em>xyz</em>, <em>grid/vtk</em>, and <em>yaml</em>
|
||
styles.</p>
|
||
<p>By default, <span class="math notranslate nohighlight">\(P\)</span> is the the number of processors, meaning one file per
|
||
processor, but <span class="math notranslate nohighlight">\(P\)</span> can be set to a smaller value via the <em>nfile</em> or
|
||
<em>fileper</em> keywords of the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command.
|
||
These options can be the most efficient way of writing out dump files
|
||
when running on large numbers of processors.</p>
|
||
<p>Note that using the “*” and “%” characters together can produce a
|
||
large number of small dump files!</p>
|
||
<div class="deprecated">
|
||
<p><span class="versionmodified deprecated">Deprecated since version 21Nov2023.</span></p>
|
||
</div>
|
||
<p>The MPIIO package and the the corresponding “/mpiio” dump styles, except
|
||
for the unrelated “netcdf/mpiio” style were removed from LAMMPS.</p>
|
||
<hr class="docutils" />
|
||
<p>Compression of dump file data:</p>
|
||
<p>If the specified filename ends with “.bin” or “.lammpsbin”, the dump
|
||
file (or files, if “*” or “%” is also used) is written in binary
|
||
format. A binary dump file will be about the same size as a text
|
||
version, but will typically write out much faster. Of course, when
|
||
post-processing, you will need to convert it back to text format (see
|
||
the <a class="reference internal" href="Tools.html#binary"><span class="std std-ref">binary2txt tool</span></a>) or write your own code to read
|
||
the binary file. The format of the binary file can be understood by
|
||
looking at the <code class="file docutils literal notranslate"><span class="pre">tools/binary2txt.cpp</span></code> file. This option is only
|
||
available for the <em>atom</em> and <em>custom</em> styles.</p>
|
||
<p>If the filename ends with “.gz”, the dump file (or files, if “*” or “%”
|
||
is also used) is written in gzipped format. A gzipped dump file will be
|
||
about <span class="math notranslate nohighlight">\(3\times\)</span> smaller than the text version, but will also take
|
||
longer to write. This option is not available for the <em>dcd</em> and <em>xtc</em>
|
||
styles.</p>
|
||
<p>Note that styles that end with <em>gz</em> are identical in command syntax to
|
||
the corresponding styles without “gz”, however, they generate
|
||
compressed files using the zlib library. Thus the filename suffix
|
||
“.gz” is mandatory. This is an alternative approach to writing
|
||
compressed files via a pipe, as done by the regular dump styles, which
|
||
may be required on clusters where the interface to the high-speed
|
||
network disallows using the fork() library call (which is needed for a
|
||
pipe). For the remainder of this page, you should thus consider the
|
||
<em>atom</em> and <em>atom/gz</em> styles (etc.) to be inter-changeable, with the
|
||
exception of the required filename suffix.</p>
|
||
<p>Similarly, styles that end with <em>zstd</em> are identical to the gz styles,
|
||
but use the Zstd compression library instead and require a “.zst”
|
||
suffix. See the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> page for details on
|
||
how to control the compression level in both variants.</p>
|
||
<hr class="docutils" />
|
||
<p>General triclinic simulation box output for the <em>atom</em> and <em>custom</em> styles:</p>
|
||
<p>As mentioned above, the simulation box can be defined as a general
|
||
triclinic box, which means that 3 arbitrary box edge vectors <strong>A</strong>,
|
||
<strong>B</strong>, <strong>C</strong> can be specified. See the <a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto triclinic</span></a> doc page for a detailed description of general
|
||
triclinic boxes.</p>
|
||
<p>This option is provided as a convenience for users who may be
|
||
converting data from solid-state crystallographic representations or
|
||
from DFT codes for input to LAMMPS. However, as explained on the
|
||
<a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto_triclinic</span></a> doc page, internally, LAMMPS
|
||
only uses restricted triclinic simulation boxes. This means the box
|
||
