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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 current"><a class="current reference internal" href="#">dump_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#dump-modify-command-for-image-movie-options"><span class="xref std std-doc">dump_modify</span> command for image/movie options</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</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-modify-command">
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<span id="index-0"></span><h1>dump_modify command<a class="headerlink" href="#dump-modify-command" title="Link to this heading"></a></h1>
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</section>
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<section id="dump-modify-command-for-image-movie-options">
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<h1><a class="reference internal" href="dump_image.html"><span class="doc">dump_modify</span></a> command for image/movie options<a class="headerlink" href="#dump-modify-command-for-image-movie-options" 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_modify </span><span class="nv nv-Identifier">dump-ID</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>
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</pre></div>
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</div>
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<ul>
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<li><p>dump-ID = ID of dump to modify</p></li>
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<li><p>one or more keyword/value pairs may be appended</p></li>
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<li><p>these keywords apply to various dump styles</p></li>
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<li><p>keyword = <em>append</em> or <em>at</em> or <em>balance</em> or <em>buffer</em> or <em>colname</em> or <em>delay</em> or <em>element</em> or <em>every</em> or <em>every/time</em> or <em>fileper</em> or <em>first</em> or <em>flush</em> or <em>format</em> or <em>header</em> or <em>image</em> or <em>label</em> or <em>maxfiles</em> or <em>nfile</em> or <em>pad</em> or <em>pbc</em> or <em>precision</em> or <em>region</em> or <em>refresh</em> or <em>scale</em> or <em>sfactor</em> or <em>skip</em> or <em>sort</em> or <em>tfactor</em> or <em>thermo</em> or <em>thresh</em> or <em>time</em> or <em>triclinic/general</em> or <em>types</em> or <em>units</em> or <em>unwrap</em></p>
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<pre class="literal-block"><em>append</em> arg = <em>yes</em> or <em>no</em>
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<em>at</em> arg = N
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N = index of frame written upon first dump
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<em>balance</em> arg = <em>yes</em> or <em>no</em>
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<em>buffer</em> arg = <em>yes</em> or <em>no</em>
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<em>colname</em> values = ID string, or <em>default</em>
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string = new column header name
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ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
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<em>or</em> a custom dump keyword or reference to compute, fix, property or variable.
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<em>delay</em> arg = Dstep
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Dstep = delay output until this timestep
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<em>element</em> args = E1 E2 ... EN, where N = # of atom types
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E1,...,EN = element name (e.g., C or Fe or Ga)
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<em>every</em> arg = N
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N = dump on timesteps which are a multiple of N
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N can be a variable (see below)
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<em>every/time</em> arg = Delta
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Delta = dump once every Delta interval of simulation time (time units)
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Delta can be a variable (see below)
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<em>fileper</em> arg = Np
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Np = write one file for every this many processors
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<em>first</em> arg = <em>yes</em> or <em>no</em>
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<em>flush</em> arg = <em>yes</em> or <em>no</em>
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<em>format</em> args = <em>line</em> string, <em>int</em> string, <em>float</em> string, ID string, or <em>none</em>
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string = C-style format string
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ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
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<em>or</em> a custom dump keyword or reference to compute, fix, property or variable.
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<em>header</em> arg = <em>yes</em> or <em>no</em>
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<em>yes</em> to write the header
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<em>no</em> to not write the header
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<em>image</em> arg = <em>yes</em> or <em>no</em>
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<em>label</em> arg = string
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string = character string (e.g., BONDS) to use in header of dump local file
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<em>maxfiles</em> arg = Fmax
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Fmax = keep only the most recent <em>Fmax</em> snapshots (one snapshot per file)
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<em>nfile</em> arg = Nf
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Nf = write this many files, one from each of Nf processors
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<em>pad</em> arg = Nchar = # of characters to convert timestep to
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<em>pbc</em> arg = <em>yes</em> or <em>no</em> = remap atoms via periodic boundary conditions
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<em>precision</em> arg = power-of-10 value from 10 to 1000000
|
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<em>region</em> arg = region-ID or "none"
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<em>refresh</em> arg = c_ID = compute ID that supports a refresh operation
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<em>scale</em> arg = <em>yes</em> or <em>no</em>
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<em>sfactor</em> arg = coordinate scaling factor (> 0.0)
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<em>skip</em> arg = v_name
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v_name = variable with name which evaluates to non-zero (skip) or 0
|
||
<em>sort</em> arg = <em>off</em> or <em>id</em> or N or -N
|
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off = no sorting of per-atom lines within a snapshot
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id = sort per-atom lines by atom ID
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N = sort per-atom lines in ascending order by the Nth column
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||
-N = sort per-atom lines in descending order by the Nth column
|
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<em>tfactor</em> arg = time scaling factor (> 0.0)
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<em>thermo</em> arg = <em>yes</em> or <em>no</em>
|
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<em>thresh</em> args = attribute operator value
|
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attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
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operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
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value = numeric value to compare to, or LAST
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these 3 args can be replaced by the word "none" to turn off thresholding
|
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<em>time</em> arg = <em>yes</em> or <em>no</em>
|
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<em>triclinic/general</em> arg = <em>yes</em> or <em>no</em>
|
||
<em>types</em> value = <em>numeric</em> or <em>labels</em>
