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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_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li 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>region command</li>
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<a href="Section_commands.html#comm">Commands</a>
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<div class="section" id="region-command">
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<span id="index-0"></span><h1>region 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">region</span> <span class="n">ID</span> <span class="n">style</span> <span class="n">args</span> <span class="n">keyword</span> <span class="n">arg</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 = user-assigned name for the region</li>
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<li>style = <em>delete</em> or <em>block</em> or <em>cone</em> or <em>cylinder</em> or <em>plane</em> or <em>prism</em> or <em>sphere</em> or <em>union</em> or <em>intersect</em></li>
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</ul>
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<pre class="literal-block">
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<em>delete</em> = no args
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<em>block</em> args = xlo xhi ylo yhi zlo zhi
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xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
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<em>cone</em> args = dim c1 c2 radlo radhi lo hi
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dim = <em>x</em> or <em>y</em> or <em>z</em> = axis of cone
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c1,c2 = coords of cone axis in other 2 dimensions (distance units)
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radlo,radhi = cone radii at lo and hi end (distance units)
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lo,hi = bounds of cone in dim (distance units)
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<em>cylinder</em> args = dim c1 c2 radius lo hi
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dim = <em>x</em> or <em>y</em> or <em>z</em> = axis of cylinder
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c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
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radius = cylinder radius (distance units)
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radius can be a variable (see below)
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lo,hi = bounds of cylinder in dim (distance units)
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<em>plane</em> args = px py pz nx ny nz
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px,py,pz = point on the plane (distance units)
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nx,ny,nz = direction normal to plane (distance units)
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<em>prism</em> args = xlo xhi ylo yhi zlo zhi xy xz yz
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xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
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xy = distance to tilt y in x direction (distance units)
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xz = distance to tilt z in x direction (distance units)
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yz = distance to tilt z in y direction (distance units)
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<em>sphere</em> args = x y z radius
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x,y,z = center of sphere (distance units)
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radius = radius of sphere (distance units)
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radius can be a variable (see below)
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<em>union</em> args = N reg-ID1 reg-ID2 ...
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N = # of regions to follow, must be 2 or greater
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reg-ID1,reg-ID2, ... = IDs of regions to join together
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<em>intersect</em> args = N reg-ID1 reg-ID2 ...
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N = # of regions to follow, must be 2 or greater
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reg-ID1,reg-ID2, ... = IDs of regions to intersect
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</pre>
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<ul class="simple">
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<li>zero or more keyword/arg pairs may be appended</li>
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<li>keyword = <em>side</em> or <em>units</em> or <em>move</em> or <em>rotate</em></li>
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</ul>
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<pre class="literal-block">
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<em>side</em> value = <em>in</em> or <em>out</em>
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<em>in</em> = the region is inside the specified geometry
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<em>out</em> = the region is outside the specified geometry
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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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<em>move</em> args = v_x v_y v_z
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v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time
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<em>rotate</em> args = v_theta Px Py Pz Rx Ry Rz
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v_theta = equal-style variable for rotaton of region over time (in radians)
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Px,Py,Pz = origin for axis of rotation (distance units)
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Rx,Ry,Rz = axis of rotation vector
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</pre>
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<ul class="simple">
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<li>accelerated styles (with same args) = <em>block/kk</em></li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">region</span> <span class="mi">1</span> <span class="n">block</span> <span class="o">-</span><span class="mf">3.0</span> <span class="mf">5.0</span> <span class="n">INF</span> <span class="mf">10.0</span> <span class="n">INF</span> <span class="n">INF</span>
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<span class="n">region</span> <span class="mi">2</span> <span class="n">sphere</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mi">5</span> <span class="n">side</span> <span class="n">out</span>
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<span class="n">region</span> <span class="n">void</span> <span class="n">cylinder</span> <span class="n">y</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">5</span> <span class="o">-</span><span class="mf">5.0</span> <span class="n">EDGE</span> <span class="n">units</span> <span class="n">box</span>
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<span class="n">region</span> <span class="mi">1</span> <span class="n">prism</span> <span class="mi">0</span> <span class="mi">10</span> <span class="mi">0</span> <span class="mi">10</span> <span class="mi">0</span> <span class="mi">10</span> <span class="mi">2</span> <span class="mi">0</span> <span class="mi">0</span>
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<span class="n">region</span> <span class="n">outside</span> <span class="n">union</span> <span class="mi">4</span> <span class="n">side1</span> <span class="n">side2</span> <span class="n">side3</span> <span class="n">side4</span>