and per-atom information (e.g. coordinates, velocities) LAMMPS stores
|
||
are converted (rotated) from general to restricted triclinic form when
|
||
the system is created.</p>
|
||
<p>For dump output, if the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify triclinic/general</span></a> command is used, the box description and per-atom
|
||
coordinates and other per-atom vectors will be converted (rotated)
|
||
from restricted to general form when each dump file snapshots is
|
||
output. This option can only be used if the simulation box was
|
||
initially created as general triclinic. If the option is not used,
|
||
and the simulation box is general triclinic, then the dump file
|
||
snapshots will reflect the internal restricted triclinic geometry.</p>
|
||
<p>The dump_modify triclinic/general option affects 3 aspects of the dump
|
||
file output.</p>
|
||
<p>First, the format for the BOX BOUNDS is as follows</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ITEM: BOX BOUNDS abc origin
|
||
ax ay az originx
|
||
bx by bz originy
|
||
cx cy cz originz
|
||
</pre></div>
|
||
</div>
|
||
<p>where the <strong>A</strong> edge vector of the box is (ax,ay,az) and similarly
|
||
for <strong>B</strong> and <strong>C</strong>. The origin of all 3 edge vectors is (originx,
|
||
originy, originz).</p>
|
||
<p>Second, the coordinates of each atom are converted (rotated) so that
|
||
the atom is inside (or near) the general triclinic box defined by the
|
||
<strong>A</strong>, <strong>B</strong>, <strong>C</strong> edge vectors. For style <em>atom</em>, this only alters
|
||
output for unscaled atom coords, via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify scaled no</span></a> setting. For style <em>custom</em>, this alters output for
|
||
either unscaled or unwrapped output of atom coords, via the <em>x,y,z</em> or
|
||
<em>xu,yu,zu</em> attributes. For output of scaled atom coords by both
|
||
styles, there is no difference between restricted and general
|
||
triclinic values.</p>
|
||
<p>Third, the output for any attribute of the <em>custom</em> style which
|
||
represents a per-atom vector quantity will be converted (rotated) to
|
||
be oriented consistent with the general triclinic box and its
|
||
orientation relative to the standard xyz coordinate axes.</p>
|
||
<p>This applies to the following <em>custom</em> style attributes:</p>
|
||
<ul class="simple">
|
||
<li><p>vx,vy,vz = atom velocities</p></li>
|
||
<li><p>fx,fy,fz = forces on atoms</p></li>
|
||
<li><p>mux,muy,muz = orientation of dipole moment of atom</p></li>
|
||
<li><p>omegax,omegay,omegaz = angular velocity of spherical particle</p></li>
|
||
<li><p>angmomx,angmomy,angmomz = angular momentum of aspherical particle</p></li>
|
||
<li><p>tqx,tqy,tqz = torque on finite-size particles</p></li>
|
||
</ul>
|
||
<p>For example, if the velocity of an atom in a restricted triclinic box
|
||
is along the x-axis, then it will be output for a general triclinic
|
||
box as a vector along the <strong>A</strong> edge vector of the box.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>For style <em>custom</em>, the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify thresh</span></a>
|
||
command may access per-atom attributes either directly or
|
||
indirectly through a compute or variable. If the attribute is an
|
||
atom coordinate or one of the vectors mentioned above, its value
|
||
will <em>NOT</em> be a general triclinic (rotated) value. Rather it will
|
||
be a restricted triclinic value.</p>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>Arguments for different styles:</p>
|
||
<p>The sections below describe per-atom, local, and per grid cell
|
||
attributes which can be used as arguments to the various styles.</p>
|
||
<p>Note that in the discussion below, for styles which can reference
|
||
values from a compute or fix or custom atom property, like the
|
||
<em>custom</em>, <em>cfg</em>, <em>grid</em> or <em>local</em> styles, the bracketed index
|
||
<span class="math notranslate nohighlight">\(i\)</span> can be specified using a wildcard asterisk with the index to
|
||
effectively specify multiple values. This takes the form “*” or
|
||
