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<div class="section" id="dump-custom-vtk-command">
<span id="index-0"></span><h1>dump custom/vtk command<a class="headerlink" href="#dump-custom-vtk-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 ID group-ID style N file args
</pre></div>
</div>
<ul class="simple">
<li>ID = user-assigned name for the dump</li>
<li>group-ID = ID of the group of atoms to be dumped</li>
<li>style = <em>custom/vtk</em></li>
<li>N = dump every this many timesteps</li>
<li>file = name of file to write dump info to</li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>custom/vtk</em> args = list of atom attributes
possible attributes = id, mol, proc, procp1, type, element, mass,
x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
spin, eradius, ervel, erforce,
c_ID, c_ID[N], f_ID, f_ID[N], v_name
</pre>
<pre class="literal-block">
id = atom ID
mol = molecule ID
proc = ID of processor that owns atom
procp1 = ID+1 of processor that owns atom
type = atom type
element = name of atom element, as defined by <code class="xref doc docutils literal"><span class="pre">dump_modify</span></code> command
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
xu,yu,zu = unwrapped atom coordinates
xsu,ysu,zsu = scaled unwrapped atom coordinates
ix,iy,iz = box image that the atom is in
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
tqx,tqy,tqz = torque on finite-size particles
c_ID = per-atom vector calculated by a compute with ID
c_ID[N] = Nth column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
f_ID[N] = Nth column of per-atom array calculated by a fix with ID
v_name = per-atom vector calculated by an atom-style variable with name
</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 dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce
</pre></div>
</div>
<p>The style <em>custom/vtk</em> is similar to the <a class="reference internal" href="dump.html"><em>custom</em></a> style but
uses the VTK library to write data to VTK simple legacy or XML format
depending on the filename extension specified. This can be either
<a href="#id1"><span class="problematic" id="id2">**</span></a>.vtk* for the legacy format or <a href="#id3"><span class="problematic" id="id4">**</span></a>.vtp* and <a href="#id5"><span class="problematic" id="id6">**</span></a>.vtu*, respectively,
for the XML format; see the <a class="reference external" href="http://www.vtk.org/VTK/img/file-formats.pdf">VTK homepage</a> for a detailed
description of these formats. Since this naming convention conflicts
with the way binary output is usually specified (see below),
<code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">binary</span></code> allows to set the binary
flag for this dump style explicitly.</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Dump a snapshot of atom quantities to one or more files every N
timesteps in a format readable by the <a class="reference external" href="http://www.vtk.org">VTK visualization toolkit</a> or other visualization tools that use it,
e.g. <a class="reference external" href="http://www.paraview.org">ParaView</a>. The timesteps on which dump
output is written can also be controlled by a variable; see the
<code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">every</span></code> command for details.</p>
<p>Only information for atoms in the specified group is dumped. The
<code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">thresh</span> <span class="pre">and</span> <span class="pre">region</span></code> commands can also
alter what atoms are included; see details below.</p>
<p>As described below, special characters (&#8220;*&#8221;, &#8220;%&#8221;) in the filename
determine the kind of output.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Because periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an
atom written to a dump file may be slightly outside the simulation
box.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Unless the <code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">sort</span></code>
option is invoked, the lines of atom information written to dump files
will be in an indeterminate order for each snapshot. This is even
true when running on a single processor, if the <a class="reference internal" href="atom_modify.html"><em>atom_modify sort</em></a> option is on, which it is by default. In this
case atoms are re-ordered periodically during a simulation, due to
spatial sorting. It is also true when running in parallel, because
data for a single snapshot is collected from multiple processors, each
of which owns a subset of the atoms.</p>
</div>
<p>For the <em>custom/vtk</em> style, sorting is off by default. See the
<code class="xref doc docutils literal"><span class="pre">dump_modify</span></code> doc page for details.</p>
<hr class="docutils" />
<p>The dimensions of the simulation box are written to a separate file
for each snapshot (either in legacy VTK or XML format depending on
the format of the main dump file) with the suffix <em>_boundingBox</em>
appended to the given dump filename.</p>
<p>For an orthogonal simulation box this information is saved as a
rectilinear grid (legacy .vtk or .vtr XML format).</p>
<p>Triclinic simulation boxes (non-orthogonal) are saved as
hexahedrons in either legacy .vtk or .vtu XML format.</p>
<p>Style <em>custom/vtk</em> allows you to specify a list of atom attributes
to be written to the dump file for each atom. Possible attributes
are listed above. In contrast to the <em>custom</em> style, the attributes
are rearranged to ensure correct ordering of vector components
(except for computes and fixes - these have to be given in the right
order) and duplicate entries are removed.</p>
<p>You cannot specify a quantity that is not defined for a particular
simulation - such as <em>q</em> for atom style <em>bond</em>, since that atom style
doesn&#8217;t assign charges. Dumps occur at the very end of a timestep,
so atom attributes will include effects due to fixes that are applied
during the timestep. An explanation of the possible dump custom/vtk attributes
is given below. Since position data is required to write VTK files &#8220;x y z&#8221;
do not have to be specified explicitly.</p>
<p>The VTK format uses a single snapshot of the system per file, thus
a wildcard &#8220;*&#8221; must be included in the filename, as discussed below.