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<span class="n">region</span> <span class="mi">2</span> <span class="n">sphere</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mi">5</span> <span class="n">side</span> <span class="n">out</span> <span class="n">move</span> <span class="n">v_left</span> <span class="n">v_up</span> <span class="n">NULL</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>This command defines a geometric region of space. Various other
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commands use regions. For example, the region can be filled with
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atoms via the <a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a> command. Or a bounding
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box around the region, can be used to define the simulation box via
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the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command. Or the atoms in the region
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can be identified as a group via the <a class="reference internal" href="group.html"><span class="doc">group</span></a> command, or
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deleted via the <a class="reference internal" href="delete_atoms.html"><span class="doc">delete_atoms</span></a> command. Or the
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surface of the region can be used as a boundary wall via the <a class="reference internal" href="fix_wall_region.html"><span class="doc">fix wall/region</span></a> command.</p>
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<p>Commands which use regions typically test whether an atom’s position
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is contained in the region or not. For this purpose, coordinates
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exactly on the region boundary are considered to be interior to the
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region. This means, for example, for a spherical region, an atom on
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the sphere surface would be part of the region if the sphere were
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defined with the <em>side in</em> keyword, but would not be part of the
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region if it were defined using the <em>side out</em> keyword. See more
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details on the <em>side</em> keyword below.</p>
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<p>Normally, regions in LAMMPS are “static”, meaning their geometric
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extent does not change with time. If the <em>move</em> or <em>rotate</em> keyword
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is used, as described below, the region becomes “dynamic”, meaning
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it’s location or orientation changes with time. This may be useful,
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for example, when thermostatting a region, via the compute temp/region
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command, or when the fix wall/region command uses a region surface as
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a bounding wall on particle motion, i.e. a rotating container.</p>
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<p>The <em>delete</em> style removes the named region. Since there is little
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overhead to defining extra regions, there is normally no need to do
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this, unless you are defining and discarding large numbers of regions
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in your input script.</p>
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<p>The lo/hi values for <em>block</em> or <em>cone</em> or <em>cylinder</em> or <em>prism</em> styles
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can be specified as EDGE or INF. EDGE means they extend all the way
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to the global simulation box boundary. Note that this is the current
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box boundary; if the box changes size during a simulation, the region
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does not. INF means a large negative or positive number (1.0e20), so
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it should encompass the simulation box even if it changes size. If a
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region is defined before the simulation box has been created (via
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<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> or <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or
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<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> commands), then an EDGE or INF
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parameter cannot be used. For a <em>prism</em> region, a non-zero tilt
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factor in any pair of dimensions cannot be used if both the lo/hi
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values in either of those dimensions are INF. E.g. if the xy tilt is
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non-zero, then xlo and xhi cannot both be INF, nor can ylo and yhi.</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">Regions in LAMMPS do not get wrapped across periodic boundaries,
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as specified by the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command. For example, a
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spherical region that is defined so that it overlaps a periodic
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boundary is not treated as 2 half-spheres, one on either side of the
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simulation box.</p>
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</div>
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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">Regions in LAMMPS are always 3d geometric objects, regardless of
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whether the <a class="reference internal" href="dimension.html"><span class="doc">dimension</span></a> of a simulation is 2d or 3d.
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Thus when using regions in a 2d simulation, you should be careful to
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define the region so that its intersection with the 2d x-y plane of
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the simulation has the 2d geometric extent you want.</p>
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</div>
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<p>For style <em>cone</em>, an axis-aligned cone is defined which is like a
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<em>cylinder</em> except that two different radii (one at each end) can be
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defined. Either of the radii (but not both) can be 0.0.</p>
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<p>For style <em>cone</em> and <em>cylinder</em>, the c1,c2 params are coordinates in
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the 2 other dimensions besides the cylinder axis dimension. For dim =
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x, c1/c2 = y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y.