|
||
<em>units</em> arg = <em>yes</em> or <em>no</em>
|
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<em>unwrap</em> arg = <em>yes</em> or <em>no</em></pre>
|
||
</li>
|
||
<li><p>these keywords apply only to the <em>image</em> and <em>movie</em> <a class="reference internal" href="dump_image.html"><span class="doc">styles</span></a></p></li>
|
||
<li><p>keyword = <em>acolor</em> or <em>adiam</em> or <em>amap</em> or <em>backcolor</em> or <em>bcolor</em> or <em>bdiam</em> or <em>boxcolor</em> or <em>color</em> or <em>bitrate</em> or <em>framerate</em></p>
|
||
<pre class="literal-block">see the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> doc page for details</pre>
|
||
</li>
|
||
<li><p>these keywords apply only to the <em>/gz</em> and <em>/zstd</em> dump styles</p></li>
|
||
<li><p>keyword = <em>compression_level</em></p>
|
||
<pre class="literal-block"><em>compression_level</em> args = level
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||
level = integer specifying the compression level that should be used (see below for supported levels)</pre>
|
||
</li>
|
||
<li><p>these keywords apply only to the <em>/zstd</em> dump styles</p></li>
|
||
<li><p>keyword = <em>checksum</em></p>
|
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<pre class="literal-block"><em>checksum</em> args = <em>yes</em> or <em>no</em> (add checksum at end of zst file)</pre>
|
||
</li>
|
||
<li><p>these keywords apply only to the vtk* dump style</p></li>
|
||
<li><p>keyword = <em>binary</em></p>
|
||
<pre class="literal-block"><em>binary</em> args = <em>yes</em> or <em>no</em> (select between binary and text mode VTK files)</pre>
|
||
</li>
|
||
</ul>
|
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</section>
|
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<section id="examples">
|
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<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_modify </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="n">format</span><span class="w"> </span><span class="n">line</span><span class="w"> </span><span class="s">"%d %d %20.15g %g %g"</span><span class="w"> </span><span class="n">scale</span><span class="w"> </span><span class="n">yes</span>
|
||
<span class="k">dump_modify </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="n">format</span><span class="w"> </span><span class="n">float</span><span class="w"> </span><span class="o">%</span><span class="m">20.15</span><span class="n">g</span><span class="w"> </span><span class="n">scale</span><span class="w"> </span><span class="n">yes</span>
|
||
<span class="k">dump_modify </span><span class="nv nv-Identifier">myDump</span><span class="w"> </span><span class="n">image</span><span class="w"> </span><span class="n">yes</span><span class="w"> </span><span class="n">scale</span><span class="w"> </span><span class="n">no</span><span class="w"> </span><span class="n">flush</span><span class="w"> </span><span class="n">yes</span>
|
||
<span class="k">dump_modify </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="k">region </span><span class="nv nv-Identifier">mySphere</span><span class="w"> </span><span class="n">thresh</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="o"><</span><span class="w"> </span><span class="m">0.0</span><span class="w"> </span><span class="n">thresh</span><span class="w"> </span><span class="n">fx</span><span class="w"> </span><span class="o">>=</span><span class="w"> </span><span class="m">3.2</span>
|
||
<span class="k">dump_modify </span><span class="nv nv-Identifier">xtcdump</span><span class="w"> </span><span class="n">precision</span><span class="w"> </span><span class="m">10000</span><span class="w"> </span><span class="n">sfactor</span><span class="w"> </span><span class="m">0.1</span>
|
||
<span class="k">dump_modify </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="n">every</span><span class="w"> </span><span class="m">1000</span><span class="w"> </span><span class="n">nfile</span><span class="w"> </span><span class="m">20</span>
|
||
<span class="k">dump_modify </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="n">every</span><span class="w"> </span><span class="n">v_myVar</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="description">
|
||
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
|
||
<p>Modify the parameters of a previously defined dump command. Not all
|
||
parameters are relevant to all dump styles.</p>
|
||
<p>Unless otherwise noted, the following keywords apply to all the
|
||
various dump styles, including the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> and
|
||
<a class="reference internal" href="dump_image.html"><span class="doc">dump movie</span></a> styles.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>append</em> keyword applies to all dump styles except <em>cfg</em> and <em>xtc</em>
|
||
and <em>dcd</em>. It also applies only to text output files, not to binary
|
||
or gzipped or image/movie files. If specified as <em>yes</em>, then dump
|
||
snapshots are appended to the end of an existing dump file. If
|
||
specified as <em>no</em>, then a new dump file will be created which will
|
||
overwrite an existing file with the same name.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>at</em> keyword only applies to the <em>netcdf</em> dump style. It can only
|
||
be used if the <em>append yes</em> keyword is also used. The <em>N</em> argument is
|
||
the index of which frame to append to. A negative value can be
|
||
specified for <em>N</em>, which means a frame counted from the end of the
|
||
file. The <em>at</em> keyword can only be used if the dump_modify command is
|
||
before the first command that causes dump snapshots to be output
|
||
(e.g., a <a class="reference internal" href="run.html"><span class="doc">run</span></a> or <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command). Once the
|
||
dump file has been opened, this keyword has no further effect.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>buffer</em> keyword applies only to dump styles <em>atom</em>, <em>cfg</em>,
|
||
<em>custom</em>, <em>local</em>, and <em>xyz</em>. It also applies only to text output
|
||
files, not to binary or gzipped files. If specified as <em>yes</em>, which
|
||
is the default, then each processor writes its output into an internal
|
||
text buffer, which is then sent to the processor(s) which perform file
|
||
writes, and written by those processors(s) as one large chunk of text.
|
||
If specified as <em>no</em>, each processor sends its per-atom data in binary
|
||
format to the processor(s) which perform file wirtes, and those
|
||
processor(s) format and write it line by line into the output file.</p>
|
||
<p>The buffering mode is typically faster since each processor does the
|
||
relatively expensive task of formatting the output for its own atoms.
|
||
However it requires about twice the memory (per processor) for the
|
||
extra buffering.</p>
|
||
<hr class="docutils" />
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 4May2022.</span></p>
|
||
</div>
|
||
<p>The <em>colname</em> keyword can be used to change the default header keyword
|
||
for dump styles: <em>atom</em>, <em>custom</em>, <em>cfg</em>, and <em>local</em> and their
|
||
compressed, ADIOS variants. The setting for <em>ID string</em> replaces the
|
||
default text with the provided string. <em>ID</em> can be a positive integer
|
||
when it represents the column number counting from the left, a negative
|
||
integer when it represents the column number from the right (i.e. -1 is
|
||
the last column/keyword), or a custom dump keyword (or compute, fix,
|
||
property, or variable reference) and then it replaces the string for
|
||
that specific keyword. For <em>atom</em> dump styles only the keywords “id”,
|
||
“type”, “x”, “y”, “z”, “ix”, “iy”, “iz” can be accessed via string
|
||
regardless of whether scaled or unwrapped coordinates were enabled or
|
||
disabled, and it always assumes 8 columns for indexing regardless of
|
||
whether image flags are enabled or not. For dump style <em>cfg</em> only
|
||
changes to the “auxiliary” keywords (6th or later keyword) will become
|
||
visible.</p>
|
||
<p>The <em>colname</em> keyword can be used multiple times. If multiple <em>colname</em>
|
||
settings refer to the same keyword, the last setting has precedence. A
|
||
setting of <em>default</em> clears all previous settings, reverting all values
|
||
to their default names. Using the <em>scale</em> or <em>image</em> keyword will also
|
||
reset all header keywords to their default values.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>delay</em> keyword applies to all dump styles. No snapshots will be
|
||
