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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>create_atoms command</li>
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<div class="section" id="create-atoms-command">
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<span id="index-0"></span><h1>create_atoms command<a class="headerlink" href="#create-atoms-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>create_atoms type style args 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>type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)</li>
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<li>style = <em>box</em> or <em>region</em> or <em>single</em> or <em>random</em></li>
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</ul>
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<pre class="literal-block">
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<em>box</em> args = none
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<em>region</em> args = region-ID
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region-ID = particles will only be created if contained in the region
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<em>single</em> args = x y z
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x,y,z = coordinates of a single particle (distance units)
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<em>random</em> args = N seed region-ID
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N = number of particles to create
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seed = random # seed (positive integer)
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region-ID = create atoms within this region, use NULL for entire simulation box
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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>mol</em> or <em>basis</em> or <em>remap</em> or <em>var</em> or <em>set</em> or <em>units</em></li>
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</ul>
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<pre class="literal-block">
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<em>mol</em> value = template-ID seed
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template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
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seed = random # seed (positive integer)
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<em>basis</em> values = M itype
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M = which basis atom
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itype = atom type (1-N) to assign to this basis atom
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<em>remap</em> value = <em>yes</em> or <em>no</em>
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<em>var</em> value = name = variable name to evaluate for test of atom creation
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<em>set</em> values = dim name
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dim = <em>x</em> or <em>y</em> or <em>z</em>
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name = name of variable to set with x, y, or z atom position
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<em>rotate</em> values = Rx Ry Rz theta
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Rx,Ry,Rz = rotation vector for single molecule
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theta = rotation angle for single molecule (degrees)
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<em>units</em> value = <em>lattice</em> or <em>box</em>
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<em>lattice</em> = the geometry is defined in lattice units
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<em>box</em> = 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<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>create_atoms 1 box
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create_atoms 3 region regsphere basis 2 3
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create_atoms 3 single 0 0 5
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create_atoms 1 box var v set x xpos set y ypos
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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>This command creates atoms (or molecules) on a lattice, or a single
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atom (or molecule), or a random collection of atoms (or molecules), as
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an alternative to reading in their coordinates explicitly via a
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<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
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command. A simulation box must already exist, which is typically
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created via the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command. Before using
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this command, a lattice must also be defined using the
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<a class="reference internal" href="lattice.html"><em>lattice</em></a> command, unless you specify the <em>single</em> style
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with units = box or the <em>random</em> style. For the remainder of this doc
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page, a created atom or molecule is referred to as a “particle”.</p>
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<p>If created particles are individual atoms, they are assigned the
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specified atom <em>type</em>, though this can be altered via the <em>basis</em>
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keyword as discussed below. If molecules are being created, the type
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of each atom in the created molecule is specified in the file read by
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the <a class="reference internal" href="molecule.html"><em>molecule</em></a> command, and those values are added to
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the specified atom <em>type</em>. E.g. if <em>type</em> = 2, and the file specifies
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atom types 1,2,3, then each created molecule will have atom types
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3,4,5.</p>
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<p>For the <em>box</em> style, the create_atoms command fills the entire
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simulation box with particles on the lattice. If your simulation box
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is periodic, you should insure its size is a multiple of the lattice
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spacings, to avoid unwanted atom overlaps at the box boundaries. If
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your box is periodic and a multiple of the lattice spacing in a
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particular dimension, LAMMPS is careful to put exactly one particle at
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the boundary (on either side of the box), not zero or two.</p>
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<p>For the <em>region</em> style, a geometric volume is filled with particles on
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the lattice. This volume what is inside the simulation box and is
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also consistent with the region volume. See the <a class="reference internal" href="region.html"><em>region</em></a>
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command for details. Note that a region can be specified so that its
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“volume” is either inside or outside a geometric boundary. Also note
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that if your region is the same size as a periodic simulation box (in
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some dimension), LAMMPS does not implement the same logic described
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above as for the <em>box</em> style, to insure exactly one particle at
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periodic boundaries. if this is what you desire, you should either
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use the <em>box</em> style, or tweak the region size to get precisely the
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particles you want.</p>
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<p>For the <em>single</em> style, a single particle is added to the system at
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the specified coordinates. This can be useful for debugging purposes
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or to create a tiny system with a handful of particles at specified
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positions.</p>
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<p>For the <em>random</em> style, N particles are added to the system at
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randomly generated coordinates, which can be useful for generating an
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amorphous system. The particles are created one by one using the
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speficied random number <em>seed</em>, resulting in the same set of particles
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coordinates, independent of how many processors are being used in the
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simulation. If the <em>region-ID</em> argument is specified as NULL, then
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the created particles will be anywhere in the simulation box. If a
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<em>region-ID</em> is specified, a geometric volume is filled which is both
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inside the simulation box and is also consistent with the region
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volume. See the <a class="reference internal" href="region.html"><em>region</em></a> command for details. Note that
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a region can be specified so that its “volume” is either inside or
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outside a geometric boundary.</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">Particles generated by the <em>random</em> style will typically be
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highly overlapped which will cause many interatomic potentials to
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compute large energies and forces. Thus you should either perform an
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<a class="reference internal" href="minimize.html"><em>energy minimization</em></a> or run dynamics with <a class="reference internal" href="fix_nve_limit.html"><em>fix nve/limit</em></a> to equilibrate such a system, before
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running normal dynamics.</p>
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</div>
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<p>Note that this command adds particles to those that already exist.
