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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<div class="section" id="dump-command">
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<span id="index-0"></span><h1>dump command<a class="headerlink" href="#dump-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="dump-custom-vtk-command">
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<h1><a class="reference internal" href="dump_custom_vtk.html"><em>dump custom/vtk</em></a> command<a class="headerlink" href="#dump-custom-vtk-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="dump-h5md-command">
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<h1><a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a> command<a class="headerlink" href="#dump-h5md-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="dump-image-command">
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<h1><a class="reference internal" href="dump_image.html"><em>dump image</em></a> command<a class="headerlink" href="#dump-image-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="dump-movie-command">
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<h1><a class="reference internal" href="dump_image.html"><em>dump movie</em></a> command<a class="headerlink" href="#dump-movie-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="dump-molfile-command">
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<h1><a class="reference internal" href="dump_molfile.html"><em>dump molfile</em></a> command<a class="headerlink" href="#dump-molfile-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>dump ID group-ID style N file args
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID = user-assigned name for the dump</li>
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<li>group-ID = ID of the group of atoms to be dumped</li>
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<li>style = <em>atom</em> or <em>atom/gz</em> or <em>atom/mpiio</em> or <em>cfg</em> or <em>cfg/gz</em> or <em>cfg/mpiio</em> or <em>dcd</em> or <em>xtc</em> or <em>xyz</em> or <em>xyz/gz</em> or <em>xyz/mpiio</em> or <em>h5md</em> or <em>image</em> or <em>movie</em> or <em>molfile</em> or <em>local</em> or <em>custom</em> or <em>custom/gz</em> or <em>custom/mpiio</em></li>
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<li>N = dump every this many timesteps</li>
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<li>file = name of file to write dump info to</li>
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<li>args = list of arguments for a particular style</li>
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</ul>
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<pre class="literal-block">
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<em>atom</em> args = none
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<em>atom/gz</em> args = none
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<em>atom/mpiio</em> args = none
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<em>cfg</em> args = same as <em>custom</em> args, see below
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<em>cfg/gz</em> args = same as <em>custom</em> args, see below
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<em>cfg/mpiio</em> args = same as <em>custom</em> args, see below
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<em>dcd</em> args = none
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<em>xtc</em> args = none
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<em>xyz</em> args = none
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</pre>
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<pre class="literal-block">
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<em>xyz/gz</em> args = none
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</pre>
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<pre class="literal-block">
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<em>xyz/mpiio</em> args = none
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</pre>
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<pre class="literal-block">
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<em>custom/vtk</em> args = similar to custom args below, discussed on <a class="reference internal" href="dump_custom_vtk.html"><em>dump custom/vtk</em></a> doc page
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</pre>
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<pre class="literal-block">
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<em>h5md</em> args = discussed on <a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a> doc page
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</pre>
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<pre class="literal-block">
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<em>image</em> args = discussed on <a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page
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</pre>
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<pre class="literal-block">
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<em>movie</em> args = discussed on <a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page
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</pre>
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<pre class="literal-block">
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<em>molfile</em> args = discussed on <a class="reference internal" href="dump_molfile.html"><em>dump molfile</em></a> doc page
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</pre>
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<pre class="literal-block">
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<em>local</em> args = list of local attributes
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possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N]
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index = enumeration of local values
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c_ID = local vector calculated by a compute with ID
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c_ID[N] = Nth column of local array calculated by a compute with ID
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f_ID = local vector calculated by a fix with ID
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f_ID[N] = Nth column of local array calculated by a fix with ID
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</pre>
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<pre class="literal-block">
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<em>custom</em> or <em>custom/gz</em> or <em>custom/mpiio</em> args = list of atom attributes
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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,
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vx, vy, vz, fx, fy, fz,
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q, mux, muy, muz, mu,
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radius, diameter, omegax, omegay, omegaz,
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angmomx, angmomy, angmomz, tqx, tqy, tqz,
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c_ID, c_ID[N], f_ID, f_ID[N], v_name
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</pre>
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<pre class="literal-block">
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id = atom ID
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mol = molecule ID
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proc = ID of processor that owns atom
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procp1 = ID+1 of processor that owns atom
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type = atom type
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element = name of atom element, as defined by <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command
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mass = atom mass