output until the specified <em>Dstep</em> timestep or later. Specifying
|
||
<em>Dstep</em> < 0 is the same as turning off the delay setting. This is a
|
||
way to turn off unwanted output early in a simulation, for example,
|
||
during an equilibration phase.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>element</em> keyword applies only to the dump <em>cfg</em>, <em>xyz</em>, and
|
||
<em>image</em> styles. It associates element names (e.g., H, C, Fe) with
|
||
LAMMPS atom types. See the list of element names at the bottom of
|
||
this page.</p>
|
||
<p>In the case of dump <em>cfg</em>, this allows the <a class="reference external" href="http://li.mit.edu/Archive/Graphics/A/">AtomEye</a>
|
||
visualization package to read the dump file and render atoms with the
|
||
appropriate size and color.</p>
|
||
<p>In the case of dump <em>image</em>, the output images will follow the same
|
||
<a class="reference external" href="http://li.mit.edu/Archive/Graphics/A/">AtomEye</a> convention. An element name is specified for each
|
||
atom type (1 to Ntype) in the simulation. The same element name can
|
||
be given to multiple atom types.</p>
|
||
<p>In the case of <em>xyz</em> format dumps, there are no restrictions to what
|
||
label can be used as an element name. Any white-space separated text
|
||
will be accepted.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>every</em> keyword can be used with any dump style except the <em>dcd</em>
|
||
and <em>xtc</em> styles. It specifies that the output of dump snapshots will
|
||
now be performed on timesteps which are a multiple of a new <span class="math notranslate nohighlight">\(N\)</span>
|
||
value, This overrides the dump frequency originally specified by the
|
||
<a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command.</p>
|
||
<p>The <em>every</em> keyword can be specified in one of two ways. It can be a
|
||
numeric value in which case it must be > 0. Or it can be an
|
||
<a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>, which should be specified as
|
||
v_name, where name is the variable name.</p>
|
||
<p>In this case, the variable is evaluated at the beginning of a run to
|
||
determine the next timestep at which a dump snapshot will be written
|
||
out. On that timestep the variable will be evaluated again to
|
||
determine the next timestep, etc. Thus the variable should return
|
||
timestep values. See the stagger() and logfreq() and stride() math
|
||
functions for <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a>, as examples of
|
||
useful functions to use in this context. Other similar math functions
|
||
could easily be added as options for <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a>. Also see the next() function, which allows use of a
|
||
file-style variable which reads successive values from a file, each
|
||
time the variable is evaluated. Used with the <em>every</em> keyword, if the
|
||
file contains a list of ascending timesteps, you can output snapshots
|
||
whenever you wish.</p>
|
||
<p>Note that when using the variable option with the <em>every</em> keyword, you
|
||
need to use the <em>first</em> option if you want an initial snapshot written
|
||
to the dump file. The <em>every</em> keyword cannot be used with the dump
|
||
<em>dcd</em> style.</p>
|
||
<p>For example, the following commands will
|
||
write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">s</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="n">logfreq</span><span class="nv">(10,3,10)</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">atom</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">tmp.dump</span>
|
||
<span class="k">dump_modify </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="n">every</span><span class="w"> </span><span class="n">v_s</span><span class="w"> </span><span class="n">first</span><span class="w"> </span><span class="n">yes</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>The following commands would write snapshots at the timesteps listed
|
||
in file tmp.times:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">f</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="n">tmp.times</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">s</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="n">next</span><span class="nv">(f)</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">atom</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">tmp.dump</span>
|
||
<span class="k">dump_modify </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="n">every</span><span class="w"> </span><span class="n">v_s</span>
|
||
</pre></div>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>When using a file-style variable with the <em>every</em> keyword, the
|
||
file of timesteps must list a first timestep that is beyond the
|
||
current timestep (e.g., it cannot be 0). And it must list one or more
|
||
timesteps beyond the length of the run you perform. This is because
|
||
the dump command will generate an error if the next timestep it reads
|
||
from the file is not a value greater than the current timestep. Thus
|
||
if you wanted output on steps 0,15,100 of a 100-timestep run, the file
|
||
should contain the values 15,100,101 and you should also use the
|
||
dump_modify first command. Any final value > 100 could be used in
|
||
place of 101.</p>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 7Jan2022.</span></p>
|
||
</div>
|
||
<p>The <em>every/time</em> keyword can be used with any dump style except the
|
||
<em>dcd</em> and <em>xtc</em> styles. It changes the frequency of dump snapshots
|
||
from being based on the current timestep to being determined by
|
||
elapsed simulation time, i.e. in time units of the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command, and specifies <em>Delta</em> for the interval between
|
||
snapshots. 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. The default is to perform output on timesteps which a
|
||
multiples of specified timestep value <span class="math notranslate nohighlight">\(N\)</span>; see the <em>every</em>
|
||
keyword.</p>
|
||
<p>The <em>every/time</em> keyword can be used with any dump style except the
|
||
<em>dcd</em> and <em>xtc</em> styles. It does two things. It specifies that the
|
||
interval between dump snapshots will be set in simulation time
|
||
(i.e. in time units of the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command). 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). The default is
|
||
to specify the interval in timesteps; see the <em>every</em> keyword. The
|
||
<em>every/time</em> command also sets the interval value.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>If you wish dump styles <em>atom</em>, <em>custom</em>, <em>local</em>, or <em>xyz</em> to
|
||
include the simulation time as a field in the header portion of
|
||
each snapshot, you also need to use the dump_modify <em>time</em> keyword
|
||
with a setting of <em>yes</em>. See its documentation below.</p>
|
||
</div>
|
||
<p>Note that since snapshots are output on simulation steps, each
|
||
snapshot will be written on the first timestep whose associated
|
||
simulation time is >= the exact snapshot time value.</p>
|
||
<p>As with the <em>every</em> option, the <em>Delta</em> value can be specified in one
|
||
of two ways. It can be a numeric value in which case it must be >
|
||
0.0. Or it can be an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>, which
|
||
should be specified as v_name, where name is the variable name.</p>
|
||
<p>In this case, the variable is evaluated at the beginning of a run to
|
||
determine the next simulation time at which a dump snapshot will be
|
||
written out. On that timestep the variable will be evaluated again to
|
||
determine the next simulation time, etc. Thus the variable should
|
||
return values in time units. Note the current timestep or simulation
|
||
time can be used in an <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a> since
|
||
they are both thermodynamic keywords. Also see the next() function,
|
||
which allows use of a file-style variable which reads successive
|
||
values from a file, each time the variable is evaluated. Used with
|
||
the <em>every/time</em> keyword, if the file contains a list of ascending
|
||
simulation times, you can output snapshots whenever you wish.</p>
|
||
<p>Note that when using the variable option with the <em>every/time</em>
|
||
keyword, you need to use the <em>first</em> option if you want an initial
|
||
snapshot written to the dump file. The <em>every/time</em> keyword cannot be
|
||
used with the dump <em>dcd</em> style.</p>
|
||
<p>For example, the following commands will write snapshots at successive
|
||
simulation times which grow by a factor of 1.5 with each interval.
