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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_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</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_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 class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li>fix deposit command</li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div class="section" id="fix-deposit-command">
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<span id="index-0"></span><h1>fix deposit 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">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">deposit</span> <span class="n">N</span> <span class="nb">type</span> <span class="n">M</span> <span class="n">seed</span> <span class="n">keyword</span> <span class="n">values</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>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
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<li>deposit = style name of this fix command</li>
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<li>N = # of atoms or molecules to insert</li>
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<li>type = atom type to assign to inserted atoms (offset for moleclue insertion)</li>
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<li>M = insert a single atom or molecule every M steps</li>
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<li>seed = random # seed (positive integer)</li>
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<li>one or more keyword/value pairs may be appended to args</li>
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<li>keyword = <em>region</em> or <em>id</em> or <em>global</em> or <em>local</em> or <em>near</em> or <em>gaussian</em> or <em>attempt</em> or <em>rate</em> or <em>vx</em> or <em>vy</em> or <em>vz</em> or <em>mol</em> or <em>rigid</em> or <em>shake</em> or <em>units</em></li>
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</ul>
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<pre class="literal-block">
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<em>region</em> value = region-ID
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region-ID = ID of region to use as insertion volume
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<em>id</em> value = <em>max</em> or <em>next</em>
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max = atom ID for new atom(s) is max ID of all current atoms plus one
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next = atom ID for new atom(s) increments by one for every deposition
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<em>global</em> values = lo hi
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lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
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<em>local</em> values = lo hi delta
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lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
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delta = lateral distance within which a neighbor is considered "nearby" (distance units)
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<em>near</em> value = R
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R = only insert atom/molecule if further than R from existing particles (distance units)
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<em>gaussian</em> values = xmid ymid zmid sigma
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xmid,ymid,zmid = center of the gaussian distribution (distance units)
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sigma = width of gaussian distribution (distance units)
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<em>attempt</em> value = Q
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Q = attempt a single insertion up to Q times
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<em>rate</em> value = V
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V = z velocity (y in 2d) at which insertion volume moves (velocity units)
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<em>vx</em> values = vxlo vxhi
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vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
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<em>vy</em> values = vylo vyhi
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vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
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<em>vz</em> values = vzlo vzhi
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vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
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<em>target</em> values = tx ty tz
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tx,ty,tz = location of target point (distance units)
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<em>mol</em> value = template-ID
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template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command
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<em>molfrac</em> values = f1 f2 ... fN
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f1 to fN = relative probability of creating each of N molecules in template-ID
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<em>rigid</em> value = fix-ID
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fix-ID = ID of <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/small</span></a> command
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<em>shake</em> value = fix-ID
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fix-ID = ID of <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> command
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<em>units</em> value = <em>lattice</em> or <em>box</em>
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lattice = the geometry is defined in lattice units
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box = the geometry is defined in simulation box units
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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">fix</span> <span class="mi">3</span> <span class="nb">all</span> <span class="n">deposit</span> <span class="mi">1000</span> <span class="mi">2</span> <span class="mi">100</span> <span class="mi">29494</span> <span class="n">region</span> <span class="n">myblock</span> <span class="n">local</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="n">units</span> <span class="n">box</span>
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<span class="n">fix</span> <span class="mi">2</span> <span class="n">newatoms</span> <span class="n">deposit</span> <span class="mi">10000</span> <span class="mi">1</span> <span class="mi">500</span> <span class="mi">12345</span> <span class="n">region</span> <span class="n">disk</span> <span class="n">near</span> <span class="mf">2.0</span> <span class="n">vz</span> <span class="o">-</span><span class="mf">1.0</span> <span class="o">-</span><span class="mf">0.8</span>
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<span class="n">fix</span> <span class="mi">4</span> <span class="n">sputter</span> <span class="n">deposit</span> <span class="mi">1000</span> <span class="mi">2</span> <span class="mi">500</span> <span class="mi">12235</span> <span class="n">region</span> <span class="n">sphere</span> <span class="n">vz</span> <span class="o">-</span><span class="mf">1.0</span> <span class="o">-</span><span class="mf">1.0</span> <span class="n">target</span> <span class="mf">5.0</span> <span class="mf">5.0</span> <span class="mf">0.0</span> <span class="n">units</span> <span class="n">lattice</span>
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<span class="n">fix</span> <span class="mi">5</span> <span class="n">insert</span> <span class="n">deposit</span> <span class="mi">200</span> <span class="mi">2</span> <span class="mi">100</span> <span class="mi">777</span> <span class="n">region</span> <span class="n">disk</span> <span class="n">gaussian</span> <span class="mf">5.0</span> <span class="mf">5.0</span> <span class="mf">9.0</span> <span class="mf">1.0</span> <span class="n">units</span> <span class="n">box</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>Insert a single atom or molecule into the simulation domain every M
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timesteps until N atoms or molecules have been inserted. This is
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useful for simulating deposition onto a surface. For the remainder of
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this doc page, a single inserted atom or molecule is referred to as a
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“particle”.</p>
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<p>If inserted particles are individual atoms, they are assigned the
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specified atom type. If they are molecules, the type of each atom in
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the inserted molecule is specified in the file read by the
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<a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command, and those values are added to the
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specified atom type. E.g. if the file specifies atom types 1,2,3, and