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x,y,z = unscaled atom coordinates
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xs,ys,zs = scaled atom coordinates
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xu,yu,zu = unwrapped atom coordinates
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xsu,ysu,zsu = scaled unwrapped atom coordinates
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ix,iy,iz = box image that the atom is in
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vx,vy,vz = atom velocities
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fx,fy,fz = forces on atoms
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q = atom charge
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mux,muy,muz = orientation of dipole moment of atom
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mu = magnitude of dipole moment of atom
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radius,diameter = radius,diameter of spherical particle
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omegax,omegay,omegaz = angular velocity of spherical particle
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angmomx,angmomy,angmomz = angular momentum of aspherical particle
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tqx,tqy,tqz = torque on finite-size particles
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c_ID = per-atom vector calculated by a compute with ID
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c_ID[N] = Nth column of per-atom array calculated by a compute with ID
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f_ID = per-atom vector calculated by a fix with ID
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f_ID[N] = Nth column of per-atom array calculated by a fix with ID
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v_name = per-atom vector calculated by an atom-style variable with name
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d_name = per-atom floating point vector with name, managed by fix property/atom
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i_name = per-atom integer vector with name, managed by fix property/atom
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>dump myDump all atom 100 dump.atom
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dump myDump all atom/mpiio 100 dump.atom.mpiio
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dump myDump all atom/gz 100 dump.atom.gz
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dump 2 subgroup atom 50 dump.run.bin
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dump 2 subgroup atom 50 dump.run.mpiio.bin
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dump 4a all custom 100 dump.myforce.* id type x y vx fx
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dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
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dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
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dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
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dump 1 all xtc 1000 file.xtc
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Dump a snapshot of atom quantities to one or more files every N
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timesteps in one of several styles. The <em>image</em> and <em>movie</em> styles are
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the exception: the <em>image</em> style renders a JPG, PNG, or PPM image file
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of the atom configuration every N timesteps while the <em>movie</em> style
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combines and compresses them into a movie file; both are discussed in
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detail on the <a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page. The timesteps on
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which dump output is written can also be controlled by a variable.
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See the <a class="reference internal" href="dump_modify.html"><em>dump_modify every</em></a> command.</p>
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<p>Only information for atoms in the specified group is dumped. The
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<a class="reference internal" href="dump_modify.html"><em>dump_modify thresh and region</em></a> commands can also
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alter what atoms are included. Not all styles support all these
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options; see details below.</p>
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<p>As described below, the filename determines the kind of output (text
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or binary or gzipped, one big file or one per timestep, one big file
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or multiple smaller files).</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Because periodic boundary conditions are enforced only on
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timesteps when neighbor lists are rebuilt, the coordinates of an atom
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written to a dump file may be slightly outside the simulation box.</p>
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</div>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Unless the <a class="reference internal" href="dump_modify.html"><em>dump_modify sort</em></a> option is
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invoked, the lines of atom information written to dump files
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(typically one line per atom) will be in an indeterminate order for
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each snapshot. This is even true when running on a single processor,
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if the <a class="reference internal" href="atom_modify.html"><em>atom_modify sort</em></a> option is on, which it is
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by default. In this case atoms are re-ordered periodically during a
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simulation, due to spatial sorting. It is also true when running in
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parallel, because data for a single snapshot is collected from
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multiple processors, each of which owns a subset of the atoms.</p>
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</div>
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<p>For the <em>atom</em>, <em>custom</em>, <em>cfg</em>, and <em>local</em> styles, sorting is off by
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default. For the <em>dcd</em>, <em>xtc</em>, <em>xyz</em>, and <em>molfile</em> styles, sorting by
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atom ID is on by default. See the <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> doc
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page for details.</p>
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<p>The <em>atom/gz</em>, <em>cfg/gz</em>, <em>custom/gz</em>, and <em>xyz/gz</em> styles are identical
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in command syntax to the corresponding styles without “gz”, however,
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they generate compressed files using the zlib library. Thus the filename
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suffix ”.gz” is mandatory. This is an alternative approach to writing
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compressed files via a pipe, as done by the regular dump styles, which
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may be required on clusters where the interface to the high-speed network
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disallows using the fork() library call (which is needed for a pipe).