|
||
The dt value used in the variable is to avoid a zero result when the
|
||
initial simulation time is 0.0.</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">increase</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="m">1.5</span><span class="o">*</span><span class="nv">(time+dt)</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">atom</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">tmp.dump</span>
|
||
<span class="k">dump_modify </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="n">every</span><span class="o">/</span><span class="n">time</span><span class="w"> </span><span class="n">v_increase</span><span class="w"> </span><span class="n">first</span><span class="w"> </span><span class="n">yes</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>The following commands would write snapshots at the times listed in
|
||
file tmp.times:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">f</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="n">tmp.times</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">s</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="n">next</span><span class="nv">(f)</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">atom</span><span class="w"> </span><span class="m">100</span><span class="w"> </span><span class="n">tmp.dump</span>
|
||
<span class="k">dump_modify </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="n">every</span><span class="o">/</span><span class="n">time</span><span class="w"> </span><span class="n">v_s</span>
|
||
</pre></div>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>When using a file-style variable with the <em>every/time</em> keyword, the
|
||
file of timesteps must list a first time that is beyond the time
|
||
associated with the current timestep (e.g., it cannot be 0.0). And
|
||
it must list one or more times beyond the length of the run you
|
||
perform. This is because the dump command will generate an error
|
||
if the next time it reads from the file is not a value greater than
|
||
the current time. Thus if you wanted output at times 0,15,100 of a
|
||
run of length 100 in simulation time, the file should contain the
|
||
values 15,100,101 and you should also use the dump_modify first
|
||
command. Any final value > 100 could be used in place of 101.</p>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>The <em>first</em> keyword determines whether a dump snapshot is written on
|
||
the very first timestep after the dump command is invoked. This will
|
||
always occur if the current timestep is a multiple of $N$, the
|
||
frequency specified in the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command or
|
||
<a class="reference internal" href="#"><span class="doc">dump_modify every</span></a> command, including timestep 0.
|
||
It will also always occur if the current simulation time is a multiple
|
||
of <em>Delta</em>, the time interval specified in the <a class="reference internal" href="#"><span class="doc">dump_modify
|
||
every/time</span></a> command.</p>
|
||
<p>But if this is not the case, a dump snapshot will only be written if
|
||
the setting of this keyword is <em>yes</em>. If it is <em>no</em>, which is the
|
||
default, then it will not be written.</p>
|
||
<p>Note that if the argument to the <a class="reference internal" href="#"><span class="doc">dump_modify every</span></a> <a class="reference internal" href="#"><span class="doc">dump_modify every/time</span></a> commands is
|
||
a variable and not a numeric value, then specifying <em>first yes</em> is the
|
||
only way to write a dump snapshot on the first timestep after the dump
|
||
command is invoked.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>flush</em> keyword determines whether a flush operation is invoked
|
||
after a dump snapshot is written to the dump file. A flush ensures
|
||
the output in that file is current (no buffering by the OS), even if
|
||
LAMMPS halts before the simulation completes. Flushes cannot be
|
||
performed with dump style <em>xtc</em>.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>format</em> keyword can be used to change the default numeric format
|
||
output by the text-based dump styles: <em>atom</em>, <em>local</em>, <em>custom</em>, <em>cfg</em>,
|
||
and <em>xyz</em> styles. Only the <em>line</em> or <em>none</em> options can be used with the
|
||
<em>atom</em> and <em>xyz</em> styles.</p>
|
||
<p>All the specified format strings are C-style formats, such as used by
|
||
the C/C++ printf() command. The <em>line</em> keyword takes a single
|
||
argument which is the format string for an entire line of output for
|
||
each atom (do not include a trailing “n”), with <span class="math notranslate nohighlight">\(N\)</span> fields, which you
|
||
must enclose in quotes if there is more than one field. The <em>int</em> and
|
||
<em>float</em> keywords take a single format argument and are applied to all
|
||
integer or floating-point quantities output. The setting for <em>M string</em>
|
||
also takes a single format argument which is used for the <span class="math notranslate nohighlight">\(M\)</span>th
|
||
value output in each line (e.g., the fifth column is output in high
|
||
precision by “format 5 %20.15g”).</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>When using the <em>line</em> keyword for the <em>cfg</em> style, the first two
|
||
fields (atom ID and type) are not actually written into the CFG file,
|
||
however you must include formats for them in the format string.</p>
|
||
</div>
|
||
<p>The <em>format</em> keyword can be used multiple times. The precedence is
|
||
that for each value in a line of output, the <em>M</em> format (if specified)
|
||
is used, else the <em>int</em> or <em>float</em> setting (if specified) is used,
|
||
else the <em>line</em> setting (if specified) for that value is used, else
|
||
the default setting is used. A setting of <em>none</em> clears all previous
|
||
settings, reverting all values to their default format.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Atom and molecule IDs are stored internally as 4-byte or 8-byte
|
||
signed integers, depending on how LAMMPS was compiled. When
|
||
specifying the <em>format int</em> option you can use a “%d”-style format
|
||
identifier in the format string and LAMMPS will convert this to the
|
||
corresponding 8-byte form if it is needed when outputting those
|
||
values. However, when specifying the <em>line</em> option or <em>format M
|
||
string</em> option for those values, you should specify a format string
|
||
appropriate for an 8-byte signed integer (e.g., one with “%ld”) if
|
||
LAMMPS was compiled with the -DLAMMPS_BIGBIG option for 8-byte IDs.</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Any value written to a text-based dump file that is a per-atom
|
||
quantity calculated by a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> or <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> is
|
||
stored internally as a floating-point value. If the value is actually
|
||
an integer and you wish it to appear in the text dump file as a
|
||
(large) integer, then you need to use an appropriate format. For
|
||
example, these commands:</p>
|
||
</div>
|
||
<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="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">100</span><span class="w"> </span><span class="n">tmp.bonds</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="k">dump_modify </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="n">format</span><span class="w"> </span><span class="n">line</span><span class="w"> </span><span class="s">"%d %0.0f %0.0f"</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>will output the two atom IDs for atoms in each bond as integers. If
|
||
the dump_modify command were omitted, they would appear as
|
||
floating-point values, assuming they were large integers (more than six
|
||
digits). The “index” keyword should use the “%d” format since it is
|
||
not generated by a compute or fix, and is stored internally as an
|
||
integer.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>fileper</em> keyword is documented below with the <em>nfile</em> keyword.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>header</em> keyword toggles whether the dump file will include a
|
||
header. Excluding a header will reduce the size of the dump file for
|
||
data produced by <a class="reference internal" href="pair_tracker.html"><span class="doc">pair tracker</span></a> or
|
||
<a class="reference internal" href="Howto_bpm.html"><span class="doc">bpm bond styles</span></a> which may not require the
|
||
information typically written to the header.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>image</em> keyword applies only to the dump <em>atom</em> style. If the
|
||
image value is <em>yes</em>, three flags are appended to each atom’s coords which
|
||
are the absolute box image of the atom in each dimension. For
|
||
example, an <span class="math notranslate nohighlight">\(x\)</span> image flag of <span class="math notranslate nohighlight">\(-2\)</span> with a normalized coord of 0.5
|
||
means the atom is in the center of the box, but has passed through the box
|
||
boundary twice and is really two box lengths to the left of its
|
||
current coordinate. Note that for dump style <em>custom</em> these various
|
||
values can be printed in the dump file by using the appropriate atom
|
||
attributes in the dump command itself.
|
||
Using this keyword will reset all custom header names set with
|
||
<em>dump_modify colname</em> to their respective default values.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>label</em> keyword applies only to the dump <em>local</em> style.
|
||
When it writes local information, such as bond or angle topology
|
||
to a dump file, it will use the specified <em>label</em> to format the header.
|
||
By default this includes two lines:</p>
|
||
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ITEM: NUMBER OF ENTRIES
|
||
ITEM: ENTRIES ...