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This means it can be used to add particles to a system previously read
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in from a data or restart file. Or the create_atoms command can be
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used multiple times, to add multiple sets of particles to the
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simulation. For example, grain boundaries can be created, by
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interleaving create_atoms with <a class="reference internal" href="lattice.html"><em>lattice</em></a> commands
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specifying different orientations. By using the create_atoms command
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in conjunction with the <a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a> command,
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reasonably complex geometries can be created, or a protein can be
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solvated with a surrounding box of water molecules.</p>
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<p>In all these cases, care should be taken to insure that new atoms do
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not overlap existing atoms inappropriately, especially if molecules
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are being added. The <a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a> command can be
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used to remove overlapping atoms or molecules.</p>
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<hr class="docutils" />
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<p>Individual atoms are inserted by this command, unless the <em>mol</em>
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keyword is used. It specifies a <em>template-ID</em> previously defined
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using the <a class="reference internal" href="molecule.html"><em>molecule</em></a> command, which reads a file that
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defines the molecule. The coordinates, atom types, charges, etc, as
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well as any bond/angle/etc and special neighbor information for the
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molecule can be specified in the molecule file. See the
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<a class="reference internal" href="molecule.html"><em>molecule</em></a> command for details. The only settings
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required to be in this file are the coordinates and types of atoms in
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the molecule.</p>
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<p>Using a lattice to add molecules, e.g. via the <em>box</em> or <em>region</em> or
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<em>single</em> styles, is exactly the same as adding atoms on lattice
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points, except that entire molecules are added at each point, i.e. on
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the point defined by each basis atom in the unit cell as it tiles the
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simulation box or region. This is done by placing the geometric
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center of the molecule at the lattice point, and giving the molecule a
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random orientation about the point. The random <em>seed</em> specified with
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the <em>mol</em> keyword is used for this operation, and the random numbers
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generated by each processor are different. This means the coordinates
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of individual atoms (in the molecules) will be different when running
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on different numbers of processors, unlike when atoms are being
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created in parallel.</p>
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<p>Also note that because of the random rotations, it may be important to
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use a lattice with a large enough spacing that adjacent molecules will
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not overlap, regardless of their relative orientations.</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 the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command is used to create
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the simulation box, followed by the create_atoms command with its
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<em>mol</em> option for adding molecules, then you typically need to use the
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optional keywords allowed by the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command
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for extra bonds (angles,etc) or extra special neighbors. This is
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because by default, the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command sets up a
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non-molecular system which doesn’t allow molecules to be added.</p>
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</div>
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<hr class="docutils" />
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<p>This is the meaning of the other allowed keywords.</p>
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<p>The <em>basis</em> keyword is only used when atoms (not molecules) are being
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created. It specifies an atom type that will be assigned to specific
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basis atoms as they are created. See the <a class="reference internal" href="lattice.html"><em>lattice</em></a>
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command for specifics on how basis atoms are defined for the unit cell
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of the lattice. By default, all created atoms are assigned the
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argument <em>type</em> as their atom type.</p>
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<p>The <em>remap</em> keyword only applies to the <em>single</em> style. If it is set
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to <em>yes</em>, then if the specified position is outside the simulation
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box, it will mapped back into the box, assuming the relevant
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dimensions are periodic. If it is set to <em>no</em>, no remapping is done
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and no particle is created if its position is outside the box.</p>
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<p>The <em>var</em> and <em>set</em> keywords can be used together to provide a
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criterion for accepting or rejecting the addition of an individual
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atom, based on its coordinates. The <em>name</em> specified for the <em>var</em>
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keyword is the name of an <a class="reference internal" href="variable.html"><em>equal-style variable</em></a> which
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should evaluate to a zero or non-zero value based on one or two or
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three variables which will store the x, y, or z coordinates of an atom
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(one variable per coordinate). If used, these other variables must be
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<a class="reference internal" href="variable.html"><em>equal-style variables</em></a> defined in the input script, but
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their formula can by anything. The <em>set</em> keyword is used to identify
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the names of these other variables, one variable for the x-coordinate
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of a created atom, one for y, and one for z.</p>
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<p>When an atom is created, its x, y, or z coordinates override the
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formula for any <em>set</em> variable that is defined. The <em>var</em> variable is
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then evaluated. If the returned value is 0.0, the atom is not