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For the remainder of this doc page, you should thus consider the <em>atom</em>
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and <em>atom/gz</em> styles (etc) to be inter-changeable, with the exception
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of the required filename suffix.</p>
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<p>As explained below, the <em>atom/mpiio</em>, <em>cfg/mpiio</em>, <em>custom/mpiio</em>, and
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<em>xyz/mpiio</em> styles are identical in command syntax and in the format
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of the dump files they create, to the corresponding styles without
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“mpiio”, except the single dump file they produce is written in
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parallel via the MPI-IO library. For the remainder of this doc page,
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you should thus consider the <em>atom</em> and <em>atom/mpiio</em> styles (etc) to
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be inter-changeable. The one exception is how the filename is
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specified for the MPI-IO styles, as explained below.</p>
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<hr class="docutils" />
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<p>The <em>style</em> keyword determines what atom quantities are written to the
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file and in what format. Settings made via the
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<a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command can also alter the format of
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individual values and the file itself.</p>
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<p>The <em>atom</em>, <em>local</em>, and <em>custom</em> styles create files in a simple text
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format that is self-explanatory when viewing a dump file. Many of the
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LAMMPS <a class="reference internal" href="Section_tools.html"><em>post-processing tools</em></a>, including
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<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a>, work with this
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format, as does the <a class="reference internal" href="rerun.html"><em>rerun</em></a> command.</p>
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<p>For post-processing purposes the <em>atom</em>, <em>local</em>, and <em>custom</em> text
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files are self-describing in the following sense.</p>
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<p>The dimensions of the simulation box are included in each snapshot.
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For an orthogonal simulation box this information is is formatted as:</p>
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<div class="highlight-python"><div class="highlight"><pre>ITEM: BOX BOUNDS xx yy zz
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xlo xhi
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ylo yhi
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zlo zhi
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</pre></div>
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</div>
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<p>where xlo,xhi are the maximum extents of the simulation box in the
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x-dimension, and similarly for y and z. The “xx yy zz” represent 6
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characters that encode the style of boundary for each of the 6
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simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi). Each of
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the 6 characters is either p = periodic, f = fixed, s = shrink wrap,
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or m = shrink wrapped with a minimum value. See the
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<a class="reference internal" href="boundary.html"><em>boundary</em></a> command for details.</p>
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<p>For triclinic simulation boxes (non-orthogonal), an orthogonal
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bounding box which encloses the triclinic simulation box is output,
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along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
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formatted as follows:</p>
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<div class="highlight-python"><div class="highlight"><pre>ITEM: BOX BOUNDS xy xz yz xx yy zz
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xlo_bound xhi_bound xy
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ylo_bound yhi_bound xz
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zlo_bound zhi_bound yz
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</pre></div>
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</div>
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<p>The presence of the text “xy xz yz” in the ITEM line indicates that
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the 3 tilt factors will be included on each of the 3 following lines.
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This bounding box is convenient for many visualization programs. The
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meaning of the 6 character flags for “xx yy zz” is the same as above.</p>
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<p>Note that the first two numbers on each line are now xlo_bound instead
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of xlo, etc, since they repesent a bounding box. See <a class="reference internal" href="Section_howto.html#howto-12"><span>this section</span></a> of the doc pages for a geometric
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description of triclinic boxes, as defined by LAMMPS, simple formulas
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for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
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calculated from the triclinic parameters, and how to transform those
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parameters to and from other commonly used triclinic representations.</p>
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<p>The “ITEM: ATOMS” line in each snapshot lists column descriptors for
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the per-atom lines that follow. For example, the descriptors would be
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“id type xs ys zs” for the default <em>atom</em> style, and would be the atom
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attributes you specify in the dump command for the <em>custom</em> style.</p>
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<p>For style <em>atom</em>, atom coordinates are written to the file, along with
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the atom ID and atom type. By default, atom coords are written in a
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scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom
|
|
is at a location 1/4 of the distance from xlo to xhi of the box
|
|
boundaries. The format can be changed to unscaled coords via the
|
|
<a class="reference internal" href="dump_modify.html"><em>dump_modify</em></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 doesn’t
|
|
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>
|
|
<p>For style <em>local</em>, local output generated by <a class="reference internal" href="compute.html"><em>computes</em></a>
|
|
and <a class="reference internal" href="fix.html"><em>fixes</em></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"><em>compute property/local</em></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"><em>read_data</em></a> command.</p>
|
|
<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://mt.seas.upenn.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"><em>dump_modify element</em></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"><em>dump_modify</em></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="http://manual.gromacs.org/current/online/xtc.html">here</a>.