“*n” or “m*” or “m*n”. If <span class="math notranslate nohighlight">\(N\)</span> is the number of columns in
|
||
the array, then an asterisk with no numeric values means all column
|
||
indices from 1 to <span class="math notranslate nohighlight">\(N\)</span>. A leading asterisk means all indices
|
||
from 1 to n (inclusive). A trailing asterisk means all indices from m
|
||
to <span class="math notranslate nohighlight">\(N\)</span> (inclusive). A middle asterisk means all indices from m
|
||
to n (inclusive).</p>
|
||
<p>Using a wildcard is the same as if the individual columns of the array
|
||
had been listed one by one. For example, these two dump commands are
|
||
equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
|
||
command creates a per-atom array with six columns:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">compute </span><span class="nv nv-Identifier">myPress</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">stress</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">NULL</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">2</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">custom</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">tmp.dump</span><span class="w"> </span><span class="n">id</span><span class="w"> </span><span class="n">myPress[</span><span class="o">*</span><span class="n">]</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">2</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">custom</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">tmp.dump</span><span class="w"> </span><span class="n">id</span><span class="w"> </span><span class="n">myPress[1]</span><span class="w"> </span><span class="n">myPress[2]</span><span class="w"> </span><span class="n">myPress[3]</span><span class="w"> </span><span class="o">&</span>
|
||
<span class="w"> </span><span class="n">myPress[4]</span><span class="w"> </span><span class="n">myPress[5]</span><span class="w"> </span><span class="n">myPress[6]</span>
|
||
</pre></div>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>Per-atom attributes used as arguments to the <em>custom</em> and <em>cfg</em> styles:</p>
|
||
<p>The <em>id</em>, <em>mol</em>, <em>proc</em>, <em>procp1</em>, <em>type</em>, <em>typelabel</em>, <em>element</em>, <em>mass</em>,
|
||
<em>vx</em>, <em>vy</em>, <em>vz</em>, <em>fx</em>, <em>fy</em>, <em>fz</em>, <em>q</em> attributes are self-explanatory.</p>
|
||
<p><em>Id</em> is the atom ID. <em>Mol</em> is the molecule ID, included in the data file
|
||
for molecular systems. <em>Proc</em> is the ID of the processor (0 to
|
||
<span class="math notranslate nohighlight">\(N_\text{procs}-1\)</span>) that currently owns the atom. <em>Procp1</em> is the
|
||
proc ID+1, which can be convenient in place of a <em>type</em> attribute (1 to
|
||
<span class="math notranslate nohighlight">\(N_\text{types}\)</span>) for coloring atoms in a visualization program.
|
||
<em>Type</em> is the atom type (1 to <span class="math notranslate nohighlight">\(N_\text{types}\)</span>). <em>Typelabel</em> is the
|
||
atom <a class="reference internal" href="Howto_type_labels.html"><span class="doc">type label</span></a>. <em>Element</em> is typically the
|
||
chemical name of an element, which you must assign to each type via the
|
||
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify element</span></a> command. More generally, it can
|
||
be any string you wish to associated with an atom type. <em>Mass</em> is the atom
|
||
mass. The quantities <em>vx</em>, <em>vy</em>, <em>vz</em>, <em>fx</em>, <em>fy</em>, <em>fz</em>, and <em>q</em> are
|
||
components of atom velocity and force and atomic charge.</p>
|
||
<p>There are several options for outputting atom coordinates. The <em>x</em>,
|
||
<em>y</em>, and <em>z</em> attributes write atom coordinates “unscaled”, in the
|
||
appropriate distance <a class="reference internal" href="units.html"><span class="doc">units</span></a> (<span class="math notranslate nohighlight">\(\AA\)</span>,
|
||
<span class="math notranslate nohighlight">\(\sigma\)</span>, etc.). Use <em>xs</em>, <em>ys</em>, and <em>zs</em> if you want the
|
||
coordinates “scaled” to the box size so that each value is 0.0 to 1.0.