|
||
</pre></div>
|
||
</div>
|
||
<p>The word “ENTRIES” will be replaced with the string specified
|
||
(e.g., BONDS or ANGLES).</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>maxfiles</em> keyword can only be used when a ‘*’ wildcard is
|
||
included in the dump file name (i.e., when writing a new file(s) for
|
||
each snapshot). The specified <em>Fmax</em> is how many snapshots will be
|
||
kept. Once this number is reached, the file(s) containing the oldest
|
||
snapshot is deleted before a new dump file is written. If the
|
||
specified <span class="math notranslate nohighlight">\(\text{Fmax} \le 0\)</span>, then all files are retained.</p>
|
||
<p>This can be useful for debugging, especially if you do not know on what
|
||
timestep something bad will happen (e.g., when LAMMPS will exit with an
|
||
error). You can dump every time step and limit the number of dump
|
||
files produced, even if you run for thousands of steps.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>nfile</em> or <em>fileper</em> keywords can be used in conjunction with the
|
||
“%” wildcard character in the specified dump file name, for all dump
|
||
styles except the <em>dcd</em>, <em>image</em>, <em>movie</em>, <em>xtc</em>, and <em>xyz</em> styles
|
||
(for which “%” is not allowed). As explained on the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a>
|
||
command doc page, the “%” character causes the dump file to be written
|
||
in pieces, one piece for each of <span class="math notranslate nohighlight">\(P\)</span> processors. By default, <span class="math notranslate nohighlight">\(P\)</span>
|
||
is the number of processors the simulation is running on. The <em>nfile</em> or
|
||
<em>fileper</em> keyword can be used to set <span class="math notranslate nohighlight">\(P\)</span> to a smaller value, which can
|
||
be more efficient when running on a large number of processors.</p>
|
||
<p>The <em>nfile</em> keyword sets <span class="math notranslate nohighlight">\(P\)</span> to the specified <span class="math notranslate nohighlight">\(N_f\)</span> value.
|
||
For example, if <span class="math notranslate nohighlight">\(N_f = 4\)</span>, and the simulation is running on 100
|
||
processors, four files will be written by processors 0, 25, 50, and 75.
|
||
Each will collect information from itself and the next 24 processors and write
|
||
it to a dump file.</p>
|
||
<p>For the <em>fileper</em> keyword, the specified value of <span class="math notranslate nohighlight">\(N_p\)</span> means write one
|
||
file for every <span class="math notranslate nohighlight">\(N_p\)</span> processors. For example, if <span class="math notranslate nohighlight">\(N_p = 4\)</span>,
|
||
every fourth processor (0, 4, 8, 12, etc.) will collect information from itself
|
||
and the next three processors and write it to a dump file.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>pad</em> keyword only applies when the dump filename is specified
|
||
with a wildcard “*” character which becomes the timestep. If <em>pad</em> is
|
||
0, which is the default, the timestep is converted into a string of
|
||
unpadded length (e.g., 100 or 12000 or 2000000). When <em>pad</em> is
|
||
specified with <em>Nchar</em> <span class="math notranslate nohighlight">\(>\)</span> 0, the string is padded with leading zeroes
|
||
so they are all the same length = <em>Nchar</em>. For example, pad 7 would
|
||
yield 0000100, 0012000, 2000000. This can be useful so that
|
||
post-processing programs can easily read the files in ascending
|
||
timestep order.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>pbc</em> keyword applies to all the dump styles. As explained on the
|
||
<a class="reference internal" href="dump.html"><span class="doc">dump</span></a> doc page, atom coordinates in a dump file may be
|
||
slightly outside the simulation box. This is because periodic
|
||
boundary conditions are enforced only on timesteps when neighbor lists
|
||
are rebuilt, which will not typically coincide with the timesteps dump
|
||
snapshots are written. If the setting of this keyword is set to
|
||
<em>yes</em>, then all atoms will be remapped to the periodic box before the
|
||
snapshot is written, then restored to their original position. If it
|
||
is set to <em>no</em> they will not be. The <em>no</em> setting is the default
|
||
because it requires no extra computation.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>precision</em> keyword only applies to the dump <em>xtc</em> style. A
|
||
specified value of <span class="math notranslate nohighlight">\(N\)</span> means that coordinates are stored to <span class="math notranslate nohighlight">\(1/N\)</span>
|
||
nanometer accuracy (e.g., for <span class="math notranslate nohighlight">\(N = 1000\)</span>, the coordinates are written to
|
||
<span class="math notranslate nohighlight">\(1/1000\)</span> nanometer accuracy).</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>refresh</em> keyword only applies to the dump <em>custom</em>, <em>cfg</em>,
|
||
<em>image</em>, and <em>movie</em> styles. It allows an “incremental” dump file to
|
||
be written, by refreshing a compute that is used as a threshold for
|
||
determining which atoms are included in a dump snapshot. The
|
||
specified <em>c_ID</em> gives the ID of the compute. It is prefixed by “c_”
|
||
to indicate a compute, which is the only current option. At some
|
||
point, other options may be added (e.g., fixes or variables).</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>This keyword can only be specified once for a dump. Refreshes
|
||
of multiple computes cannot yet be performed.</p>
|
||
</div>
|
||
<p>The definition and motivation of an incremental dump file is as
|
||
follows. Instead of outputting all atoms at each snapshot (with some
|
||
associated values), you may only wish to output the subset of atoms
|
||
with a value that has changed in some way compared to the value the
|
||
last time that atom was output. In some scenarios this can result in
|
||
a dramatically smaller dump file. If desired, by post-processing the
|
||
sequence of snapshots, the values for all atoms at all timesteps can
|
||
be inferred.</p>
|
||
<p>A concrete example is a simulation of atom diffusion in a solid,
|
||
represented as atoms on a lattice. Diffusive hops are rare. Imagine
|
||
that when a hop occurs an atom moves more than a distance <em>Dhop</em>. For
|
||
any snapshot we only want to output atoms that have hopped since the
|
||
last snapshot. This can be accomplished with something the following
|
||
commands:</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">Dhop</span><span class="w"> </span><span class="n">equal</span><span class="w"> </span><span class="m">0.6</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">check</span><span class="w"> </span><span class="n">atom</span><span class="w"> </span><span class="s">"c_dsp[4] > v_Dhop"</span>
|
||
<span class="k">compute </span><span class="nv nv-Identifier">dsp</span><span class="w"> </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">displace</span><span class="o">/</span><span class="n">atom</span><span class="w"> </span><span class="n">refresh</span><span class="w"> </span><span class="n">check</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">custom</span><span class="w"> </span><span class="m">20</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">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="k">dump_modify </span><span class="nv nv-Identifier">1</span><span class="w"> </span><span class="n">append</span><span class="w"> </span><span class="n">yes</span><span class="w"> </span><span class="n">thresh</span><span class="w"> </span><span class="n">c_dsp[4]</span><span class="w"> </span><span class="o">></span><span class="w"> </span><span class="nv">${Dhop}</span><span class="w"> </span><span class="n">refresh</span><span class="w"> </span><span class="n">c_dsp</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>The <a class="reference internal" href="compute_displace_atom.html"><span class="doc">compute displace/atom</span></a> command
|
||
calculates the displacement of each atom from its reference position.