|
|
The precision used in XTC files can be adjusted via the
|
|
<a class="reference internal" href="dump_modify.html"><em>dump_modify</em></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"><em>dump_modify</em></a> command allows
|
|
XTC coordinates to be written “unwrapped” by the image flags for each
|
|
atom. Unwrapped means that if the atom has passed thru 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 x-, y-, and z-coordinate of that atom. You can use the
|
|
<a class="reference internal" href="dump_modify.html"><em>dump_modify element</em></a> option to change the output
|
|
from using the (numerical) atom type to an element name (or some
|
|
other label). This will help many visualization programs to guess
|
|
bonds and colors.</p>
|
|
<p>Note that <em>atom</em>, <em>custom</em>, <em>dcd</em>, <em>xtc</em>, and <em>xyz</em> style dump files
|
|
can be read directly by <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a>, a
|
|
popular molecular viewing program. See <a class="reference internal" href="Section_tools.html#vmd"><span>Section tools</span></a> of the manual and the
|
|
tools/lmp2vmd/README.txt file for more information about support in
|
|
VMD for reading and visualizing LAMMPS dump files.</p>
|
|
<hr class="docutils" />
|
|
<p>Dumps are performed on timesteps that are a multiple of N (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 N. This behavior can be
|
|
changed via the <a class="reference internal" href="dump_modify.html"><em>dump_modify first</em></a> command, which
|
|
can also be useful if the dump command is invoked after a minimization
|
|
ended on an arbitrary timestep. N can be changed between runs by
|
|
using the <a class="reference internal" href="dump_modify.html"><em>dump_modify every</em></a> command (not allowed
|
|
for <em>dcd</em> style). The <a class="reference internal" href="dump_modify.html"><em>dump_modify every</em></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"><em>dump_modify first</em></a> command is used.</p>
|
|
<p>The specified 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"><em>undump</em></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>Dump filenames can contain 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"><em>dump_modify pad</em></a>
|
|
command can be used to insure 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 0 to P-1. For example, tmp.dump.% becomes
|
|
tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, 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 not available for the
|
|
<em>dcd</em>, <em>xtc</em>, and <em>xyz</em> styles.</p>
|
|
<p>By default, P = the number of processors meaning one file per
|
|
processor, but P 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"><em>dump_modify</em></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>
|
|
<p>For the <em>atom/mpiio</em>, <em>cfg/mpiio</em>, <em>custom/mpiio</em>, and <em>xyz/mpiio</em>
|
|
styles, a single dump file is written in parallel via the MPI-IO
|
|
library, which is part of the MPI standard for versions 2.0 and above.
|
|
Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO
|
|
package installed, e.g.</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-mpiio # installs the MPIIO package
|
|
make g++ # build LAMMPS for your platform
|
|
</pre></div>
|
|
</div>
|
|
<p>Second, use a dump filename which contains ”.mpiio”. Note that it
|
|
does not have to end in ”.mpiio”, just contain those characters.
|
|
Unlike MPI-IO restart files, which must be both written and read using
|
|
MPI-IO, the dump files produced by these MPI-IO styles are identical
|
|
in format to the files produced by their non-MPI-IO style
|
|
counterparts. This means you can write a dump file using MPI-IO and
|
|
use the <a class="reference internal" href="read_dump.html"><em>read_dump</em></a> command or perform other
|
|
post-processing, just as if the dump file was not written using
|
|
MPI-IO.</p>
|
|
<p>Note that MPI-IO dump files are one large file which all processors
|
|
write to. You thus cannot use the “%” wildcard character described
|
|
above in the filename since that specifies generation of multiple
|
|
files. You can use the ”.bin” suffix described below in an MPI-IO
|
|
dump file; again this file will be written in parallel and have the
|
|
same binary format as if it were written without MPI-IO.</p>
|
|
<p>If the filename ends with ”.bin”, 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="Section_tools.html#binary"><span>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 tools/binary2txt.cpp 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 3x 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>
|
|
<hr class="docutils" />
|
|
<p>This section explains the local attributes that can be specified as
|
|
part of 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[N]</em> attributes allow local vectors or arrays
|
|
calculated by a <a class="reference internal" href="compute.html"><em>compute</em></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"><em>compute</em></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"><em>thermo_style custom</em></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[N]</em> is used, then N must be in the
|
|
range from 1-M, which will print the Nth column of the M-length local
|
|
array calculated by the compute.</p>
|
|
<p>The <em>f_ID</em> and <em>f_ID[N]</em> attributes allow local vectors or arrays
|
|
calculated by a <a class="reference internal" href="fix.html"><em>fix</em></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[N]</em> is used, then N must be in the
|
|
range from 1-M, which will print the Nth column of the M-length local
|
|
array calculated by the fix.</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-python"><div class="highlight"><pre>compute 1 all property/local batom1 batom2 btype
