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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">read_dump command</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_restart.html">read_restart command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="shell.html">shell command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_modify.html">thermo_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timer.html">timer command</a></li>
<li class="toctree-l2"><a class="reference internal" href="timestep.html">timestep command</a></li>
<li class="toctree-l2"><a class="reference internal" href="uncompute.html">uncompute command</a></li>
<li class="toctree-l2"><a class="reference internal" href="undump.html">undump command</a></li>
<li class="toctree-l2"><a class="reference internal" href="unfix.html">unfix command</a></li>
<li class="toctree-l2"><a class="reference internal" href="units.html">units command</a></li>
<li class="toctree-l2"><a class="reference internal" href="variable.html">variable command</a></li>
<li class="toctree-l2"><a class="reference internal" href="velocity.html">velocity command</a></li>
<li class="toctree-l2"><a class="reference internal" href="write_coeff.html">write_coeff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
<li class="toctree-l2"><a class="reference internal" href="write_dump.html">write_dump command</a></li>
<li class="toctree-l2"><a class="reference internal" href="write_restart.html">write_restart command</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
<section id="read-dump-command">
<span id="index-0"></span><h1>read_dump command<a class="headerlink" href="#read-dump-command" title="Link to this heading"></a></h1>
<section id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">read_dump</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="n">Nstep</span><span class="w"> </span><span class="n">field1</span><span class="w"> </span><span class="n">field2</span><span class="w"> </span><span class="n">...</span><span class="w"> </span><span class="n">keyword</span><span class="w"> </span><span class="n">values</span><span class="w"> </span><span class="n">...</span>
</pre></div>
</div>
<ul>
<li><p>file = name of dump file to read</p></li>
<li><p>Nstep = snapshot timestep to read from file</p></li>
<li><p>one or more fields may be appended</p>
<pre class="literal-block">field = <em>x</em> or <em>y</em> or <em>z</em> or <em>vx</em> or <em>vy</em> or <em>vz</em> or <em>q</em> or <em>ix</em> or <em>iy</em> or <em>iz</em> or <em>fx</em> or <em>fy</em> or <em>fz</em>
<em>x</em>,<em>y</em>,<em>z</em> = atom coordinates
<em>vx</em>,<em>vy</em>,<em>vz</em> = velocity components
<em>q</em> = charge
<em>ix</em>,<em>iy</em>,<em>iz</em> = image flags in each dimension
<em>fx</em>,<em>fy</em>,<em>fz</em> = force components</pre>
</li>
<li><p>zero or more keyword/value pairs may be appended</p></li>
<li><p>keyword = <em>nfile</em> or <em>box</em> or <em>timestep</em> or <em>replace</em> or <em>purge</em> or <em>trim</em> or <em>add</em> or <em>label</em> or <em>scaled</em> or <em>wrapped</em> or <em>format</em></p>
<pre class="literal-block"><em>nfile</em> value = Nfiles = how many parallel dump files exist
<em>box</em> value = <em>yes</em> or <em>no</em> = replace simulation box with dump box
<em>timestep</em> value = <em>yes</em> or <em>no</em> = reset simulation timestep with dump timestep
<em>replace</em> value = <em>yes</em> or <em>no</em> = overwrite atoms with dump atoms
<em>purge</em> value = <em>yes</em> or <em>no</em> = delete all atoms before adding dump atoms
<em>trim</em> value = <em>yes</em> or <em>no</em> = trim atoms not in dump snapshot
<em>add</em> value = <em>yes</em> or <em>keep</em> or <em>no</em> = add new dump atoms to system
<em>label</em> value = field column
field = one of the listed fields or <em>id</em> or <em>type</em>
column = label on corresponding column in dump file
<em>scaled</em> value = <em>yes</em> or <em>no</em> = coords in dump file are scaled/unscaled
<em>wrapped</em> value = <em>yes</em> or <em>no</em> = coords in dump file are wrapped/unwrapped
<em>format</em> values = format of dump file, must be last keyword if used
<em>native</em> = native LAMMPS dump file
<em>xyz</em> = XYZ file
<em>adios</em> [<em>timeout</em> value] = dump file written by the <a class="reference internal" href="dump_adios.html"><span class="doc">dump adios</span></a> command
<em>timeout</em> = specify waiting time for the arrival of the timestep when running concurrently.