|
||
The “4” index is the scalar displacement; 1, 2, and 3 are the <span class="math notranslate nohighlight">\(xyz\)</span>
|
||
components of the displacement. The <a class="reference internal" href="#"><span class="doc">dump_modify thresh</span></a>
|
||
command will cause only atoms that have displaced more than
|
||
<span class="math notranslate nohighlight">\(0.6~\AA\)</span> to be output on a given snapshot (assuming
|
||
metal units). However, note that when an atom is output, we also need to
|
||
update the reference position for that atom to its new coordinates. So that it
|
||
will not be output in every snapshot thereafter. That reference position is
|
||
stored by <a class="reference internal" href="compute_displace_atom.html"><span class="doc">compute displace/atom</span></a>. So the
|
||
dump_modify <em>refresh</em> option triggers a call to compute displace/atom at the
|
||
end of every dump to perform that update. The <em>refresh check</em> option
|
||
shown as part of the <a class="reference internal" href="compute_displace_atom.html"><span class="doc">compute displace/atom</span></a>
|
||
command enables the compute to respond to the call from the dump command, and
|
||
update the appropriate reference positions. This is done be defining an
|
||
<a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a>, <em>check</em> in this example, which
|
||
calculates a Boolean value (0 or 1) for each atom, based on the same
|
||
criterion used by dump_modify thresh.</p>
|
||
<p>See the <a class="reference internal" href="compute_displace_atom.html"><span class="doc">compute displace/atom</span></a> command for
|
||
more details, including an example of how to produce output that
|
||
includes an initial snapshot with the reference position of all atoms.</p>
|
||
<p>Note that only computes with a <em>refresh</em> option will work with
|
||
dump_modify refresh. See individual compute doc pages for details.
|
||
Currently, only compute displace/atom supports this option. Others
|
||
may be added at some point. If you use a compute that does not support
|
||
refresh operations, LAMMPS will not complain; dump_modify refresh will
|
||
simply do nothing.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>region</em> keyword only applies to the dump <em>custom</em>, <em>cfg</em>,
|
||
<em>image</em>, and <em>movie</em> styles. If specified, only atoms in the region
|
||
will be written to the dump file or included in the image/movie. Only
|
||
one region can be applied as a filter (the last one specified). See
|
||
the <a class="reference internal" href="region.html"><span class="doc">region</span></a> command for more details. Note that a region
|
||
can be defined as the “inside” or “outside” of a geometric shape, and
|
||
it can be the “union” or “intersection” of a series of simpler
|
||
regions.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>scale</em> keyword applies only to the dump <em>atom</em> style. A scale
|
||
value of <em>yes</em> means atom coords are written in normalized units from
|
||
0.0 to 1.0 in each box dimension. If the simulation box is triclinic
|
||
(tilted), then all atom coords will still be between 0.0 and 1.0. A
|
||
value of <em>no</em> means they are written in absolute distance units
|
||
(e.g., <span class="math notranslate nohighlight">\(\AA\)</span> or <span class="math notranslate nohighlight">\(\sigma\)</span>).
|
||
Using this keyword will reset all custom header names set with
|
||
<em>dump_modify colname</em> to their respective default values.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>sfactor</em> and <em>tfactor</em> keywords only apply to the dump <em>xtc</em>
|
||
style. They allow customization of the unit conversion factors used
|
||
when writing to XTC files. By default, they are initialized for
|
||
whatever <a class="reference internal" href="units.html"><span class="doc">units</span></a> style is being used, to write out
|
||
coordinates in nanometers and time in picoseconds. For example, for <em>real</em>
|
||
units, LAMMPS defines <em>sfactor</em> = 0.1 and <em>tfactor</em> = 0.001, since the
|
||
<span class="math notranslate nohighlight">\(\AA\)</span> and fs used by <em>real</em> units are 0.1 nm and
|
||
0.001 ps, respectively. If you are using a units system with distance and time
|
||
units far from nm and ps, you may wish to write XTC files with
|
||
different units, since the compression algorithm used in XTC files is
|
||
most effective when the typical magnitude of position data is between
|
||
10.0 and 0.1.</p>
|
||
<hr class="docutils" />
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 15Sep2022.</span></p>
|
||
</div>
|
||
<p>The <em>skip</em> keyword can be used with all dump styles. It allows a dump
|
||
snapshot to be skipped (not written to the dump file), if a condition
|
||
is met. The condition is computed by an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>, which should be specified as v_name, where name is the
|
||
variable name. If the variable evaluation returns a non-zero value,
|
||
then the dump snapshot is skipped. If it returns zero, the dump
|
||
proceeds as usual. Note that <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>
|
||
can contain Boolean operators which effectively evaluate as a true
|
||
(non-zero) or false (zero) result.</p>
|
||
<p>The <em>skip</em> keyword can be useful for debugging purposes, e.g. to dump
|
||
only on a particular timestep. Or to limit output to conditions of
|
||
interest, e.g. only when the force on some atom exceeds a threshold
|
||
value.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>sort</em> keyword determines whether lines of per-atom output in a
|
||
snapshot are sorted or not. A sort value of <em>off</em> means they will
|
||
typically be written in indeterminate order, either in serial or
|
||
parallel. This is the case even in serial if the <a class="reference internal" href="atom_modify.html"><span class="doc">atom_modify sort</span></a> option is turned on, which it is by default, to improve
|
||
performance. A sort value of <em>id</em> means sort the output by atom ID. A
|
||
sort value of <span class="math notranslate nohighlight">\(N\)</span> or <span class="math notranslate nohighlight">\(-N\)</span> means sort the output by the value
|
||
in the <span class="math notranslate nohighlight">\(N\)</span>th column of per-atom info in either ascending or
|
||
descending order.</p>
|
||
<p>The dump <em>local</em> style cannot be sorted by atom ID, since there are
|
||
typically multiple lines of output per atom. Some dump styles, such
|
||
as <em>dcd</em> and <em>xtc</em>, require sorting by atom ID to format the output
|
||
file correctly. If multiple processors are writing the dump file, via
|
||
the “%” wildcard in the dump filename and the <em>nfile</em> or <em>fileper</em>
|
||
keywords are set to non-default values (i.e., the number of dump file
|
||
pieces is not equal to the number of procs), then sorting cannot be
|
||
performed.</p>
|
||
<p>In a parallel run, the per-processor dump file pieces can have
|
||
significant imbalance in number of lines of per-atom info. The <em>balance</em>
|
||
keyword determines whether the number of lines in each processor
|
||
snapshot are balanced to be nearly the same. A balance value of <em>no</em>
|
||
means no balancing will be done, while <em>yes</em> means balancing will be
|
||
performed. This balancing preserves dump sorting order. For a serial
|
||
run, this option is ignored since the output is already balanced.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>Unless it is required by the dump style, sorting dump file
|
||
output requires extra overhead in terms of CPU and communication cost,
|
||
as well as memory, versus unsorted output.</p>
|
||
</div>
|
||
<hr class="docutils" />
|
||
<p>The <em>thermo</em> keyword only applies the dump styles <em>netcdf</em> and <em>yaml</em>.