|
||
If the simulation box is triclinic (tilted), then all atom coords will
|
||
still be between 0.0 and 1.0. The actual unscaled <span class="math notranslate nohighlight">\((x,y,z)\)</span>
|
||
coordinate is <span class="math notranslate nohighlight">\(x_s a + y_s b + z_s c\)</span>, where <span class="math notranslate nohighlight">\((a,b,c)\)</span> are
|
||
the non-orthogonal vectors of the simulation box edges, as discussed on
|
||
the <a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto triclinic</span></a> page.</p>
|
||
<p>Use <em>xu</em>, <em>yu</em>, and <em>zu</em> if you want the coordinates “unwrapped” by the
|
||
image flags for each atom. Unwrapped means that if the atom has passed
|
||
through a periodic boundary one or more times, the value is printed for
|
||
what the coordinate would be if it had not been wrapped back into the
|
||
periodic box. Note that using <em>xu</em>, <em>yu</em>, and <em>zu</em> means that the
|
||
coordinate values may be far outside the box bounds printed with the
|
||
snapshot. Using <em>xsu</em>, <em>ysu</em>, and <em>zsu</em> is similar to using <em>xu</em>, <em>yu</em>,
|
||
and <em>zu</em>, except that the unwrapped coordinates are scaled by the box
|
||
size. Atoms that have passed through a periodic boundary will have the
|
||
corresponding coordinate increased or decreased by 1.0.</p>
|
||
<p>The image flags can be printed directly using the <em>ix</em>, <em>iy</em>, and <em>iz</em>
|
||
attributes. For periodic dimensions, they specify which image of the
|
||
simulation box the atom is considered to be in. An image of 0 means
|
||
it is inside the box as defined. A value of 2 means add 2 box lengths
|
||
to get the true value. A value of <span class="math notranslate nohighlight">\(-1\)</span> means subtract 1 box length to
|
||
get the true value. LAMMPS updates these flags as atoms cross
|
||
periodic boundaries during the simulation.</p>
|
||
<p>The <em>mux</em>, <em>muy</em>, and <em>muz</em> attributes are specific to dipolar systems
|
||
defined with an atom style of <em>dipole</em>. They give the orientation of
|
||
the atom’s point dipole moment. The <em>mu</em> attribute gives the magnitude
|
||
of the atom’s dipole moment.</p>
|
||
<p>The <em>radius</em> and <em>diameter</em> attributes are specific to spherical
|
||
particles that have a finite size, such as those defined with an atom
|
||
style of <em>sphere</em>.</p>
|
||
<p>The <em>omegax</em>, <em>omegay</em>, and <em>omegaz</em> attributes are specific to
|
||
finite-size spherical particles that have an angular velocity. Only
|
||
certain atom styles, such as <em>sphere</em>, define this quantity.</p>
|
||
<p>The <em>angmomx</em>, <em>angmomy</em>, and <em>angmomz</em> attributes are specific to
|
||
finite-size aspherical particles that have an angular momentum. Only
|
||
the <em>ellipsoid</em> atom style defines this quantity.</p>
|
||
<p>The <em>tqx</em>, <em>tqy</em>, and <em>tqz</em> attributes are for finite-size particles
|
||
that can sustain a rotational torque due to interactions with other
|
||
particles.</p>
|
||
<p>The <em>c_ID</em> and <em>c_ID[I]</em> attributes allow per-atom vectors or arrays
|
||
calculated by a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> to be output. The ID in the
|
||
attribute should be replaced by the actual ID of the compute that has
|
||
been defined previously in the input script. See the <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command for details. There are computes for calculating the
|
||
per-atom energy, stress, centro-symmetry parameter, and coordination
|
||
number of individual atoms.</p>
|
||
<p>Note that computes which calculate global or local quantities, as
|
||
opposed to per-atom quantities, cannot be output in a dump custom
|
||
command. Instead, global quantities can be output by the
|
||
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command, and local quantities
|
||
can be output by the dump local command.</p>
|
||
<p>If <em>c_ID</em> is used as a attribute, then the per-atom vector calculated by
|
||
the compute is printed. If <em>c_ID[i]</em> is used, then <span class="math notranslate nohighlight">\(i\)</span> must be in
|
||
the range from 1 to <span class="math notranslate nohighlight">\(M\)</span>, which will print the <span class="math notranslate nohighlight">\(i\)</span>th column
|
||
of the per-atom array with <span class="math notranslate nohighlight">\(M\)</span> columns calculated by the compute.