The value is a float number and is interpreted in seconds.
<em>molfile</em> style path = VMD molfile plugin interface
style = <em>dcd</em> or <em>xyz</em> or others supported by molfile plugins
path = optional path for location of molfile plugins</pre>
</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">read_dump</span><span class="w"> </span><span class="n">dump.file</span><span class="w"> </span><span class="m">5000</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="k">read_dump</span><span class="w"> </span><span class="n">dump.xyz</span><span class="w"> </span><span class="m">5</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">box</span><span class="w"> </span><span class="n">no</span><span class="w"> </span><span class="n">format</span><span class="w"> </span><span class="n">xyz</span>
<span class="k">read_dump</span><span class="w"> </span><span class="n">dump.xyz</span><span class="w"> </span><span class="m">10</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">box</span><span class="w"> </span><span class="n">no</span><span class="w"> </span><span class="n">format</span><span class="w"> </span><span class="n">molfile</span><span class="w"> </span><span class="n">xyz</span><span class="w"> </span><span class="s">&quot;../plugins&quot;</span>
<span class="k">read_dump</span><span class="w"> </span><span class="n">dump.dcd</span><span class="w"> </span><span class="m">0</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">box</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="n">molfile</span><span class="w"> </span><span class="n">dcd</span>
<span class="k">read_dump</span><span class="w"> </span><span class="n">dump.file</span><span class="w"> </span><span class="m">1000</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">box</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="n">molfile</span><span class="w"> </span><span class="n">lammpstrj</span><span class="w"> </span><span class="o">/</span><span class="n">usr</span><span class="o">/</span><span class="n">local</span><span class="o">/</span><span class="n">lib</span><span class="o">/</span><span class="n">vmd</span><span class="o">/</span><span class="n">plugins</span><span class="o">/</span><span class="n">LINUXAMD64</span><span class="o">/</span><span class="n">plugins</span><span class="o">/</span><span class="n">molfile</span>
<span class="k">read_dump</span><span class="w"> </span><span class="n">dump.file</span><span class="w"> </span><span class="m">5000</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">vy</span><span class="w"> </span><span class="n">trim</span><span class="w"> </span><span class="n">yes</span>
<span class="k">read_dump</span><span class="w"> </span><span class="n">dump.file</span><span class="w"> </span><span class="m">5000</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">vy</span><span class="w"> </span><span class="n">add</span><span class="w"> </span><span class="n">yes</span><span class="w"> </span><span class="n">box</span><span class="w"> </span><span class="n">no</span><span class="w"> </span><span class="n">timestep</span><span class="w"> </span><span class="n">no</span>
<span class="k">read_dump</span><span class="w"> </span><span class="n">..</span><span class="o">/</span><span class="n">run7</span><span class="o">/</span><span class="n">dump.file.gz</span><span class="w"> </span><span class="m">10000</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">box</span><span class="w"> </span><span class="n">yes</span>
<span class="k">read_dump</span><span class="w"> </span><span class="n">dump.xyz</span><span class="w"> </span><span class="m">10</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">box</span><span class="w"> </span><span class="n">no</span><span class="w"> </span><span class="n">format</span><span class="w"> </span><span class="n">molfile</span><span class="w"> </span><span class="n">xyz</span><span class="w"> </span><span class="n">..</span><span class="o">/</span><span class="n">plugins</span>
<span class="k">read_dump</span><span class="w"> </span><span class="n">dump.dcd</span><span class="w"> </span><span class="m">0</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">format</span><span class="w"> </span><span class="n">molfile</span><span class="w"> </span><span class="n">dcd</span>
<span class="k">read_dump</span><span class="w"> </span><span class="n">dump.file</span><span class="w"> </span><span class="m">1000</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">format</span><span class="w"> </span><span class="n">molfile</span><span class="w"> </span><span class="n">lammpstrj</span><span class="w"> </span><span class="o">/</span><span class="n">usr</span><span class="o">/</span><span class="n">local</span><span class="o">/</span><span class="n">lib</span><span class="o">/</span><span class="n">vmd</span><span class="o">/</span><span class="n">plugins</span><span class="o">/</span><span class="n">LINUXAMD64</span><span class="o">/</span><span class="n">plugins</span><span class="o">/</span><span class="n">molfile</span>
<span class="k">read_dump</span><span class="w"> </span><span class="n">dump.bp</span><span class="w"> </span><span class="m">5000</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">format</span><span class="w"> </span><span class="n">adios</span>
<span class="k">read_dump</span><span class="w"> </span><span class="n">dump.bp</span><span class="w"> </span><span class="m">5000</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">format</span><span class="w"> </span><span class="n">adios</span><span class="w"> </span><span class="n">timeout</span><span class="w"> </span><span class="m">60.0</span>