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those are the atom types you want for inserted molecules, then specify
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<em>type</em> = 0. If you specify <em>type</em> = 2, the in the inserted molecule
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will have atom types 3,4,5.</p>
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<p>All atoms in the inserted particle are assigned to two groups: the
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default group “all” and the group specified in the fix deposit command
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(which can also be “all”).</p>
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<p>If you are computing temperature values which include inserted
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particles, you will want to use the
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<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> dynamic option, which insures the
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current number of atoms is used as a normalizing factor each time the
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temperature is computed.</p>
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<p>Care must be taken that inserted particles are not too near existing
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atoms, using the options described below. When inserting particles
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above a surface in a non-periodic box (see the
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<a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command), the possibility of a particle
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escaping the surface and flying upward should be considered, since the
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particle may be lost or the box size may grow infinitely large. A
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<a class="reference internal" href="fix_wall_reflect.html"><span class="doc">fix wall/reflect</span></a> command can be used to
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prevent this behavior. Note that if a shrink-wrap boundary is used,
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it is OK to insert the new particle outside the box, however the box
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will immediately be expanded to include the new particle. When
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simulating a sputtering experiment it is probably more realistic to
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ignore those atoms using the <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a>
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command with the <em>lost ignore</em> option and a fixed
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<a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a>.</p>
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<p>The fix deposit command must use the <em>region</em> keyword to define an
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insertion volume. The specified region must have been previously
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defined with a <a class="reference internal" href="region.html"><span class="doc">region</span></a> command. It must be defined with
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side = <em>in</em>.</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">LAMMPS checks that the specified region is wholly inside the
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simulation box. It can do this correctly for orthonormal simulation
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boxes. However for <a class="reference internal" href="Section_howto.html#howto-12"><span class="std std-ref">triclinic boxes</span></a>, it
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only tests against the larger orthonormal box that bounds the tilted
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simulation box. If the specified region includes volume outside the
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tilted box, then an insertion will likely fail, leading to a “lost
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atoms” error. Thus for triclinic boxes you should insure the
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specified region is wholly inside the simulation box.</p>
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</div>
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<p>The locations of inserted particles are taken from uniform distributed
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random numbers, unless the <em>gaussian</em> keyword is used. Then the
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individual coordinates are taken from a gaussian distribution of
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width <em>sigma</em> centered on <em>xmid,ymid,zmid</em>.</p>
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<p>Individual atoms are inserted, unless the <em>mol</em> keyword is used. It
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specifies a <em>template-ID</em> previously defined using the
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<a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command, which reads files that define one or
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more molecules. The coordinates, atom types, charges, etc, as well as
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any bond/angle/etc and special neighbor information for the molecule
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can be specified in the molecule file. See the
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<a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command for details. The only settings
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required to be in each file are the coordinates and types of atoms in
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the molecule.</p>
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<p>If the molecule template contains more than one molecule, the relative
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probability of depositing each molecule can be specified by the
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<em>molfrac</em> keyword. N relative probablities, each from 0.0 to 1.0, are
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specified, where N is the number of molecules in the template. Each
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time a molecule is deposited, a random number is used to sample from
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the list of relative probabilities. The N values must sum to 1.0.</p>
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<p>If you wish to insert molecules via the <em>mol</em> keyword, that will be
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treated as rigid bodies, use the <em>rigid</em> keyword, specifying as its
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value the ID of a separate <span class="xref doc">fix rigid/small</span>
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command which also appears in your input script.</p>
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<p>If you wish to insert molecules via the <em>mol</em> keyword, that will have
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their bonds or angles constrained via SHAKE, use the <em>shake</em> keyword,
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specifying as its value the ID of a separate <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> command which also appears in your input script.</p>
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<p>Each timestep a particle is inserted, the coordinates for its atoms
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are chosen as follows. For insertion of individual atoms, the
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“position” referred to in the following description is the coordinate
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of the atom. For insertion of molecule, the “position” is the
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geometric center of the molecule; see the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> doc
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page for details. A random rotation of the molecule around its center
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point is performed, which determines the coordinates all the
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individual atoms.</p>
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<p>A random position within the region insertion volume is generated. If
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neither the <em>global</em> or <em>local</em> keyword is used, the random position
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is the trial position. If the <em>global</em> keyword is used, the random
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x,y values are used, but the z position of the new particle is set
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above the highest current atom in the simulation by a distance
