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<div class="section" id="fix-bond-create-command">
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<span id="index-0"></span><h1>fix bond/create command<a class="headerlink" href="#fix-bond-create-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>fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
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<li>bond/create = style name of this fix command</li>
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<li>Nevery = attempt bond creation every this many steps</li>
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<li>itype,jtype = atoms of itype can bond to atoms of jtype</li>
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<li>Rmin = 2 atoms separated by less than Rmin can bond (distance units)</li>
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<li>bondtype = type of created bonds</li>
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<li>zero or more keyword/value pairs may be appended to args</li>
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<li>keyword = <em>iparam</em> or <em>jparam</em> or <em>prob</em> or <em>atype</em> or <em>dtype</em> or <em>itype</em></li>
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</ul>
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<pre class="literal-block">
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<em>iparam</em> values = maxbond, newtype
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maxbond = max # of bonds of bondtype the itype atom can have
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newtype = change the itype atom to this type when maxbonds exist
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<em>jparam</em> values = maxbond, newtype
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maxbond = max # of bonds of bondtype the jtype atom can have
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newtype = change the jtype atom to this type when maxbonds exist
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<em>prob</em> values = fraction seed
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fraction = create a bond with this probability if otherwise eligible
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seed = random number seed (positive integer)
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<em>atype</em> value = angletype
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angletype = type of created angles
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<em>dtype</em> value = dihedraltype
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dihedraltype = type of created dihedrals
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<em>itype</em> value = impropertype
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impropertype = type of created impropers
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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<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix 5 all bond/create 10 1 2 0.8 1
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fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3
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fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2
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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>Create bonds between pairs of atoms as a simulation runs according to
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specified criteria. This can be used to model cross-linking of
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polymers, the formation of a percolation network, etc. In this
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context, a bond means an interaction between a pair of atoms computed
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by the <a class="reference internal" href="bond_style.html"><em>bond_style</em></a> command. Once the bond is created
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it will be permanently in place. Optionally, the creation of a bond
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can also create angle, dihedral, and improper interactions that bond
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is part of. See the discussion of the <em>atype</em>, <em>dtype</em>, and <em>itype</em>
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keywords below.</p>
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<p>This is different than a <a class="reference internal" href="pair_style.html"><em>pairwise</em></a> bond-order
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potential such as Tersoff or AIREBO which infers bonds and many-body
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interactions based on the current geometry of a small cluster of atoms
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and effectively creates and destroys bonds and higher-order many-body
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interactions from timestep to timestep as atoms move.</p>
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<p>A check for possible new bonds is performed every <em>Nevery</em> timesteps.
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If two atoms I,J are within a distance <em>Rmin</em> of each other, if I is
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of atom type <em>itype</em>, if J is of atom type <em>jtype</em>, if both I and J
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are in the specified fix group, if a bond does not already exist
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between I and J, and if both I and J meet their respective <em>maxbond</em>
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requirement (explained below), then I,J is labeled as a “possible”
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bond pair.</p>
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<p>If several atoms are close to an atom, it may have multiple possible
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bond partners. Every atom checks its list of possible bond partners
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and labels the closest such partner as its “sole” bond partner. After
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this is done, if atom I has atom J as its sole partner, and atom J has
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atom I as its sole partner, then the I,J bond is “eligible” to be
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formed.</p>
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<p>Note that these rules mean an atom will only be part of at most one
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created bond on a given timestep. It also means that if atom I
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chooses atom J as its sole partner, but atom J chooses atom K is its
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sole partner (due to Rjk < Rij), then this means atom I will not form
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a bond on this timestep, even if it has other possible bond partners.</p>
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<p>It is permissible to have <em>itype</em> = <em>jtype</em>. <em>Rmin</em> must be <= the
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pairwise cutoff distance between <em>itype</em> and <em>jtype</em> atoms, as defined
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by the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command.</p>
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<p>The <em>iparam</em> and <em>jparam</em> keywords can be used to limit the bonding
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functionality of the participating atoms. Each atom keeps track of
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how many bonds of <em>bondtype</em> it already has. If atom I of
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itype already has <em>maxbond</em> bonds (as set by the <em>iparam</em>
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keyword), then it will not form any more. Likewise for atom J. If
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<em>maxbond</em> is set to 0, then there is no limit on the number of bonds
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that can be formed with that atom.</p>
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<p>The <em>newtype</em> value for <em>iparam</em> and <em>jparam</em> can be used to change
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the atom type of atom I or J when it reaches <em>maxbond</em> number of bonds
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of type <em>bondtype</em>. This means it can now interact in a pairwise
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fashion with other atoms in a different way by specifying different
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<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> coefficients. If you do not wish the
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atom type to change, simply specify <em>newtype</em> as <em>itype</em> or <em>jtype</em>.</p>
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<p>The <em>prob</em> keyword can also effect whether an eligible bond is
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actually created. The <em>fraction</em> setting must be a value between 0.0
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and 1.0. A uniform random number between 0.0 and 1.0 is generated and
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the eligible bond is only created if the random number < fraction.</p>
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<p>Any bond that is created is assigned a bond type of <em>bondtype</em></p>
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<p>When a bond is created, data structures within LAMMPS that store bond
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topology are updated to reflect the creation. If the bond is part of
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new 3-body (angle) or 4-body (dihedral, improper) interactions, you
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can choose to create new angles, dihedrals, impropers as well, using
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the <em>atype</em>, <em>dtype</em>, and <em>itype</em> keywords. All of these changes
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typically affect pairwise interactions between atoms that are now part
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of new bonds, angles, etc.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">One data structure that is not updated when a bond
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breaks are the molecule IDs stored by each atom. Even though two
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molecules become one moleclue due to the created bond, all atoms in
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the new moleclue retain their original molecule IDs.</p>
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</div>
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<p>If the <em>atype</em> keyword is used and if an angle potential is defined
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via the <code class="xref doc docutils literal"><span class="pre">angle_style</span></code> command, then any new 3-body