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created. If it is non-zero, the atom is created. After all atoms are
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created, the formulas defined for all of the <em>set</em> variables are
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restored to their original strings.</p>
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<p>As an example, these commands can be used in a 2d simulation, to
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create a sinusoidal surface. Note that the surface is “rough” due to
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individual lattice points being “above” or “below” the mathematical
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expression for the sinusoidal curve. If a finer lattice were used,
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the sinusoid would appear to be “smoother”. Also note the use of the
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“xlat” and “ylat” <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> keywords which
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converts lattice spacings to distance. Click on the image for a
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larger version.</p>
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<div class="highlight-python"><div class="highlight"><pre>variable x equal 100
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variable y equal 25
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lattice hex 0.8442
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region box block 0 $x 0 $y -0.5 0.5
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create_box 1 box
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>variable xx equal 0.0
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variable yy equal 0.0
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variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
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create_atoms 1 box var v set x xx set y yy
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</pre></div>
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</div>
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<a data-lightbox="group-default"
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href="_images/sinusoid.jpg"
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class=""
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title=""
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data-title=""
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><img src="_images/sinusoid.jpg"
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class="align-center"
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width="25%"
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height="auto"
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alt=""/>
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</a><p>The <em>rotate</em> keyword can be used with the <em>single</em> style, when adding
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a single molecule to specify the orientation at which the molecule is
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inserted. The axis of rotation is determined by the rotation vector
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(Rx,Ry,Rz) that goes through the insertion point. The specified
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<em>theta</em> determines the angle of rotation around that axis. Note that
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the direction of rotation for the atoms around the rotation axis is
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consistent with the right-hand rule: if your right-hand’s thumb points
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along <em>R</em>, then your fingers wrap around the axis in the direction of
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rotation.</p>
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<p>The <em>units</em> keyword determines the meaning of the distance units used
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to specify the coordinates of the one particle created by the <em>single</em>
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style. A <em>box</em> value selects standard distance units as defined by
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the <a class="reference internal" href="units.html"><em>units</em></a> command, e.g. Angstroms for units = real or
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metal. A <em>lattice</em> value means the distance units are in lattice
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spacings.</p>
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<hr class="docutils" />
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<p>Atom IDs are assigned to created atoms in the following way. The
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collection of created atoms are assigned consecutive IDs that start
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immediately following the largest atom ID existing before the
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create_atoms command was invoked. When a simulation is performed on
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different numbers of processors, there is no guarantee a particular
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created atom will be assigned the same ID. If molecules are being
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created, molecule IDs are assigned to created molecules in a similar
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fashion.</p>
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<p>Aside from their ID, atom type, and xyz position, other properties of
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created atoms are set to default values, depending on which quantities
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are defined by the chosen <a class="reference internal" href="atom_style.html"><em>atom style</em></a>. See the <a class="reference internal" href="atom_style.html"><em>atom style</em></a> command for more details. See the
|
|
<a class="reference internal" href="set.html"><em>set</em></a> and <a class="reference internal" href="velocity.html"><em>velocity</em></a> commands for info on how
|
|
to change these values.</p>
|
|
<ul class="simple">
|
|
<li>charge = 0.0</li>
|
|
<li>dipole moment magnitude = 0.0</li>
|
|
<li>diameter = 1.0</li>
|
|
<li>shape = 0.0 0.0 0.0</li>
|
|
<li>density = 1.0</li>
|
|
<li>volume = 1.0</li>
|
|
<li>velocity = 0.0 0.0 0.0</li>
|
|
<li>angular velocity = 0.0 0.0 0.0</li>
|
|
<li>angular momentum = 0.0 0.0 0.0</li>
|
|
<li>quaternion = (1,0,0,0)</li>
|
|
<li>bonds, angles, dihedrals, impropers = none</li>
|
|
</ul>
|
|
<p>If molecules are being created, these defaults can be overridden by
|
|
values specified in the file read by the <a class="reference internal" href="molecule.html"><em>molecule</em></a>
|
|
command. E.g. the file typically defines bonds (angles,etc) between
|
|
atoms in the molecule, and can optionally define charges on each atom.</p>
|
|
<p>Note that the <em>sphere</em> atom style sets the default particle diameter
|
|
to 1.0 as well as the density. This means the mass for the particle
|
|
is not 1.0, but is PI/6 * diameter^3 = 0.5236.</p>
|
|
<p>Note that the <em>ellipsoid</em> atom style sets the default particle shape
|
|
to (0.0 0.0 0.0) and the density to 1.0 which means it is a point
|
|
particle, not an ellipsoid, and has a mass of 1.0.</p>
|
|
<p>Note that the <em>peri</em> style sets the default volume and density to 1.0
|
|
and thus also set the mass for the particle to 1.0.</p>
|
|
<p>The <a class="reference internal" href="set.html"><em>set</em></a> command can be used to override many of these
|
|
default settings.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
|
<p>An <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> must be previously defined to use this
|
|
command.</p>
|
|
<p>A rotation vector specified for a single molecule must be in
|
|
the z-direction for a 2d model.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p><a class="reference internal" href="lattice.html"><em>lattice</em></a>, <a class="reference internal" href="region.html"><em>region</em></a>, <a class="reference internal" href="create_box.html"><em>create_box</em></a>,
|
|
<a class="reference internal" href="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="read_restart.html"><em>read_restart</em></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
|
<p>The default for the <em>basis</em> keyword is that all created atoms are
|
|
assigned the argument <em>type</em> as their atom type (when single atoms are
|
|
being created). The other defaults are <em>remap</em> = no, <em>rotate</em> =
|
|
random, and <em>units</em> = lattice.</p>
|
|
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