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<div class="section" id="dump-modify-command">
<span id="index-0"></span><h1>dump_modify command<a class="headerlink" href="#dump-modify-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>dump_modify dump-ID keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>dump-ID = ID of dump to modify</li>
<li>one or more keyword/value pairs may be appended</li>
<li>these keywords apply to the dump custom/vtk style</li>
<li>keyword = <em>binary</em> or <em>element</em> or <em>every</em> or <em>fileper</em> or <em>first</em> or <em>label</em> or <em>nfile</em> or <em>pad</em> or <em>region</em> or <em>sort</em> or <em>thresh</em></li>
</ul>
<pre class="literal-block">
<em>binary</em> arg = <em>yes</em> or <em>no</em>
<em>element</em> args = E1 E2 ... EN, where N = # of atom types
E1,...,EN = element name, e.g. C or Fe or Ga
<em>every</em> arg = N
N = dump every this many timesteps
N can be a variable (see below)
<em>fileper</em> arg = Np
Np = write one file for every this many processors
<em>first</em> arg = <em>yes</em> or <em>no</em>
<em>label</em> arg = string
string = character string to use in header of legacy VTK file
<em>nfile</em> arg = Nf
Nf = write this many files, one from each of Nf processors
<em>pad</em> arg = Nchar = # of characters to convert timestep to
<em>region</em> arg = region-ID or "none"
<em>sort</em> arg = <em>off</em> or <em>id</em> or N or -N
off = no sorting of per-atom lines within a snapshot
id = sort per-atom lines by atom ID
N = sort per-atom lines in ascending order by the Nth column
-N = sort per-atom lines in descending order by the Nth column
<em>thresh</em> args = attribute operation value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operation = "<" or "<=" or ">" or ">=" or "==" or "!="
value = numeric value to compare to
these 3 args can be replaced by the word "none" to turn off thresholding
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>dump_modify dmpvtp binary yes
dump_modify e_data region mySphere thresh x < 0.0 thresh ervel >= 0.2
dump_modify dmpvtk every 1000 nfile 20
dump_modify dmpvtk every v_myVar
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Modify the parameters of a previously defined dump command.</p>
<p>These keywords apply to the <a class="reference internal" href="dump_custom_vtk.html"><em>dump custom/vtk</em></a> style.
The description gives details.</p>
<hr class="docutils" />
<p>The <em>binary</em> keyword, if specified as <em>yes</em>, causes the output to be
written in binary format. If specified as <em>no</em>, which is the default,
the data is written in ASCII format to the output file.</p>
<hr class="docutils" />
<p>The <em>element</em> keyword associates element names (e.g. H, C, Fe) with
LIGGGHTS(R)-PUBLIC atom types. There are no restrictions to what
label can be used as an element name. Any whitespace separated text
will be accepted.</p>
<hr class="docutils" />
<p>The <em>every</em> keyword changes the dump frequency originally specified by
the <a class="reference internal" href="dump_custom_vtk.html"><em>dump custom/vtk</em></a> command to a new value.
The every 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"><em>equal-style variable</em></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"><em>equal-style variables</em></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"><em>equal-style variables</em></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.</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-python"><div class="highlight"><pre>variable s equal logfreq(10,3,10)
dump 1 all custom/vtk 100 tmp.dump*.vtk vx vy vz
dump_modify 1 every v_s first yes
</pre></div>
</div>
<p>The following commands would write snapshots at the timesteps listed
in file tmp.times:</p>
<div class="highlight-python"><div class="highlight"><pre>variable f file tmp.times
variable s equal next(f)
dump 1 all custom/vtk 100 tmp.dump*.vtk vx vy vz
dump_modify 1 every v_s
</pre></div>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">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" />
<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_custom_vtk.html"><em>dump custom/vtk</em></a> command,
including timestep 0. 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>
<hr class="docutils" />
<p>The <em>fileper</em> keyword is documented below with the <em>nfile</em> keyword.</p>
<hr class="docutils" />
<p>When writing to legacy VTK files, the dump <em>custom/vtk</em> style will
use the specified <em>label</em> as the header line. By default this header line is:</p>
<div class="highlight-python"><div class="highlight"><pre>Generated by LIGGGHTS(R)-PUBLIC
</pre></div>
</div>
<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, if an XML file
format was specified. As explained on the <a class="reference internal" href="dump_custom_vtk.html"><em>dump custom_vtk</em></a>
command doc page, the “%” character causes the dump file to be written
in pieces, one piece for each of P processors. By default P = the
number of processors the simulation is running on. The <em>nfile</em> or
<em>fileper</em> keyword can be used to set P to a smaller value, which can
be more efficient when running on a large number of processors.</p>
<p>The <em>nfile</em> keyword sets P to the specified Nf value. For example, if
Nf = 4, and the simulation is running on 100 processors, 4 files will
be written, by processors 0,25,50,75. Each will collect information
from itself and the next 24 processors and write it to a dump file.</p>
<p>For the <em>fileper</em> keyword, the specified value of Np means write one
file for every Np processors. For example, if Np = 4, every 4th
processor (0,4,8,12,etc) will collect information from itself and the
next 3 processors and write it to a 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> > 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>If the <em>region</em> keyword is specified, only atoms in the region
will be written to the dump file. Only one region can be applied as
a filter (the last one specified). See the <a class="reference internal" href="region.html"><em>region</em></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>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"><em>atom_modify sort</em></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 N or -N means sort the output by the value
in the Nth column of per-atom info in either ascending or descending
order.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">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>Using the <em>thresh</em> keyword, multiple thresholds can be specified.
Specifying “none” turns off all threshold criteria. If thresholds are
specified, only atoms whose attributes meet all the threshold criteria
are written to the dump file. 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_custom_vtk.html"><em>dump custom/vtk</em></a> command, with the exception
of the <em>element</em> attribute, since it is not a numeric value. Note
that different attributes can be output by the dump custom/vtk command
than are used as threshold criteria by the dump_modify command.
E.g. you can output the coordinates and stress of atoms whose energy
is above some threshold.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="dump_custom_vtk.html"><em>dump custom/vtk</em></a>, <a class="reference internal" href="dump_image.html"><em>dump image</em></a>, <a class="reference internal" href="undump.html"><em>undump</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
<p>The option defaults are</p>
<ul class="simple">
<li>binary = no</li>
<li>element = “C” for every atom type</li>
<li>every = whatever it was set to via the <a class="reference internal" href="dump_custom_vtk.html"><em>dump custom/vtk</em></a> command</li>
<li>fileper = # of processors</li>
<li>first = no</li>
<li>label = “Generated by LIGGGHTS”</li>
<li>nfile = 1</li>
<li>pad = 0</li>
<li>region = none</li>
<li>sort = off</li>
<li>thresh = none</li>
</ul>
</div>
</div>
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