</pre></div>
</div>
</section>
<section id="description">
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
<p>Read atom information from a dump file to overwrite the current atom
coordinates, and optionally the atom velocities and image flags, the
simulation timestep, and the simulation box dimensions. This is useful
for restarting a run from a particular snapshot in a dump file. See the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> and <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>
commands for alternative methods to do this. Also see the
<a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command for a means of reading multiple snapshots
from a dump file.</p>
<p>Note that a simulation box must already be defined before using the
read_dump command. This can be done by the
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>, <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, or
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> commands. The read_dump command can
reset the simulation box dimensions, as explained below.</p>
<p>Also note that reading per-atom information from a dump snapshot is
limited to the atom coordinates, velocities and image flags, as
explained below. Other atom properties, which may be necessary to run
a valid simulation, such as atom charge, or bond topology information
for a molecular system, are not read from (or may not even be contained
in) dump files. Thus this auxiliary information should be defined in
the usual way, e.g. in a data file read in by a <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>
command, before using the read_dump command, or by the <a class="reference internal" href="set.html"><span class="doc">set</span></a>
command, after the dump snapshot is read.</p>
<hr class="docutils" />
<p>If the dump filename specified as <em>file</em> ends with “.gz”, the dump
file is read in gzipped format.</p>
<p>You can read dump files that were written (in parallel) to multiple
files via the “%” wild-card character in the dump file name. If any
specified dump file name contains a “%”, they must all contain it.
See the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command for details.
The “%” wild-card character is only supported by the <em>native</em> format
for dump files, described next.</p>
<p>If reading parallel dump files, you must also use the <em>nfile</em> keyword
to tell LAMMPS how many parallel files exist, via its specified
<em>Nfiles</em> value.</p>
<p>The format of the dump file is selected through the <em>format</em> keyword.
If specified, it must be the last keyword used, since all remaining
arguments are passed on to the dump reader. The <em>native</em> format is for
native LAMMPS dump files, written with a <a class="reference internal" href="dump.html"><span class="doc">dump atom</span></a> or
<a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command. The <em>xyz</em> format is for generic XYZ
formatted dump files (see details below). These formats take no
additional values.</p>
<p>The <em>molfile</em> format supports reading data through using the <a class="reference external" href="https://www.ks.uiuc.edu/Research/vmd">VMD</a>
molfile plugin interface. This dump reader format is only available,
if the MOLFILE package has been installed when compiling
LAMMPS.</p>
<p>The <em>molfile</em> format takes one or two additional values. The <em>style</em>
value determines the file format to be used and can be any format that
the molfile plugins support, such as DCD or XYZ. Note that DCD dump
files can be written by LAMMPS via the <a class="reference internal" href="dump.html"><span class="doc">dump dcd</span></a> command.
The <em>path</em> value specifies a list of directories which LAMMPS will
search for the molfile plugins appropriate to the specified <em>style</em>.
The syntax of the <em>path</em> value is like other search paths: it can
contain multiple directories separated by a colon (or semicolon on
windows). The <em>path</em> keyword is optional and defaults to “.”,
i.e. the current directory.</p>
<p>The <em>adios</em> format supports reading data that was written by the
<a class="reference internal" href="dump_adios.html"><span class="doc">dump adios</span></a> command. The
entire dump is read in parallel across all the processes, dividing
the atoms evenly among the processes. The number of writers that
has written the dump file does not matter. Using the adios style for
dump and read_dump is a convenient way to dump all atoms from <em>N</em>
writers and read it back by <em>M</em> readers. If one is running two
LAMMPS instances concurrently where one dumps data and the other is
reading it with the rerun command, the timeout option can be specified
to wait on the reader side for the arrival of the requested step.</p>
<p>Support for other dump format readers may be added in the future.</p>
<hr class="docutils" />
<p>Global information is first read from the dump file, namely timestep
and box information.</p>
<p>The dump file is scanned for a snapshot with a timestamp that matches
the specified <em>Nstep</em>. This means the LAMMPS timestep the dump file
snapshot was written on for the <em>native</em> or <em>adios</em> formats.</p>
<p>The list of timestamps available in an adios .bp file is stored in the
variable <em>ntimestep</em>:</p>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>console
$ bpls dump.bp -d ntimestep
uint64_t ntimestep 5*scalar
(0) 0 50 100 150 200
</pre></div>
</div>
<p>Note that the <em>xyz</em> and <em>molfile</em> formats do not store the timestep.