|
||
It triggers writing of <a class="reference internal" href="thermo.html"><span class="doc">thermo</span></a> information to the dump
|
||
file alongside per-atom data. The values included in the dump file are
|
||
cached values from the last thermo output and include the exact same the
|
||
values as specified by the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command.
|
||
Because these are cached values, they are only up-to-date when dump
|
||
output is on a timestep that also has thermo output. Dump style <em>yaml</em>
|
||
will skip thermo output on incompatible steps.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>thresh</em> keyword only applies to the dump <em>custom</em>, <em>cfg</em>,
|
||
<em>image</em>, and <em>movie</em> styles. Multiple thresholds can be specified.
|
||
Specifying <em>none</em> turns off all threshold criteria. If thresholds are
|
||
specified, only atoms whose attributes meet all the threshold criteria
|
||
are written to the dump file or included in the image. The possible
|
||
attributes that can be tested for are the same as those that can be
|
||
specified in the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command, with the exception
|
||
of the <em>element</em> attribute, since it is not a numeric value. Note
|
||
that a different attributes can be used than those output by the
|
||
<a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command. For example, you can output the
|
||
coordinates and stress of atoms whose energy is above some threshold.</p>
|
||
<p>If an atom-style variable is used as the attribute, then it can
|
||
produce continuous numeric values or effective Boolean 0/1 values,
|
||
which may be useful for the comparison operator. Boolean values can
|
||
be generated by variable formulas that use comparison or Boolean math
|
||
operators or special functions like gmask() and rmask() and grmask().
|
||
See the <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> command page for details.</p>
|
||
<p>The specified value must be a simple numeric value or the word LAST.
|
||
If LAST is used, it refers to the value of the attribute the last time
|
||
the dump command was invoked to produce a snapshot. This is a way to
|
||
only dump atoms whose attribute has changed (or not changed).
|
||
Three examples follow.</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">dump_modify </span><span class="nv nv-Identifier">...</span><span class="w"> </span><span class="n">thresh</span><span class="w"> </span><span class="n">ix</span><span class="w"> </span><span class="o">!=</span><span class="w"> </span><span class="n">LAST</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>This will dump atoms which have crossed the periodic <span class="math notranslate nohighlight">\(x\)</span> boundary of the
|
||
simulation box since the last dump. (Note that atoms that crossed
|
||
once and then crossed back between the two dump timesteps would not be
|
||
included.)</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">region </span><span class="nv nv-Identifier">foo</span><span class="w"> </span><span class="n">sphere</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">15</span>
|
||
<span class="k">variable </span><span class="nv nv-Identifier">inregion</span><span class="w"> </span><span class="n">atom</span><span class="w"> </span><span class="n">rmask</span><span class="nv">(foo)</span>
|
||
<span class="k">dump_modify </span><span class="nv nv-Identifier">...</span><span class="w"> </span><span class="n">thresh</span><span class="w"> </span><span class="n">v_inregion</span><span class="w"> </span><span class="o">|^</span><span class="w"> </span><span class="n">LAST</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>This will dump atoms which crossed the boundary of the spherical
|
||
region since the last dump.</p>
|
||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">variable </span><span class="nv nv-Identifier">charge</span><span class="w"> </span><span class="n">atom</span><span class="w"> </span><span class="s">"(q > 0.5) || (q < -0.5)"</span>
|
||
<span class="k">dump_modify </span><span class="nv nv-Identifier">...</span><span class="w"> </span><span class="n">thresh</span><span class="w"> </span><span class="n">v_charge</span><span class="w"> </span><span class="o">|^</span><span class="w"> </span><span class="n">LAST</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>This will dump atoms whose charge has changed from an absolute value
|
||
less than <span class="math notranslate nohighlight">\(\frac12\)</span> to greater than <span class="math notranslate nohighlight">\(\frac12\)</span> (or vice
|
||
versa) since the last dump (e.g., due to reactions and subsequent
|
||
charge equilibration in a reactive force field).</p>
|
||
<p>The choice of operators listed above are the usual comparison
|
||
operators. The XOR operation (exclusive or) is also included as “|^”.
|
||
In this context, XOR means that if either the attribute or value is
|
||
0.0 and the other is non-zero, then the result is “true” and the
|
||
threshold criterion is met. Otherwise it is not met.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>For style <em>custom</em>, the <em>triclinic/general</em> keyword can alter dump
|
||
output for general triclinic simulation boxes and their atoms. See
|
||
the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command for details of how this changes the
|
||
format of dump file snapshots. The thresh keyword may access
|
||
per-atom attributes either directly or indirectly through a compute
|
||
or variable. If the attribute is an atom coordinate or a per-atom
|
||
vector (such as velocity, force, or dipole moment), 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>The <em>time</em> keyword only applies to the dump <em>atom</em>, <em>custom</em>, <em>local</em>,
|
||
and <em>xyz</em> styles (and their COMPRESS package versions <em>atom/gz</em>,
|
||
<em>custom/gz</em> and <em>local/gz</em>). For the first three styles, if set to
|
||
<em>yes</em>, each frame will will contain two extra lines before the “ITEM:
|
||
TIMESTEP” entry:</p>
|
||
<pre class="literal-block">ITEM: TIME
|
||
<elapsed time></pre>
|
||
<p>For the <em>xyz</em> style, the simulation time is included on the same line
|
||
as the timestep value.</p>
|
||
<p>This will output the current elapsed simulation time in current
|
||
time units equivalent to the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo keyword</span></a> <em>time</em>.
|
||
This is to simplify post-processing of trajectories using a variable time
|
||
step (e.g., when using <a class="reference internal" href="fix_dt_reset.html"><span class="doc">fix dt/reset</span></a>).