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randomly chosen between lo/hi. (For a 2d simulation, this is done for
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the y position.) If the <em>local</em> keyword is used, the z position is
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set a distance between lo/hi above the highest current atom in the
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simulation that is “nearby” the chosen x,y position. In this context,
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“nearby” means the lateral distance (in x,y) between the new and old
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particles is less than the <em>delta</em> setting.</p>
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<p>Once a trial x,y,z position has been selected, the insertion is only
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performed if no current atom in the simulation is within a distance R
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of any atom in the new particle, including the effect of periodic
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boundary conditions if applicable. R is defined by the <em>near</em>
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keyword. Note that the default value for R is 0.0, which will allow
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atoms to strongly overlap if you are inserting where other atoms are
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present. This distance test is performed independently for each atom
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in an inserted molecule, based on the randomly rotated configuration
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of the molecule. If this test fails, a new random position within the
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insertion volume is chosen and another trial is made. Up to Q
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attempts are made. If the particle is not successfully inserted,
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LAMMPS prints a warning message.</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">If you are inserting finite size particles or a molecule or
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rigid body consisting of finite-size particles, then you should
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typically set R larger than the distance at which any inserted
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particle may overlap with either a previouly inserted particle or an
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existing particle. LAMMPS will issue a warning if R is smaller than
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this value, based on the radii of existing and inserted particles.</p>
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</div>
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<p>The <em>rate</em> option moves the insertion volume in the z direction (3d)
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or y direction (2d). This enables particles to be inserted from a
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successively higher height over time. Note that this parameter is
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ignored if the <em>global</em> or <em>local</em> keywords are used, since those
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options choose a z-coordinate for insertion independently.</p>
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<p>The vx, vy, and vz components of velocity for the inserted particle
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are set using the values specified for the <em>vx</em>, <em>vy</em>, and <em>vz</em>
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keywords. Note that normally, new particles should be a assigned a
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negative vertical velocity so that they move towards the surface. For
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molecules, the same velocity is given to every particle (no rotation
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or bond vibration).</p>
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<p>If the <em>target</em> option is used, the velocity vector of the inserted
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particle is changed so that it points from the insertion position
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towards the specified target point. The magnitude of the velocity is
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unchanged. This can be useful, for example, for simulating a
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sputtering process. E.g. the target point can be far away, so that
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all incident particles strike the surface as if they are in an
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incident beam of particles at a prescribed angle.</p>
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<p>The <em>id</em> keyword determines how atom IDs and molecule IDs are assigned
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to newly deposited particles. Molecule IDs are only assigned if
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molecules are being inserted. For the <em>max</em> setting, the atom and
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molecule IDs of all current atoms are checked. Atoms in the new
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particle are assigned IDs starting with the current maximum plus one.
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If a molecule is inserted it is assigned an ID = current maximum plus
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one. This means that if particles leave the system, the new IDs may
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replace the lost ones. For the <em>next</em> setting, the maximum ID of any
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atom and molecule is stored at the time the fix is defined. Each time
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a new particle is added, this value is incremented to assign IDs to
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the new atom(s) or molecule. Thus atom and molecule IDs for deposited
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particles will be consecutive even if particles leave the system over
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time.</p>
|
|
<p>The <em>units</em> keyword determines the meaning of the distance units used
|
|
for the other deposition parameters. A <em>box</em> value selects standard
|
|
distance units as defined by the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command,
|
|
e.g. Angstroms for units = real or metal. A <em>lattice</em> value means the
|
|
distance units are in lattice spacings. The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a>
|
|
command must have been previously used to define the lattice spacing.
|
|
Note that the units choice affects all the keyword values that have
|
|
units of distance or velocity.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">If you are monitoring the temperature of a system where the atom
|
|
count is changing due to adding particles, you typically should use
|
|
the <a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify dynamic yes</span></a> command for the
|
|
temperature compute you are using.</p>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
|
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
|
<p>This fix writes the state of the deposition to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. This includes information about how many
|
|
particles have been depositied, the random number generator seed, the
|
|
next timestep for deposition, etc. See the
|
|
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
|
|
a fix in an input script that reads a restart file, so that the
|
|
operation of the fix continues in an uninterrupted fashion.</p>
|
|
<p>None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options are relevant to this
|
|
fix. No global or per-atom quantities are stored by this fix for
|
|
access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No
|
|
parameter of this fix can be used with the <em>start/stop</em> keywords of
|
|
the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>This fix is part of the MISC 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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
|
<p>The specified insertion region cannot be a “dynamic” region, as
|
|
defined by the <a class="reference internal" href="region.html"><span class="doc">region</span></a> command.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>, <a class="reference internal" href="region.html"><span class="doc">region</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>Insertions are performed for individual atoms, i.e. no <em>mol</em> setting
|
|
is defined. If the <em>mol</em> keyword is used, the default for <em>molfrac</em>
|
|
is an equal probabilities for all molecules in the template.
|
|
Additional option defaults are id = max, delta = 0.0, near = 0.0,
|
|
attempt = 10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0,
|
|
and units = lattice.</p>
|
|
</div>
|
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