Otherwise the dump files will get overwritten with the new snapshot
each time.</p>
<hr class="docutils" />
<p>Dumps are performed on timesteps that are a multiple of N (including
timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
changed via the <code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">first</span></code> command, which
can also be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
using the <code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">every</span></code> command.
The <code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">every</span></code> command
also allows a variable to be used to determine the sequence of
timesteps on which dump files are written. In this mode a dump on the
first timestep of a run will also not be written unless the
<code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">first</span></code> command is used.</p>
<p>Dump filenames can contain two wildcard characters. If a &#8220;*&#8221;
character appears in the filename, then one file per snapshot is
written and the &#8220;*&#8221; character is replaced with the timestep value.
For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
tmp.dump20000.vtk, etc. Note that the <code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">pad</span></code>
command can be used to insure all timestep numbers are the same length
(e.g. 00010), which can make it easier to read a series of dump files
in order with some post-processing tools.</p>
<p>If a &#8220;%&#8221; character appears in the filename, then each of P processors
writes a portion of the dump file, and the &#8220;%&#8221; character is replaced
with the processor ID from 0 to P-1 preceded by an underscore character.
For example, tmp.dump%.vtp becomes tmp.dump_0.vtp, tmp.dump_1.vtp, ...
tmp.dump_P-1.vtp, etc. This creates smaller files and can be a fast
mode of output on parallel machines that support parallel I/O for output.</p>
<p>By default, P = the number of processors meaning one file per
processor, but P can be set to a smaller value via the <em>nfile</em> or
<em>fileper</em> keywords of the <code class="xref doc docutils literal"><span class="pre">dump_modify</span></code> command.
These options can be the most efficient way of writing out dump files
when running on large numbers of processors.</p>
<p>For the legacy VTK format &#8220;%&#8221; is ignored and P = 1, i.e., only
processor 0 does write files.</p>
<p>Note that using the &#8220;*&#8221; and &#8220;%&#8221; characters together can produce a
large number of small dump files!</p>
<p>If <em>dump_modify binary</em> is used, the dump file (or files, if &#8220;*&#8221; or
&#8220;%&#8221; is also used) is written in binary format. A binary dump file
will be about the same size as a text version, but will typically
write out much faster.</p>
<hr class="docutils" />
<p>This section explains the atom attributes that can be specified as
part of the <em>custom/vtk</em> style.</p>
<p>The <em>id</em>, <em>mol</em>, <em>proc</em>, <em>procp1</em>, <em>type</em>, <em>element</em>, <em>mass</em>, <em>vx</em>,
<em>vy</em>, <em>vz</em>, <em>fx</em>, <em>fy</em>, <em>fz</em>, <em>q</em> attributes are self-explanatory.</p>
<p><em>id</em> is the atom ID. <em>mol</em> is the molecule ID, included in the data
file for molecular systems. <em>type</em> is the atom type. <em>element</em> is
typically the chemical name of an element, which you must assign to
each type via the <code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">element</span></code> command.
More generally, it can be any string you wish to associate with an
atom type. <em>mass</em> is the atom mass. <em>vx</em>, <em>vy</em>, <em>vz</em>, <em>fx</em>, <em>fy</em>,
<em>fz</em>, and <em>q</em> are components of atom velocity and force and atomic
charge.</p>
<p>There are several options for outputting atom coordinates. The <em>x</em>,
<em>y</em>, <em>z</em> attributes are used to write atom coordinates &#8220;unscaled&#8221;, in
the appropriate distance <a class="reference internal" href="units.html"><em>units</em></a> (Angstroms, sigma, etc).
Additionaly, you can use <em>xs</em>, <em>ys</em>, <em>zs</em> if you want to also save the
coordinates &#8220;scaled&#8221; to the box size, so that each value is 0.0 to
1.0. If the simulation box is triclinic (tilted), then all atom
coords will still be between 0.0 and 1.0. Use <em>xu</em>, <em>yu</em>, <em>zu</em> if you
want the coordinates &#8220;unwrapped&#8221; by the image flags for each atom.
Unwrapped means that if the atom has passed through a periodic
boundary one or more times, the value is printed for what the
coordinate would be if it had not been wrapped back into the periodic
box. Note that using <em>xu</em>, <em>yu</em>, <em>zu</em> means that the coordinate
values may be far outside the box bounds printed with the snapshot.