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interactions inferred by the creation of a bond will create new angles
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of type <em>angletype</em>, with parameters assigned by the corresponding
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<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command. Likewise, the <em>dtype</em> and
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<em>itype</em> keywords will create new dihedrals and impropers of type
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<em>dihedraltype</em> and <em>impropertype</em>.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">To create a new bond, the internal LAMMPS data
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structures that store this information must have space for it. When
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LAMMPS is initialized from a data file, the list of bonds is scanned
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and the maximum number of bonds per atom is tallied. If some atom
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will acquire more bonds than this limit as this fix operates, then the
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“extra bond per atom” parameter must be set to allow for it. Ditto
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for “extra angle per atom”, “extra dihedral per atom”, and “extra
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improper per atom” if angles, dihedrals, or impropers are being added
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when bonds are created. See the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
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<a class="reference internal" href="create_box.html"><em>create_box</em></a> command for more details. Note that a
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data file with no atoms can be used if you wish to add unbonded atoms
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via the <a class="reference internal" href="create_atoms.html"><em>create atoms</em></a> command, e.g. for a
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percolation simulation.</p>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">LAMMPS stores and maintains a data structure with a
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list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
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topology of the system) for use in weighting pairwise interactions for
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bonded atoms. Note that adding a single bond always adds a new 1st
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neighbor but may also induce <em>many</em> new 2nd and 3rd neighbors,
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depending on the molecular topology of your system. The “extra
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special per atom” parameter must typically be set to allow for the new
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maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list.
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There are 3 ways to do this. See the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
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<a class="reference internal" href="create_box.html"><em>create_box</em></a> or “special_bonds extra” commands for
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details.</p>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">Even if you do not use the <em>atype</em>, <em>dtype</em>, or
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<em>itype</em> keywords, the list of topological neighbors is updated for
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atoms affected by the new bond. This in turn affects which neighbors
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are considered for pairwise interactions, using the weighting rules
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set by the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command. Consider a new
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bond created between atoms I,J. If J has a bonded neighbor K, then K
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becomes a 2nd neighbor of I. Even if the <em>atype</em> keyword is not used
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to create angle I-J-K, the pairwise interaction between I and K will
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be potentially turned off or weighted by the 1-3 weighting specified
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by the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command. This is the case
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even if the “angle yes” option was used with that command. The same
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is true for 3rd neighbors (1-4 interactions), the <em>dtype</em> keyword, and
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the “dihedral yes” option used with the
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<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command.</p>
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</div>
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<p>Note that even if your simulation starts with no bonds, you must
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define a <a class="reference internal" href="bond_style.html"><em>bond_style</em></a> and use the
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<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command to specify coefficients for the
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<em>bondtype</em>. Similarly, if new atom types are specified by the
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<em>iparam</em> or <em>jparam</em> keywords, they must be within the range of atom
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types allowed by the simulation and pairwise coefficients must be
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specified for the new types.</p>
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<p>Computationally, each timestep this fix operates, it loops over
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neighbor lists and computes distances between pairs of atoms in the
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list. It also communicates between neighboring processors to
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coordinate which bonds are created. Moreover, if any bonds are
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created, neighbor lists must be immediately updated on the same
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timestep. This is to insure that any pairwise interactions that
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should be turned “off” due to a bond creation, because they are now
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excluded by the presence of the bond and the settings of the
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<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command, will be immediately
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recognized. All of these operations increase the cost of a timestep.
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Thus you should be cautious about invoking this fix too frequently.</p>
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<p>You can dump out snapshots of the current bond topology via the <a class="reference internal" href="dump.html"><em>dump local</em></a> command.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">Creating a bond typically alters the energy of a
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system. You should be careful not to choose bond creation criteria
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that induce a dramatic change in energy. For example, if you define a
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very stiff harmonic bond and create it when 2 atoms are separated by a
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distance far from the equilibribum bond length, then the 2 atoms will
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oscillate dramatically when the bond is formed. More generally, you
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may need to thermostat your system to compensate for energy changes
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resulting from created bonds (and angles, dihedrals, impropers).</p>
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</div>
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</div>
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<hr class="docutils" />
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<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
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<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
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<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options
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are relevant to this fix.</p>
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<p>This fix computes two statistics which it stores in a global vector of
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length 2, which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The vector values calculated
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by this fix are “intensive”.</p>
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<p>These are the 2 quantities:</p>
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<ul class="simple">
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<li><ol class="first arabic">
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<li># of bonds created on the most recent creation timestep</li>
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</ol>
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</li>
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<li><ol class="first arabic" start="2">
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<li>cummulative # of bonds created</li>
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</ol>
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</li>
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</ul>
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<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
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the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</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 fix is part of the MC package. It is only enabled if LAMMPS was
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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>
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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="fix_bond_break.html"><em>fix bond/break</em></a>, <a class="reference internal" href="fix_bond_swap.html"><em>fix bond/swap</em></a>, <a class="reference internal" href="dump.html"><em>dump local</em></a>,
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<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
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