forked from lijiext/lammps
329 lines
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HTML
329 lines
14 KiB
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<a href="Manual.html" class="icon icon-home"> LAMMPS
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li><a href="Manual.html">Docs</a> »</li>
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<li>delete_atoms command</li>
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<a href="http://lammps.sandia.gov">Website</a>
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<a href="Section_commands.html#comm">Commands</a>
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<div itemprop="articleBody">
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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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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_atoms</span> <span class="n">style</span> <span class="n">args</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>style = <em>group</em> or <em>region</em> or <em>overlap</em> or <em>porosity</em></li>
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</ul>
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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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<ul class="simple">
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>compress</em> or <em>bond</em> or <em>mol</em></li>
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</ul>
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<pre class="literal-block">
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<em>compress</em> value = <em>no</em> or <em>yes</em>
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<em>bond</em> value = <em>no</em> or <em>yes</em>
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<em>mol</em> value = <em>no</em> or <em>yes</em>
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_atoms</span> <span class="n">group</span> <span class="n">edge</span>
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<span class="n">delete_atoms</span> <span class="n">region</span> <span class="n">sphere</span> <span class="n">compress</span> <span class="n">no</span>
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<span class="n">delete_atoms</span> <span class="n">overlap</span> <span class="mf">0.3</span> <span class="nb">all</span> <span class="nb">all</span>
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<span class="n">delete_atoms</span> <span class="n">overlap</span> <span class="mf">0.5</span> <span class="n">solvent</span> <span class="n">colloid</span>
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<span class="n">delete_atoms</span> <span class="n">porosity</span> <span class="n">cube</span> <span class="mf">0.1</span> <span class="mi">482793</span> <span class="n">bond</span> <span class="n">yes</span>
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description</h2>
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<p>Delete the specified atoms. This command can be used to carve out
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voids from a block of material or to delete created atoms that are too
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close to each other (e.g. at a grain boundary).</p>
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<p>For style <em>group</em>, all atoms belonging to the group are deleted.</p>
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<p>For style <em>region</em>, all atoms in the region volume are deleted.
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Additional atoms can be deleted if they are in a molecule for which
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one or more atoms were deleted within the region; see the <em>mol</em>
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keyword discussion below.</p>
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<p>For style <em>overlap</em> pairs of atoms whose distance of separation is
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within the specified cutoff distance are searched for, and one of the
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2 atoms is deleted. Only pairs where one of the two atoms is in the
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first group specified and the other atom is in the second group are
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considered. The atom that is in the first group is the one that is
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deleted.</p>
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<p>Note that it is OK for the two group IDs to be the same (e.g. group
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<em>all</em>), or for some atoms to be members of both groups. In these
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cases, either atom in the pair may be deleted. Also note that if
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there are atoms which are members of both groups, the only guarantee
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is that at the end of the deletion operation, enough deletions will
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have occurred that no atom pairs within the cutoff will remain
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(subject to the group restriction). There is no guarantee that the
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minimum number of atoms will be deleted, or that the same atoms will
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be deleted when running on different numbers of processors.</p>
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<p>For style <em>porosity</em> a specified <em>fraction</em> of atoms are deleted
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within the specified region. For example, if fraction is 0.1, then
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10% of the atoms will be deleted. The atoms to delete are chosen
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randomly. There is no guarantee that the exact fraction of atoms will
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be deleted, or that the same atoms will be deleted when running on
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different numbers of processors.</p>
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<p>If the <em>compress</em> keyword is set to <em>yes</em>, then after atoms are
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deleted, then atom IDs are re-assigned so that they run from 1 to the
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number of atoms in the system. Note that this is not done for
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molecular systems (see the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> command),
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regardless of the <em>compress</em> setting, since it would foul up the bond
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connectivity that has already been assigned.</p>
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<p>A molecular system with fixed bonds, angles, dihedrals, or improper
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interactions, is one where the topology of the interactions is
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typically defined in the data file read by the
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<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command, and where the interactions
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themselves are defined with the <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a>,
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<a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a>, etc commands. If you delete atoms
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from such a system, you must be careful not to end up with bonded
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interactions that are stored by remaining atoms but which include
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deleted atoms. This will cause LAMMPS to generate a “missing atoms”
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error when the bonded interaction is computed. The <em>bond</em> and <em>mol</em>
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keywords offer two ways to do that.</p>
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<p>It the <em>bond</em> keyword is set to <em>yes</em> then any bond or angle or
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dihedral or improper interaction that includes a deleted atom is also
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removed from the lists of such interactions stored by non-deleted
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atoms. Note that simply deleting interactions due to dangling bonds
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(e.g. at a surface) may result in a inaccurate or invalid model for
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the remaining atoms.</p>
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<p>It the <em>mol</em> keyword is set to <em>yes</em>, then for every atom that is
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deleted, all other atoms in the same molecule (with the same molecule
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ID) will also be deleted. This is not done for atoms with molecule ID
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= 0, since such an ID is assumed to flag isolated atoms that are not
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part of molecules.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">The molecule deletion operation in invoked after all individual
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atoms have been deleted using the rules described above for each
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style. This means additional atoms may be deleted that are not in the
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group or region, that are not required by the overlap cutoff
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criterion, or that will create a higher fraction of porosity than was
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requested.</p>
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</div>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<p>The <em>overlap</em> styles requires inter-processor communication to acquire
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ghost atoms and build a neighbor list. This means that your system
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must be ready to perform a simulation before using this command (force
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fields setup, atom masses set, etc). Since a neighbor list is used to
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find overlapping atom pairs, it also means that you must define a
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<a class="reference internal" href="pair_style.html"><span class="doc">pair style</span></a> with the minimum force cutoff distance
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between any pair of atoms types (plus the <a class="reference internal" href="neighbor.html"><span class="doc">neighbor</span></a>
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skin) >= the specified overlap cutoff.</p>
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<p>If the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command is used with a
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setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not
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appear in the neighbor list, and thus will not be considered for
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deletion by the <em>overlap</em> styles. You probably don’t want to be
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deleting one atom in a bonded pair anyway.</p>
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<p>The <em>bond yes</em> option cannot be used with molecular systems defined
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using molecule template files via the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> and
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<a class="reference internal" href="atom_style.html"><span class="doc">atom_style template</span></a> commands.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default</h2>
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<p>The option defaults are compress = yes, bond = no, mol = no.</p>
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</div>
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</div>
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