For these formats, timesteps are numbered logically, in a sequential
manner, starting from 0. Thus to access the 10th snapshot in an <em>xyz</em>
or <em>mofile</em> formatted dump file, use <em>Nstep</em> = 9.</p>
<p>The dimensions of the simulation box for the selected snapshot are
also read; see the <em>box</em> keyword discussion below. For the <em>native</em>
format, an error is generated if the snapshot is for a triclinic box
and the current simulation box is orthogonal or vice versa. A warning
will be generated if the snapshot box boundary conditions (periodic,
shrink-wrapped, etc) do not match the current simulation boundary
conditions, but the boundary condition information in the snapshot is
otherwise ignored. See the “boundary” command for more details. The
<em>adios</em> reader does the same as the <em>native</em> format reader.</p>
<p>For the <em>xyz</em> format, no information about the box is available, so
you must set the <em>box</em> flag to <em>no</em>. See details below.</p>
<p>For the <em>molfile</em> format, reading simulation box information is
typically supported, but the location of the simulation box origin is
lost and no explicit information about periodicity or
orthogonal/triclinic box shape is available. The MOLFILE package
makes a best effort to guess based on heuristics, but this may not
always work perfectly.</p>
<hr class="docutils" />
<p>Per-atom information from the dump file snapshot is then read from the
dump file snapshot. This corresponds to the specified <em>fields</em> listed
in the read_dump command. It is an error to specify a z-dimension
field, namely <em>z</em>, <em>vz</em>, or <em>iz</em>, for a 2d simulation.</p>
<p>For dump files in <em>native</em> format, each column of per-atom data has a
text label listed in the file. A matching label for each field must
appear, e.g. the label “vy” for the field <em>vy</em>. For the <em>x</em>, <em>y</em>, <em>z</em>
fields any of the following labels are considered a match:</p>
<pre class="literal-block">x, xs, xu, xsu for field <em>x</em>
y, ys, yu, ysu for field <em>y</em>
z, zs, zu, zsu for field <em>z</em></pre>
<p>The meaning of xs (scaled), xu (unwrapped), and xsu (scaled and
unwrapped) is explained on the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command doc page.
These labels are searched for in the list of column labels in the dump
file, in order, until a match is found.</p>
<p>The dump file must also contain atom IDs, with a column label of “id”.</p>
<p>If the <em>add</em> keyword is specified with a value of <em>yes</em> or <em>keep</em>, as
discussed below, the dump file must contain atom types, with a column
label of “type”.</p>
<p>If a column label you want to read from the dump file is not a match
to a specified field, the <em>label</em> keyword can be used to specify the
specific column label from the dump file to associate with that field.
An example is if a time-averaged coordinate is written to the dump
file via the <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a> command. The column
will then have a label corresponding to the fix-ID rather than “x” or
“xs”. The <em>label</em> keyword can also be used to specify new column
labels for fields <em>id</em> and <em>type</em>.</p>
<p>For dump files in <em>xyz</em> format, only the <em>type</em>, <em>x</em>, <em>y</em>, and <em>z</em>
fields are supported. There are many variants of the XYZ file format.