|
|
compute 2 all bond/local dist eng
|
|
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
|
|
</pre></div>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>This section explains the atom attributes that can be specified as
|
|
part of 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>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
|
|
Nprocs-1) 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 Ntypes)
|
|
for coloring atoms in a visualization program. <em>Type</em> is the atom
|
|
type (1 to Ntypes). <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"><em>dump_modify element</em></a> command. More generally, it can be any
|
|
string you wish to associated with an atom type. <em>Mass</em> is the atom
|
|
mass. <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>, <em>z</em> attributes write atom coordinates “unscaled”, in the
|
|
appropriate distance <a class="reference internal" href="units.html"><em>units</em></a> (Angstroms, sigma, etc). Use
|
|
<em>xs</em>, <em>ys</em>, <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. Use
|
|
<em>xu</em>, <em>yu</em>, <em>zu</em> if you want the coordinates “unwrapped” by the image
|
|
flags for each atom. Unwrapped means that if the atom has passed thru
|
|
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>, <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>, <em>zsu</em> is similar to using <em>xu</em>, <em>yu</em>, <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
|
|
cooordinate increased or decreased by 1.0.</p>
|
|
<p>The image flags can be printed directly using the <em>ix</em>, <em>iy</em>, <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 -1 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>, <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>, <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[N]</em> attributes allow per-atom vectors or arrays
|
|
calculated by a <a class="reference internal" href="compute.html"><em>compute</em></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"><em>compute</em></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"><em>thermo_style custom</em></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[N]</em> is used, then N must be in
|
|
the range from 1-M, which will print the Nth column of the M-length
|
|
per-atom array calculated by the compute.</p>
|
|
<p>The <em>f_ID</em> and <em>f_ID[N]</em> attributes allow vector or array per-atom
|
|
quantities calculated by a <a class="reference internal" href="fix.html"><em>fix</em></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"><em>fix ave/atom</em></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"><em>compute</em></a>, <a class="reference internal" href="fix.html"><em>fix</em></a>, or atom-style
|
|
<a class="reference internal" href="variable.html"><em>variable</em></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[N]</em> is used, then N must be in the
|
|
range from 1-M, which will print the Nth column of the M-length
|
|
per-atom array calculated by the fix.</p>
|
|
<p>The <em>v_name</em> attribute allows per-atom vectors calculated by a
|
|
<a class="reference internal" href="variable.html"><em>variable</em></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 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>d_name</em> and <em>i_name</em> attributes allow to output custom per atom
|
|
floating point or integer properties that are managed by
|
|
<a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a>.</p>
|
|
<p>See <a class="reference internal" href="Section_modify.html"><em>Section_modify</em></a> of the manual 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>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</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="Section_start.html#start-2"><span>Making LAMMPS</span></a> section of
|
|
the documentation.</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="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
|
|
<p>The <em>atom/mpiio</em>, <em>cfg/mpiio</em>, <em>custom/mpiio</em>, and <em>xyz/mpiio</em> styles
|
|
are part of the MPIIO package. They are only enabled if LAMMPS was
|
|
built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
|
|
<p>The <em>xtc</em> style is part of the MISC package. It is only enabled if
|
|
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info. This is
|
|
because some machines may not support the low-level XDR data format
|
|
that XTC files are written with, which will result in a compile-time
|
|
error when a low-level include file is not found. Putting this style
|
|
in a package makes it easy to exclude from a LAMMPS build for those
|
|
machines. However, the MISC package also includes two compatibility
|
|
header files and associated functions, which should be a suitable
|
|
substitute on machines that do not have the appropriate native header
|
|
files. This option can be invoked at build time by adding
|
|
-DLAMMPS_XDR to the CCFLAGS variable in the appropriate low-level
|
|
Makefile, e.g. src/MAKE/Makefile.foo. This compatibility mode has
|
|
been tested successfully on Cray XT3/XT4/XT5 and IBM BlueGene/L
|
|
machines and should also work on IBM BG/P, and Windows XP/Vista/7
|
|
machines.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p><a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a>, <a class="reference internal" href="dump_image.html"><em>dump image</em></a>,
|
|
<a class="reference internal" href="dump_molfile.html"><em>dump molfile</em></a>, <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a>,
|
|
<a class="reference internal" href="undump.html"><em>undump</em></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</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"><em>dump image</em></a> doc page.</p>
|
|
</div>
|
|
</div>
|
|
|
|
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