|
||
The default setting is <em>no</em>.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>types</em> keyword applies only to the dump xyz style. If this keyword is
|
||
used with a value of <em>numeric</em>, then numeric atom types are printed in the
|
||
xyz file (default). If the value <em>labels</em> is specified, then
|
||
<a class="reference internal" href="Howto_type_labels.html"><span class="doc">type labels</span></a> are printed for atom types.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>triclinic/general</em> keyword only applies to the dump <em>atom</em> and
|
||
<em>custom</em> styles. It can only be used with a value of <em>yes</em> if the
|
||
simulation box was created as a general triclinic box. See the
|
||
<a class="reference internal" href="Howto_triclinic.html"><span class="doc">Howto_triclinic</span></a> doc page for a detailed
|
||
explanation of orthogonal, restricted triclinic, and general triclinic
|
||
simulation boxes.</p>
|
||
<p>If this keyword is used with a value of <em>yes</em>, the box information at
|
||
the beginning of each snapshot will include information about the 3
|
||
arbitrary edge vectors <strong>A</strong>, <strong>B</strong>, <strong>C</strong> that define the general
|
||
triclinic box as well as their origin. The format is described on the
|
||
<a class="reference internal" href="dump.html"><span class="doc">dump</span></a> doc page.</p>
|
||
<p>The coordinates of each atom will likewise be output as values in (or
|
||
near) the general triclinic box. Likewise, per-atom vector quantities
|
||
such as velocity, omega, dipole moment, etc will have orientations
|
||
consistent with the general triclinic box, meaning they will be
|
||
rotated relative to the standard xyz coordinate axes. See the
|
||
<a class="reference internal" href="dump.html"><span class="doc">dump</span></a> doc page for a full list of which dump attributes
|
||
this affects.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>units</em> keyword only applies to the dump <em>atom</em>, <em>custom</em>, and
|
||
<em>local</em> styles (and their COMPRESS package versions <em>atom/gz</em>,
|
||
<em>custom/gz</em> and <em>local/gz</em>). If set to <em>yes</em>, each individual dump
|
||
file will contain two extra lines at the very beginning with:</p>
|
||
<pre class="literal-block">ITEM: UNITS
|
||
<units style></pre>
|
||
<p>This will output the current selected <a class="reference internal" href="units.html"><span class="doc">units</span></a> style
|
||
to the dump file and thus allows visualization and post-processing
|
||
tools to determine the choice of units of the data in the dump file.
|
||
The default setting is <em>no</em>.</p>
|
||
<hr class="docutils" />
|
||
<p>The <em>unwrap</em> keyword only applies to the dump <em>dcd</em> and <em>xtc</em> styles.
|
||
If set to <em>yes</em>, coordinates will 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>
|
||
<hr class="docutils" />
|
||
<p>The <a class="reference internal" href="Packages_details.html#pkg-compress"><span class="std std-ref">COMPRESS package</span></a> offers both GZ and Zstd
|
||
compression variants of styles atom, custom, local, cfg, and xyz. When
|
||
using these styles the compression level can be controlled by the
|
||
<code class="code docutils literal notranslate"><span class="pre">compression_level</span></code> keyword. File names with these styles have to
|
||
end in either <code class="code docutils literal notranslate"><span class="pre">.gz</span></code> or <code class="code docutils literal notranslate"><span class="pre">.zst</span></code>.</p>
|
||
<p>GZ supports compression levels from <span class="math notranslate nohighlight">\(-1\)</span> (default), 0 (no compression),
|
||
and 1 to 9, 9 being the best compression. The COMPRESS <code class="code docutils literal notranslate"><span class="pre">/gz</span></code> styles use 9
|
||
as default compression level.</p>
|
||
<p>Zstd offers a wider range of compression levels, including negative
|
||
levels that sacrifice compression for performance. 0 is the default,
|
||
positive levels are 1 to 22, with 22 being the most expensive
|
||
compression. Zstd promises higher compression/decompression speeds for
|
||
similar compression ratios. For more details see
|
||
<cite>https://facebook.github.io/zstd/</cite>.</p>
|
||
<p>In addition, Zstd compressed files can include a checksum of the
|
||
entire contents. The Zstd enabled dump styles enable this feature by
|
||
default and it can be disabled with the <code class="code docutils literal notranslate"><span class="pre">checksum</span></code> keyword.</p>
|
||
<hr class="docutils" />
|
||
<p>The <a class="reference internal" href="Packages_details.html#pkg-vtk"><span class="std std-ref">VTK package</span></a> offers writing dump files in <a class="reference external" href="https://www.vtk.org/">VTK file
|
||
formats</a> that can be read by a variety of
|
||
visualization tools based on the VTK library. These VTK files follow
|
||
naming conventions that collide with the LAMMPS convention to append
|
||
“.bin” to a file name in order to switch to a binary output. Thus for
|
||
<a class="reference internal" href="dump_vtk.html"><span class="doc">vtk style dumps</span></a> the dump_modify command supports the
|
||
keyword <em>binary</em> which selects between generating text mode and binary
|
||
style VTK files.</p>
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="restrictions">
|
||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
||
<p>Not all <em>dump_modify</em> options can be applied to all dump styles.
|
||
Details are in the discussions of the individual options.</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_image.html"><span class="doc">dump image</span></a>, <a class="reference internal" href="undump.html"><span class="doc">undump</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</p>
|
||
<ul class="simple">
|
||
<li><p>append = no</p></li>
|
||
<li><p>balance = no</p></li>
|
||
<li><p>buffer = yes for dump styles <em>atom</em>, <em>custom</em>, <em>loca</em>, and <em>xyz</em></p></li>
|
||
<li><p>element = “C” for every atom type</p></li>
|
||
<li><p>every = whatever it was set to via the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command</p></li>
|
||
<li><p>fileper = # of processors</p></li>
|
||
<li><p>first = no</p></li>
|
||
<li><p>flush = yes</p></li>
|
||
<li><p>format = %d and %g for each integer or floating point value</p></li>
|
||
<li><p>image = no</p></li>
|
||
<li><p>label = ENTRIES</p></li>
|
||
<li><p>maxfiles = -1</p></li>
|
||
<li><p>nfile = 1</p></li>
|
||
<li><p>pad = 0</p></li>
|
||
<li><p>pbc = no</p></li>
|
||
<li><p>precision = 1000</p></li>
|
||
<li><p>region = none</p></li>
|
||
<li><p>scale = yes</p></li>
|
||
<li><p>sort = off for dump styles <em>atom</em>, <em>custom</em>, <em>cfg</em>, and <em>local</em></p></li>
|
||
<li><p>sort = id for dump styles <em>dcd</em>, <em>xtc</em>, and <em>xyz</em></p></li>
|
||
<li><p>thresh = none</p></li>
|
||
<li><p>time = no</p></li>
|
||
<li><p>triclinic/general = no</p></li>
|
||
<li><p>types = numeric</p></li>
|
||
<li><p>units = no</p></li>
|
||
<li><p>unwrap = no</p></li>
|
||
<li><p>compression_level = 9 (gz variants)</p></li>
|
||
<li><p>compression_level = 0 (zstd variants)</p></li>
|
||
<li><p>checksum = yes (zstd variants)</p></li>
|
||
</ul>
|
||
</section>
|
||
</section>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
|
||
<a href="dump_image.html" class="btn btn-neutral float-left" title="dump image command" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
|
||
<a href="dump_molfile.html" class="btn btn-neutral float-right" title="dump molfile command" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
|
||
</div>
|
||
|
||
<hr/>
|
||
|
||
<div role="contentinfo">
|
||
<p>© Copyright 2003-2025 Sandia Corporation.</p>
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