LAMMPS will read the number of atoms from the first line of each frame,
ignore the second (title) line, and then read one line for each atom in the format:</p>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>&lt;label&gt; &lt;x coordinate&gt; &lt;y coordinate&gt; &lt;z coordinate&gt;
</pre></div>
</div>
<p>If the atom label is a numeric integer (like with XYZ files created by
created with default settings by <a class="reference internal" href="dump.html"><span class="doc">dump style</span></a> <em>xyz</em>), that
number will be used as the atom type. If the atom label is a string,
then a type map must be created using the <a class="reference internal" href="labelmap.html"><span class="doc">labelmap command</span></a>. This map needs to associate each (numeric) atom type with
a string label. The numeric atom type is stored internally.</p>
<p>The xyz format dump file does not store atom IDs, so these are assigned
consecutively to the atoms as they appear in the dump file, starting
from 1. Thus you should ensure that the order of atoms is consistent
from snapshot to snapshot in the XYZ dump file. See the
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify sort</span></a> command if the XYZ dump file was
written by LAMMPS.</p>
<p>For dump files in <em>molfile</em> format, the <em>x</em>, <em>y</em>, <em>z</em>, <em>vx</em>, <em>vy</em>, and
<em>vz</em> fields can be specified. However, not all molfile formats store
velocities, or their respective plugins may not support reading of
velocities. The molfile dump files do not store atom IDs, so these are
assigned consecutively to the atoms as they appear in the dump file,
starting from 1. Thus you should ensure that the order of atoms are
consistent from snapshot to snapshot in the molfile dump file. See the
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify sort</span></a> command if the dump file was
written by LAMMPS.</p>
<p>The <em>adios</em> format supports all fields that the <em>native</em> format supports
except for the <em>q</em> charge field.
The list of fields stored in an adios .bp file is recorded in the attributes
<em>columns</em> (array of short strings) and <em>columnstr</em> (space-separated single string).</p>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>console
$ bpls -la dump.bp column*
string columns attr = {&quot;id&quot;, &quot;type&quot;, &quot;x&quot;, &quot;y&quot;, &quot;z&quot;, &quot;vx&quot;, &quot;vy&quot;, &quot;vz&quot;}
string columnstr attr = &quot;id type x y z vx vy vz &quot;
</pre></div>
</div>
<hr class="docutils" />
<p>Information from the dump file snapshot is used to overwrite or
replace properties of the current system. There are various options
for how this is done, determined by the specified fields and optional
keywords.</p>
<div class="versionchanged">
<p><span class="versionmodified changed">Changed in version 3Aug2022.</span></p>
</div>
<p>The timestep of the snapshot becomes the current timestep for the
simulation unless the <em>timestep</em> keyword is specified with a <em>no</em> value
(default setting is <em>yes</em>). See the <a class="reference internal" href="reset_timestep.html"><span class="doc">reset_timestep</span></a>
command if you wish to change this to a different value after the dump
snapshot is read.</p>
<p>If the <em>box</em> keyword is specified with a <em>yes</em> value, then the current
simulation box dimensions are replaced by the dump snapshot box
dimensions. If the <em>box</em> keyword is specified with a <em>no</em> value, the
current simulation box is unchanged.</p>
<p>If the <em>purge</em> keyword is specified with a <em>yes</em> value, then all
current atoms in the system are deleted before any of the operations
invoked by the <em>replace</em>, <em>trim</em>, or <em>add</em> keywords take place.</p>
<p>If the <em>replace</em> keyword is specified with a <em>yes</em> value, then atoms
with IDs that are in both the current system and the dump snapshot
have their properties overwritten by field values. If the <em>replace</em>
keyword is specified with a <em>no</em> value, atoms with IDs that are in
both the current system and the dump snapshot are not modified.</p>
<p>If the <em>trim</em> keyword is specified with a <em>yes</em> value, then atoms with
IDs that are in the current system but not in the dump snapshot are
deleted. These atoms are unaffected if the <em>trim</em> keyword is
specified with a <em>no</em> value.</p>
<p>If the <em>add</em> keyword is specified with a <em>no</em> value (default), then
dump file atoms with IDs that are not in the current system are not
added to the system. They are simply ignored.</p>
<p>If a <em>yes</em> value is specified, the atoms with new IDs are added to the
system but their atom IDs are not preserved. Instead, after all the
atoms are added, new IDs are assigned to them in the same manner as is
described for the <a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a> command. Basically
the largest existing atom ID in the system is identified, and all the
added atoms are assigned IDs that consecutively follow the largest ID.</p>
<p>If a <em>keep</em> value is specified, the atoms with new IDs are added to
the system and their atom IDs are preserved. This may lead to
non-contiguous IDs for the combined system.</p>
<p>Note that atoms added via the <em>add</em> keyword will only have the
attributes read from the dump file due to the <em>field</em> arguments. For
example, if <em>x</em> or <em>y</em> or <em>z</em> or <em>q</em> is not specified as a field, a
value of 0.0 is used for added atoms. Added atoms must have an atom
type, so this value must appear in the dump file.</p>
<p>Any other attributes (e.g. charge or particle diameter for spherical
particles) will be set to default values, the same as if the
<a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a> command were used.</p>
<hr class="docutils" />
<p>Atom coordinates read from the dump file are first converted into
unscaled coordinates, relative to the box dimensions of the snapshot.