Using <em>xsu</em>, <em>ysu</em>, <em>zsu</em> is similar to using <em>xu</em>, <em>yu</em>, <em>zu</em>, except
that the unwrapped coordinates are scaled by the box size. Atoms that
have passed through a periodic boundary will have the corresponding
cooordinate increased or decreased by 1.0.</p>
<p>The image flags can be printed directly using the <em>ix</em>, <em>iy</em>, <em>iz</em>
attributes. For periodic dimensions, they specify which image of the
simulation box the atom is considered to be in. An image of 0 means
it is inside the box as defined. A value of 2 means add 2 box lengths
to get the true value. A value of -1 means subtract 1 box length to
get the true value. LAMMPS updates these flags as atoms cross
periodic boundaries during the simulation.</p>
<p>The <em>mux</em>, <em>muy</em>, <em>muz</em> attributes are specific to dipolar systems
defined with an atom style of <em>dipole</em>. They give the orientation of
the atom&#8217;s point dipole moment. The <em>mu</em> attribute gives the
magnitude of the atom&#8217;s dipole moment.</p>
<p>The <em>radius</em> and <em>diameter</em> attributes are specific to spherical
particles that have a finite size, such as those defined with an atom
style of <em>sphere</em>.</p>
<p>The <em>omegax</em>, <em>omegay</em>, and <em>omegaz</em> attributes are specific to
finite-size spherical particles that have an angular velocity. Only
certain atom styles, such as <em>sphere</em> define this quantity.</p>
<p>The <em>angmomx</em>, <em>angmomy</em>, and <em>angmomz</em> attributes are specific to
finite-size aspherical particles that have an angular momentum. Only
the <em>ellipsoid</em> atom style defines this quantity.</p>
<p>The <em>tqx</em>, <em>tqy</em>, <em>tqz</em> attributes are for finite-size particles that
can sustain a rotational torque due to interactions with other
particles.</p>
<p>The <em>spin</em>, <em>eradius</em>, <em>ervel</em>, and <em>erforce</em> attributes are for
particles that represent nuclei and electrons modeled with the
electronic force field (EFF). See <a class="reference internal" href="atom_style.html"><em>atom_style electron</em></a> and <a class="reference internal" href="pair_eff.html"><em>pair_style eff</em></a> for more
details.</p>
<p>The <em>c_ID</em> and <em>c_ID[N]</em> attributes allow per-atom vectors or arrays
calculated by a <a class="reference internal" href="compute.html"><em>compute</em></a> to be output. The ID in the
attribute should be replaced by the actual ID of the compute that has
been defined previously in the input script. See the
<a class="reference internal" href="compute.html"><em>compute</em></a> command for details. There are computes for
calculating the per-atom energy, stress, centro-symmetry parameter,
and coordination number of individual atoms.</p>
<p>Note that computes which calculate global or local quantities, as
opposed to per-atom quantities, cannot be output in a dump custom/vtk
command. Instead, global quantities can be output by the
<a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> command, and local quantities
can be output by the dump local command.</p>
<p>If <em>c_ID</em> is used as an attribute, then the per-atom vector calculated
by the compute is printed. If <em>c_ID[N]</em> is used, then N must be in
the range from 1-M, which will print the Nth column of the M-length
per-atom array calculated by the compute.</p>
<p>The <em>f_ID</em> and <em>f_ID[N]</em> attributes allow vector or array per-atom
quantities calculated by a <a class="reference internal" href="fix.html"><em>fix</em></a> to be output. The ID in the
attribute should be replaced by the actual ID of the fix that has been
defined previously in the input script. The <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a> command is one that calculates per-atom
quantities. Since it can time-average per-atom quantities produced by
any <a class="reference internal" href="compute.html"><em>compute</em></a>, <a class="reference internal" href="fix.html"><em>fix</em></a>, or atom-style
<a class="reference internal" href="variable.html"><em>variable</em></a>, this allows those time-averaged results to
be written to a dump file.</p>
<p>If <em>f_ID</em> is used as a attribute, then the per-atom vector calculated
by the fix is printed. If <em>f_ID[N]</em> is used, then N must be in the
range from 1-M, which will print the Nth column of the M-length
per-atom array calculated by the fix.</p>
<p>The <em>v_name</em> attribute allows per-atom vectors calculated by a
<a class="reference internal" href="variable.html"><em>variable</em></a> to be output. The name in the attribute
should be replaced by the actual name of the variable that has been
defined previously in the input script. Only an atom-style variable
can be referenced, since it is the only style that generates per-atom
values. Variables of style <em>atom</em> can reference individual atom
attributes, per-atom atom attributes, thermodynamic keywords, or
invoke other computes, fixes, or variables when they are evaluated, so
this is a very general means of creating quantities to output to a
dump file.</p>
<p>See <a class="reference internal" href="Section_modify.html"><em>Section_modify</em></a> of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The <em>custom/vtk</em> style does not support writing of gzipped dump files.</p>
<p>The <em>custom/vtk</em> dump style is part of the USER-VTK package. It is
only enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>To use this dump style, you also must link to the VTK library. See
the info in lib/vtk/README and insure the Makefile.lammps file in that
directory is appropriate for your machine.</p>
<p>The <em>custom/vtk</em> dump style neither supports buffering nor custom
format strings.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="dump_image.html"><em>dump image</em></a>,
<a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a>, <a class="reference internal" href="undump.html"><em>undump</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>By default, files are written in ASCII format. If the file extension
is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used.</p>
</div>
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