forked from lijiext/lammps
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HTML
483 lines
27 KiB
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<title>delete_atoms command — LAMMPS documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute.html">compute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_modify.html">compute_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_atoms.html">create_atoms command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">delete_atoms command</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="delete_bonds.html">delete_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="displace_atoms.html">displace_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-custom-vtk-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">custom/vtk</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-h5md-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">h5md</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-molfile-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">molfile</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_molfile.html">dump molfile command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="special_bonds.html">special_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timer.html">timer command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timestep.html">timestep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="uncompute.html">uncompute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="undump.html">undump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="unfix.html">unfix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="units.html">units command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_coeff.html">write_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
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<li>delete_atoms command</li>
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<div class="section" id="delete-atoms-command">
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<span id="index-0"></span><h1>delete_atoms command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<pre class="literal-block">
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delete_atoms style args keyword value ...
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</pre>
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<ul>
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<li><p class="first">style = <em>group</em> or <em>region</em> or <em>overlap</em> or <em>porosity</em></p>
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<pre class="literal-block">
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<em>group</em> args = group-ID
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<em>region</em> args = region-ID
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<em>overlap</em> args = cutoff group1-ID group2-ID
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cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
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group1-ID = one atom in pair must be in this group
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group2-ID = other atom in pair must be in this group
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<em>porosity</em> args = region-ID fraction seed
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region-ID = region within which to perform deletions
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fraction = delete this fraction of atoms
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seed = random number seed (positive integer)
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</pre>
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</li>
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<li><p class="first">zero or more keyword/value pairs may be appended</p>
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</li>
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<li><p class="first">keyword = <em>compress</em> or <em>bond</em> or <em>mol</em></p>
|
|
<pre class="literal-block">
|
|
<em>compress</em> value = <em>no</em> or <em>yes</em>
|
|
<em>bond</em> value = <em>no</em> or <em>yes</em>
|
|
<em>mol</em> value = <em>no</em> or <em>yes</em>
|
|
</pre>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<pre class="literal-block">
|
|
delete_atoms group edge
|
|
delete_atoms region sphere compress no
|
|
delete_atoms overlap 0.3 all all
|
|
delete_atoms overlap 0.5 solvent colloid
|
|
delete_atoms porosity cube 0.1 482793 bond yes
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Delete the specified atoms. This command can be used to carve out
|
|
voids from a block of material or to delete created atoms that are too
|
|
close to each other (e.g. at a grain boundary).</p>
|
|
<p>For style <em>group</em>, all atoms belonging to the group are deleted.</p>
|
|
<p>For style <em>region</em>, all atoms in the region volume are deleted.
|
|
Additional atoms can be deleted if they are in a molecule for which
|
|
one or more atoms were deleted within the region; see the <em>mol</em>
|
|
keyword discussion below.</p>
|
|
<p>For style <em>overlap</em> pairs of atoms whose distance of separation is
|
|
within the specified cutoff distance are searched for, and one of the
|
|
2 atoms is deleted. Only pairs where one of the two atoms is in the
|
|
first group specified and the other atom is in the second group are
|
|
considered. The atom that is in the first group is the one that is
|
|
deleted.</p>
|
|
<p>Note that it is OK for the two group IDs to be the same (e.g. group
|
|
<em>all</em>), or for some atoms to be members of both groups. In these
|
|
cases, either atom in the pair may be deleted. Also note that if
|
|
there are atoms which are members of both groups, the only guarantee
|
|
is that at the end of the deletion operation, enough deletions will
|
|
have occurred that no atom pairs within the cutoff will remain
|
|
(subject to the group restriction). There is no guarantee that the
|
|
minimum number of atoms will be deleted, or that the same atoms will
|
|
be deleted when running on different numbers of processors.</p>
|
|
<p>For style <em>porosity</em> a specified <em>fraction</em> of atoms are deleted
|
|
within the specified region. For example, if fraction is 0.1, then
|
|
10% of the atoms will be deleted. The atoms to delete are chosen
|
|
randomly. There is no guarantee that the exact fraction of atoms will
|
|
be deleted, or that the same atoms will be deleted when running on
|
|
different numbers of processors.</p>
|
|
<p>If the <em>compress</em> keyword is set to <em>yes</em>, then after atoms are
|
|
deleted, then atom IDs are re-assigned so that they run from 1 to the
|
|
number of atoms in the system. Note that this is not done for
|
|
molecular systems (see the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> command),
|
|
regardless of the <em>compress</em> setting, since it would foul up the bond
|
|
connectivity that has already been assigned.</p>
|
|
<p>A molecular system with fixed bonds, angles, dihedrals, or improper
|
|
interactions, is one where the topology of the interactions is
|
|
typically defined in the data file read by the
|
|
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command, and where the interactions
|
|
themselves are defined with the <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a>,
|
|
<a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a>, etc commands. If you delete atoms
|
|
from such a system, you must be careful not to end up with bonded
|
|
interactions that are stored by remaining atoms but which include
|
|
deleted atoms. This will cause LAMMPS to generate a “missing atoms”
|
|
error when the bonded interaction is computed. The <em>bond</em> and <em>mol</em>
|
|
keywords offer two ways to do that.</p>
|
|
<p>It the <em>bond</em> keyword is set to <em>yes</em> then any bond or angle or
|
|
dihedral or improper interaction that includes a deleted atom is also
|
|
removed from the lists of such interactions stored by non-deleted
|
|
atoms. Note that simply deleting interactions due to dangling bonds
|
|
(e.g. at a surface) may result in a inaccurate or invalid model for
|
|
the remaining atoms.</p>
|
|
<p>It the <em>mol</em> keyword is set to <em>yes</em>, then for every atom that is
|
|
deleted, all other atoms in the same molecule (with the same molecule
|
|
ID) will also be deleted. This is not done for atoms with molecule ID
|
|
= 0, since such an ID is assumed to flag isolated atoms that are not
|
|
part of molecules.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">The molecule deletion operation in invoked after all individual
|
|
atoms have been deleted using the rules described above for each
|
|
style. This means additional atoms may be deleted that are not in the
|
|
group or region, that are not required by the overlap cutoff
|
|
criterion, or that will create a higher fraction of porosity than was
|
|
requested.</p>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>The <em>overlap</em> styles requires inter-processor communication to acquire
|
|
ghost atoms and build a neighbor list. This means that your system
|
|
must be ready to perform a simulation before using this command (force
|
|
fields setup, atom masses set, etc). Since a neighbor list is used to
|
|
find overlapping atom pairs, it also means that you must define a
|
|
<a class="reference internal" href="pair_style.html"><span class="doc">pair style</span></a> with the minimum force cutoff distance
|
|
between any pair of atoms types (plus the <a class="reference internal" href="neighbor.html"><span class="doc">neighbor</span></a>
|
|
skin) >= the specified overlap cutoff.</p>
|
|
<p>If the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command is used with a
|
|
setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not
|
|
appear in the neighbor list, and thus will not be considered for
|
|
deletion by the <em>overlap</em> styles. You probably don’t want to be
|
|
deleting one atom in a bonded pair anyway.</p>
|
|
<p>The <em>bond yes</em> option cannot be used with molecular systems defined
|
|
using molecule template files via the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> and
|
|
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style template</span></a> commands.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults are compress = yes, bond = no, mol = no.</p>
|
|
</div>
|
|
</div>
|
|
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