These coordinates are then be assigned to an existing or new atom in
the current simulation. The coordinates will then be remapped to the
simulation box, whether it is the original box or the dump snapshot
box. If periodic boundary conditions apply, this means the atom will
be remapped back into the simulation box if necessary. If shrink-wrap
boundary conditions apply, the new coordinates may change the
simulation box dimensions. If fixed boundary conditions apply, the
atom will be lost if it is outside the simulation box.</p>
<p>For <em>native</em> format dump files, the 3 xyz image flags for an atom in
the dump file are set to the corresponding values appearing in the
dump file if the <em>ix</em>, <em>iy</em>, <em>iz</em> fields are specified. If not
specified, the image flags for replaced atoms are not changed and
image flags for new atoms are set to default values. If coordinates
read from the dump file are in unwrapped format (e.g. <em>xu</em>) then the
image flags for read-in atoms are also set to default values. The
remapping procedure described in the previous paragraph will then
change images flags for all atoms (old and new) if periodic boundary
conditions are applied to remap an atom back into the simulation box.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>If you get a warning about inconsistent image flags after
reading in a dump snapshot, it means one or more pairs of bonded atoms
now have inconsistent image flags. As discussed on the <a class="reference internal" href="Errors_common.html"><span class="doc">Errors common</span></a> page this may or may not cause problems
for subsequent simulations. One way this can happen is if you read
image flag fields from the dump file but do not also use the dump file
box parameters.</p>
</div>
<p>LAMMPS knows how to compute unscaled and remapped coordinates for the
snapshot column labels discussed above, e.g. <em>x</em>, <em>xs</em>, <em>xu</em>, <em>xsu</em>.
If another column label is assigned to the <em>x</em> or <em>y</em> or <em>z</em> field via
the <em>label</em> keyword, e.g. for coordinates output by the <a class="reference internal" href="fix_ave_atom.html"><span class="doc">fix ave/atom</span></a> command, then LAMMPS needs to know whether
the coordinate information in the dump file is scaled and/or wrapped.
This can be set via the <em>scaled</em> and <em>wrapped</em> keywords. Note that
the value of the <em>scaled</em> and <em>wrapped</em> keywords is ignored for fields
<em>x</em> or <em>y</em> or <em>z</em> if the <em>label</em> keyword is not used to assign a
column label to that field.</p>
<p>The scaled/unscaled and wrapped/unwrapped setting must be identical
for any of the <em>x</em>, <em>y</em>, <em>z</em> fields that are specified. Thus you
cannot read <em>xs</em> and <em>yu</em> from the dump file. Also, if the dump file
coordinates are scaled and the simulation box is triclinic, then all 3
of the <em>x</em>, <em>y</em>, <em>z</em> fields must be specified, since they are all
needed to generate absolute, unscaled coordinates.</p>
</section>
<hr class="docutils" />
<section id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
<p>To read gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option. See the <a class="reference internal" href="Build_settings.html"><span class="doc">Build settings</span></a>
doc page for details.</p>
<p>The <em>molfile</em> dump file formats are part of the MOLFILE package.
They are only enabled if LAMMPS was built with that packages. See the
<a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info.</p>
<p>To write and read adios .bp files, you must compile LAMMPS with the
<a class="reference internal" href="Packages_details.html#pkg-adios"><span class="std std-ref">ADIOS</span></a> package.</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.html"><span class="doc">dump</span></a>, <a class="reference internal" href="dump_molfile.html"><span class="doc">dump molfile</span></a>,
<a class="reference internal" href="dump_adios.html"><span class="doc">dump adios</span></a>,
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>,
<a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a></p>
</section>
<section id="default">
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
<p>The option defaults are box = yes, timestep = yes, replace = yes, purge = no,
trim = no, add = no, scaled = no, wrapped = yes, and format = native.</p>
</section>
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