|
||
See the discussion above for how <span class="math notranslate nohighlight">\(i\)</span> can be specified with a
|
||
wildcard asterisk to effectively specify multiple values.</p>
|
||
<p>The <em>f_ID</em> and <em>f_ID[I]</em> attributes allow vector or array per-atom
|
||
quantities calculated by a <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> to be output. The ID in the
|
||
attribute should be replaced by the actual ID of the fix that has been
|
||
defined previously in the input script. The <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a> command is one that calculates per-atom quantities.
|
||
Since it can time-average per-atom quantities produced by any
|
||
<a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix.html"><span class="doc">fix</span></a>, or atom-style <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>, this allows those time-averaged results to be written to a
|
||
dump file.</p>
|
||
<p>If <em>f_ID</em> is used as a attribute, then the per-atom vector calculated by
|
||
the fix is printed. If <em>f_ID[i]</em> is used, then <span class="math notranslate nohighlight">\(i\)</span> must be in the
|
||
range from 1 to <span class="math notranslate nohighlight">\(M\)</span>, which will print the <span class="math notranslate nohighlight">\(i\)</span>th column of
|
||
the per-atom array with <span class="math notranslate nohighlight">\(M\)</span> columns calculated by the fix. See
|
||
the discussion above for how <span class="math notranslate nohighlight">\(i\)</span> can be specified with a wildcard
|
||
asterisk to effectively specify multiple values.</p>
|
||
<p>The <em>v_name</em> attribute allows per-atom vectors calculated by a
|
||
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a> to be output. The name in the attribute
|
||
should be replaced by the actual name of the variable that has been
|
||
defined previously in the input script. Only an atom-style variable can
|
||
be referenced, since it is the only style that generates per-atom
|
||
values. Variables of style <em>atom</em> can reference individual atom
|
||
attributes, per-atom attributes, thermodynamic keywords, or invoke other
|
||
computes, fixes, or variables when they are evaluated, so this is a very
|
||
general means of creating quantities to output to a dump file.</p>
|
||
<p>The <em>i_name</em>, <em>d_name</em>, <em>i2_name</em>, <em>d2_name</em> attributes refer to
|
||
custom per-atom integer and floating-point vectors or arrays that have
|
||
been added via the <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a>
|
||
command. When that command is used specific names are given to each
|
||
attribute which are the “name” portion of these keywords. For arrays
|
||
<em>i2_name</em> and <em>d2_name</em>, the column of the array must also be included
|
||
following the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where
|
||
<span class="math notranslate nohighlight">\(i\)</span> is in the range from 1 to <span class="math notranslate nohighlight">\(M\)</span>, where <span class="math notranslate nohighlight">\(M\)</span> is the
|
||
number of columns in the custom array). See the discussion above for
|
||
how <span class="math notranslate nohighlight">\(i\)</span> can be specified with a wildcard asterisk to effectively
|
||
specify multiple values.</p>
|
||
<p>See the <a class="reference internal" href="Modify.html"><span class="doc">Modify</span></a> page for information on how to add
|
||
new compute and fix styles to LAMMPS to calculate per-atom quantities
|
||
which could then be output into dump files.</p>
|
||
<hr class="docutils" />
|
||
<p>Attributes used as arguments to the <em>local</em> style:</p>
|
||
<p>The <em>index</em> attribute can be used to generate an index number from 1
|
||
to N for each line written into the dump file, where N is the total
|
||
number of local datums from all processors, or lines of output that
|
||
will appear in the snapshot. Note that because data from different
|
||
processors depend on what atoms they currently own, and atoms migrate
|
||
between processor, there is no guarantee that the same index will be
|
||
used for the same info (e.g. a particular bond) in successive
|
||
snapshots.</p>
|
||
<p>The <em>c_ID</em> and <em>c_ID[I]</em> attributes allow local vectors or arrays
|
||
calculated by a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> to be output. The ID in the
|
||
attribute should be replaced by the actual ID of the compute that has
|
||
been defined previously in the input script. See the
|
||
<a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command for details. There are computes for
|
||
calculating local information such as indices, types, and energies for
|
||
bonds and angles.</p>
|
||
<p>Note that computes which calculate global or per-atom quantities, as
|
||
opposed to local quantities, cannot be output in a dump local command.
