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<title>delete_bonds command — LAMMPS 15 May 2015 version documentation</title>
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<div class="section" id="delete-bonds-command">
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<span id="index-0"></span><h1>delete_bonds command<a class="headerlink" href="#delete-bonds-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>delete_bonds group-ID style arg keyword ...
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</pre></div>
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</div>
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<ul>
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<li><p class="first">group-ID = group ID</p>
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</li>
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<li><dl class="first docutils">
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<dt>style = <em>multi</em> or <em>atom</em> or <em>bond</em> or <em>angle</em> or <em>dihedral</em> or</dt>
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<dd><p class="first last"><em>improper</em> or <em>stats</em></p>
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</dd>
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</dl>
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</li>
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</ul>
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<pre class="literal-block">
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<em>multi</em> arg = none
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<em>atom</em> arg = an atom type or range of types (see below)
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<em>bond</em> arg = a bond type or range of types (see below)
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<em>angle</em> arg = an angle type or range of types (see below)
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<em>dihedral</em> arg = a dihedral type or range of types (see below)
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<em>improper</em> arg = an improper type or range of types (see below)
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<em>stats</em> arg = none
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</pre>
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<ul class="simple">
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<li>zero or more keywords may be appended</li>
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<li>keyword = <em>any</em> or <em>undo</em> or <em>remove</em> or <em>special</em></li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>delete_bonds frozen multi remove
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delete_bonds all atom 4 special
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delete_bonds all bond 0*3 special
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delete_bonds all stats
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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<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Turn off (or on) molecular topology interactions, i.e. bonds, angles,
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dihedrals, impropers. This command is useful for deleting
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interactions that have been previously turned off by bond-breaking
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potentials. It is also useful for turning off topology interactions
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between frozen or rigid atoms. Pairwise interactions can be turned
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off via the <a class="reference internal" href="neigh_modify.html"><em>neigh_modify exclude</em></a> command. The
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<a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command also effectively turns off certain
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bond and angle interactions.</p>
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<p>For all styles, by default, an interaction is only turned off (or on)
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if all the atoms involved are in the specified group. See the <em>any</em>
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keyword to change the behavior.</p>
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<p>Several of the styles (<em>atom</em>, <em>bond</em>, <em>angle</em>, <em>dihedral</em>,
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<em>improper</em>) take a <em>type</em> as an argument. The specified <em>type</em> should
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be an integer from 0 to N, where N is the number of relevant types
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(atom types, bond types, etc). A value of 0 is only relevant for
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style <em>bond</em>; see details below. In all cases, a wildcard asterisk
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can be used in place of or in conjunction with the <em>type</em> argument to
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specify a range of types. This takes the form “*” or “<em>n” or “n</em>” or
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“m*n”. If N = the number of types, then an asterisk with no numeric
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values means all types from 0 to N. A leading asterisk means all
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types from 0 to n (inclusive). A trailing asterisk means all types
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from n to N (inclusive). A middle asterisk means all types from m to
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n (inclusive). Note that it is fine to include a type of 0 for
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non-bond styles; it will simply be ignored.</p>
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<p>For style <em>multi</em> all bond, angle, dihedral, and improper interactions
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of any type, involving atoms in the group, are turned off.</p>
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<p>Style <em>atom</em> is the same as style <em>multi</em> except that in addition, one
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or more of the atoms involved in the bond, angle, dihedral, or
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improper interaction must also be of the specified atom type.</p>
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<p>For style <em>bond</em>, only bonds are candidates for turn-off, and the bond
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must also be of the specified type. Styles <em>angle</em>, <em>dihedral</em>, and
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<em>improper</em> are treated similarly.</p>
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<p>For style <em>bond</em>, you can set the type to 0 to delete bonds that have
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been previously broken by a bond-breaking potential (which sets the
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bond type to 0 when a bond is broken); e.g. see the <a class="reference internal" href="bond_style.html"><em>bond_style quartic</em></a> command.</p>
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<p>For style <em>stats</em> no interactions are turned off (or on); the status
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of all interactions in the specified group is simply reported. This
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is useful for diagnostic purposes if bonds have been turned off by a
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bond-breaking potential during a previous run.</p>
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<p>The default behavior of the delete_bonds command is to turn off
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interactions by toggling their type to a negative value, but not to
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permanently remove the interaction. E.g. a bond_type of 2 is set to
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-2. The neighbor list creation routines will not include such an
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interaction in their interaction lists. The default is also to not
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alter the list of 1-2, 1-3, 1-4 neighbors computed by the
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<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command and used to weight pairwise
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force and energy calculations. This means that pairwise computations
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will proceed as if the bond (or angle, etc) were still turned on.</p>
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<p>Several keywords can be appended to the argument list to alter the
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default behaviors.</p>
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<p>The <em>any</em> keyword changes the requirement that all atoms in the bond
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(angle, etc) must be in the specified group in order to turn-off the
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interaction. Instead, if any of the atoms in the interaction are in
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the specified group, it will be turned off (or on if the <em>undo</em>
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keyword is used).</p>
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<p>The <em>undo</em> keyword inverts the delete_bonds command so that the
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specified bonds, angles, etc are turned on if they are currently
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turned off. This means a negative value is toggled to positive. For
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example, for style <em>angle</em>, if <em>type</em> is specified as 2, then all
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angles with current type = -2, are reset to type = 2. Note that the
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<a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command also sets bond and angle types
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negative, so this option should not be used on those interactions.</p>
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<p>The <em>remove</em> keyword is invoked at the end of the delete_bonds
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operation. It causes turned-off bonds (angles, etc) to be removed
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from each atom’s data structure and then adjusts the global bond
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(angle, etc) counts accordingly. Removal is a permanent change;
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removed bonds cannot be turned back on via the <em>undo</em> keyword.
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Removal does not alter the pairwise 1-2, 1-3, 1-4 weighting list.</p>
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<p>The <em>special</em> keyword is invoked at the end of the delete_bonds
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operation, after (optional) removal. It re-computes the pairwise 1-2,
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1-3, 1-4 weighting list. The weighting list computation treats
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turned-off bonds the same as turned-on. Thus, turned-off bonds must
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be removed if you wish to change the weighting list.</p>
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<p>Note that the choice of <em>remove</em> and <em>special</em> options affects how
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1-2, 1-3, 1-4 pairwise interactions will be computed across bonds that
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have been modified by the delete_bonds command.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>This command requires inter-processor communication to coordinate the
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deleting of bonds. This means that your system must be ready to
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perform a simulation before using this command (force fields setup,
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atom masses set, etc).</p>
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<p>If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4
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weighting list is not recomputed, this can cause a later <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command to fail due to an atom’s bonds being
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inconsistent with the weighting list. This should only happen if the
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group used in the fix command includes both atoms in the bond, in
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which case you probably should be recomputing the weighting list.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a> exclude,
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<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a>, <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a></p>
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<p><strong>Default:</strong> none</p>
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