|
||
Instead, global quantities can be output by the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style
|
||
custom</span></a> command, and per-atom quantities can be output
|
||
by the dump custom command.</p>
|
||
<p>If <em>c_ID</em> is used as a attribute, then the local vector calculated by
|
||
the compute is printed. If <em>c_ID[I]</em> is used, then I must be in the
|
||
range from 1-M, which will print the Ith column of the local array
|
||
with M columns calculated by the compute. See the discussion above
|
||
for how I can be specified with a wildcard asterisk to effectively
|
||
specify multiple values.</p>
|
||
<p>The <em>f_ID</em> and <em>f_ID[I]</em> attributes allow local vectors or arrays
|
||
calculated by a <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> to be output. The ID in the attribute
|
||
should be replaced by the actual ID of the fix that has been defined
|
||
previously in the input script.</p>
|
||
<p>If <em>f_ID</em> is used as a attribute, then the local vector calculated by
|
||
the fix is printed. If <em>f_ID[I]</em> is used, then I must be in the
|
||
range from 1-M, which will print the Ith column of the local with M
|
||
columns calculated by the fix. See the discussion above for how I can
|
||
be specified with a wildcard asterisk to effectively specify multiple
|
||
values.</p>
|
||
<p>Here is an example of how to dump bond info for a system, including
|
||
the distance and energy of each bond:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">compute </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">property</span><span class="o">/</span><span class="n">local</span><span class="w"> </span><span class="n">batom1</span><span class="w"> </span><span class="n">batom2</span><span class="w"> </span><span class="n">btype</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">2</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">bond</span><span class="o">/</span><span class="n">local</span><span class="w"> </span><span class="n">dist</span><span class="w"> </span><span class="n">eng</span>
|
||
<span class="k">dump </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">local</span><span class="w"> </span><span class="m">1000</span><span class="w"> </span><span class="n">tmp.dump</span><span class="w"> </span><span class="n">index</span><span class="w"> </span><span class="n">c_1[1]</span><span class="w"> </span><span class="n">c_1[2]</span><span class="w"> </span><span class="n">c_1[3]</span><span class="w"> </span><span class="n">c_2[1]</span><span class="w"> </span><span class="n">c_2[2]</span>
|
||
</pre></div>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>Attributes used as arguments to the <em>grid</em> and <em>grid/vtk</em> styles:</p>
|
||
<p>The attributes that begin with <em>c_ID</em> and <em>f_ID</em> both take
|
||
colon-separated fields <em>gname</em> and <em>dname</em>. These refer to a grid
|
||
name and data field name which is defined by the compute or fix. Note
|
||
that a compute or fix can define one or more grids (of different
|
||
sizes) and one or more data fields for each of those grids. The sizes
|
||
of all grids output in a single dump grid command must be the same.</p>
|
||
<p>The <em>c_ID:gname:dname</em> and <em>c_ID:gname:dname[I]</em> attributes allow
|
||
per-grid vectors or arrays calculated by a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> to
|
||
be output. The ID in the attribute should be replaced by the actual
|
||
ID of the compute that has been defined previously in the input
|
||
script.</p>
|
||
<p>If <em>c_ID:gname:dname</em> is used as a attribute, then the per-grid vector
|
||
calculated by the compute is printed. If <em>c_ID:gname:dname[I]</em> is
|
||
used, then I must be in the range from 1-M, which will print the Ith
|
||
column of the per-grid array with M columns calculated by the compute.
|
||
See the discussion above for how I can be specified with a wildcard
|
||
asterisk to effectively specify multiple values.</p>
|
||
<p>The <em>f_ID:gname:dname</em> and <em>f_ID:gname:dname[I]</em> attributes allow
|
||
per-grid vectors or arrays calculated by a <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> to be
|
||
output. The ID in the attribute should be replaced by the actual ID
|
||
of the fix that has been defined previously in the input script.</p>
|
||
<p>If <em>f_ID:gname:dname</em> is used as a attribute, then the per-grid vector
|
||
calculated by the fix is printed. If <em>f_ID:gname:dname[I]</em> is used,
|
||
then I must be in the range from 1-M, which will print the Ith column
|
||
of the per-grid with M columns calculated by the fix. See the
|
||
discussion above for how I can be specified with a wildcard asterisk
|
||
to effectively specify multiple values.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>To write gzipped dump files, you must either compile LAMMPS with the
|
||
-DLAMMPS_GZIP option or use the styles from the COMPRESS package.
|
||
See the <a class="reference internal" href="Build_settings.html"><span class="doc">Build settings</span></a> page for details.</p>
|
||
<p>While a dump command is active (i.e., has not been stopped by using
|
||
the <a class="reference internal" href="undump.html"><span class="doc">undump command</span></a>), no commands may be used that will
|
||
change the timestep (e.g., <a class="reference internal" href="reset_timestep.html"><span class="doc">reset_timestep</span></a>).
|
||
LAMMPS will terminate with an error otherwise.</p>
|
||
<p>The <em>atom/gz</em>, <em>cfg/gz</em>, <em>custom/gz</em>, and <em>xyz/gz</em> styles are part of
|
||
the COMPRESS package. They are only enabled if LAMMPS was built with
|
||
that package. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for
|
||
more info.</p>
|
||
<p>The <em>xtc</em>, <em>dcd</em>, and <em>yaml</em> styles are part of the EXTRA-DUMP package.
|
||
They are only enabled if LAMMPS was built with that package. See the
|
||
<a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info.</p>
|
||
</section>
|
||
<section id="related-commands">
|
||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
|
||
<p><a class="reference internal" href="dump_adios.html"><span class="doc">dump atom/adios</span></a>, <a class="reference internal" href="dump_adios.html"><span class="doc">dump custom/adios</span></a>,
|
||
<a class="reference internal" href="dump_cfg_uef.html"><span class="doc">dump cfg/uef</span></a>, <a class="reference internal" href="dump_h5md.html"><span class="doc">dump h5md</span></a>,
|
||
<a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a>, <a class="reference internal" href="dump_molfile.html"><span class="doc">dump molfile</span></a>,
|
||
<a class="reference internal" href="dump_netcdf.html"><span class="doc">dump netcdf</span></a>, <a class="reference internal" href="dump_netcdf.html"><span class="doc">dump netcdf/mpiio</span></a>,
|
||
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a>, <a class="reference internal" href="undump.html"><span class="doc">undump</span></a>,
|
||
<a class="reference internal" href="write_dump.html"><span class="doc">write_dump</span></a></p>
|
||
</section>
|
||
<section id="default">
|
||
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
||
<p>The defaults for the <em>image</em> and <em>movie</em> styles are listed on the
|
||
<a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> page.</p>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
|
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<a href="dumps.html" class="btn btn-neutral float-left" title="Dump Styles" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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|
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|
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