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Thus the third example above specifies a cylinder with its axis in the
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y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
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extending in the y-direction from -5.0 to the upper box boundary.</p>
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<p>For style <em>plane</em>, a plane is defined which contain the point
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(px,py,pz) and has a normal vector (nx,ny,nz). The normal vector does
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not have to be of unit length. The “inside” of the plane is the
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half-space in the direction of the normal vector; see the discussion
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of the <em>side</em> option below.</p>
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<p>For style <em>prism</em>, a parallelepiped is defined (it’s too hard to spell
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parallelepiped in an input script!). The parallelepiped has its
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“origin” at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
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from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
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(xz,yz,zhi-zlo). <em>Xy,xz,yz</em> can be 0.0 or positive or negative values
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and are called “tilt factors” because they are the amount of
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displacement applied to faces of an originally orthogonal box to
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transform it into the parallelepiped.</p>
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<p>A prism region that will be used with the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>
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command to define a triclinic simulation box must have tilt factors
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(xy,xz,yz) that do not skew the box more than half the distance of
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corresponding the parallel box length. For example, if xlo = 2 and
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xhi = 12, then the x box length is 10 and the xy tilt factor must be
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between -5 and 5. Similarly, both xz and yz must be between
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-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
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since if the maximum tilt factor is 5 (as in this example), then
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configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
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geometrically equivalent.</p>
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<p>The <em>radius</em> value for style <em>sphere</em> and <em>cylinder</em> can be specified
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as an equal-style <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>. If the value is a
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variable, it should be specified as v_name, where name is the variable
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name. In this case, the variable will be evaluated each timestep, and
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its value used to determine the radius of the region.</p>
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<p>Equal-style variables can specify formulas with various mathematical
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functions, and include <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command
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keywords for the simulation box parameters and timestep and elapsed
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time. Thus it is easy to specify a time-dependent radius.</p>
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<p>See <a class="reference internal" href="Section_howto.html#howto-12"><span class="std std-ref">Section_howto 12</span></a> of the doc pages
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for a geometric description of triclinic boxes, as defined by LAMMPS,
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and how to transform these parameters to and from other commonly used
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triclinic representations.</p>
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<p>The <em>union</em> style creates a region consisting of the volume of all the
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listed regions combined. The <em>intersect</em> style creates a region
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consisting of the volume that is common to all the listed regions.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">The <em>union</em> and <em>intersect</em> regions operate by invoking methods
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from their list of sub-regions. Thus you cannot delete the
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sub-regions after defining the <em>union</em> or <em>intersection</em> region.</p>
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</div>
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<hr class="docutils" />
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<p>The <em>side</em> keyword determines whether the region is considered to be
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inside or outside of the specified geometry. Using this keyword in
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conjunction with <em>union</em> and <em>intersect</em> regions, complex geometries
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can be built up. For example, if the interior of two spheres were
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each defined as regions, and a <em>union</em> style with <em>side</em> = out was
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constructed listing the region-IDs of the 2 spheres, the resulting
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region would be all the volume in the simulation box that was outside
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both of the spheres.</p>
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<p>The <em>units</em> keyword determines the meaning of the distance units used
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to define the region for any argument above listed as having distance
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units. It also affects the scaling of the velocity vector specfied
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with the <em>vel</em> keyword, the amplitude vector specified with the
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<em>wiggle</em> keyword, and the rotation point specified with the <em>rotate</em>
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keyword, since they each involve a distance metric.</p>
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<p>A <em>box</em> value selects standard distance units as defined by the
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<a class="reference internal" href="units.html"><span class="doc">units</span></a> command, e.g. Angstroms for units = real or metal.
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A <em>lattice</em> value means the distance units are in lattice spacings.
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The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have been previously used to
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define the lattice spacings which are used as follows:</p>
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<ul class="simple">
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|
<li>For style <em>block</em>, the lattice spacing in dimension x is applied to
|
|
xlo and xhi, similarly the spacings in dimensions y,z are applied to
|
|
ylo/yhi and zlo/zhi.</li>
|
|
<li>For style <em>cone</em>, the lattice spacing in argument <em>dim</em> is applied to
|
|
lo and hi. The spacings in the two radial dimensions are applied to
|
|
c1 and c2. The two cone radii are scaled by the lattice
|
|
spacing in the dimension corresponding to c1.</li>
|
|
<li>For style <em>cylinder</em>, the lattice spacing in argument <em>dim</em> is applied
|
|
to lo and hi. The spacings in the two radial dimensions are applied
|
|
to c1 and c2. The cylinder radius is scaled by the lattice
|
|
spacing in the dimension corresponding to c1.</li>
|
|
<li>For style <em>plane</em>, the lattice spacing in dimension x is applied to
|
|
px and nx, similarly the spacings in dimensions y,z are applied to
|
|
py/ny and pz/nz.</li>
|
|
<li>For style <em>prism</em>, the lattice spacing in dimension x is applied to
|
|
xlo and xhi, similarly for ylo/yhi and zlo/zhi. The lattice spacing
|
|
in dimension x is applied to xy and xz, and the spacing in dimension y
|
|
to yz.</li>
|
|
<li>For style <em>sphere</em>, the lattice spacing in dimensions x,y,z are
|
|
applied to the sphere center x,y,z. The spacing in dimension x is
|
|
applied to the sphere radius.</li>
|
|
</ul>
|
|
<hr class="docutils" />
|
|
<p>If the <em>move</em> or <em>rotate</em> keywords are used, the region is “dynamic”,
|
|
meaning its location or orientation changes with time. These keywords
|
|
cannot be used with a <em>union</em> or <em>intersect</em> style region. Instead,
|
|
the keywords should be used to make the individual sub-regions of the
|
|
<em>union</em> or <em>intersect</em> region dynamic. Normally, each sub-region
|
|
should be “dynamic” in the same manner (e.g. rotate around the same
|
|
point), though this is not a requirement.</p>
|
|
<p>The <em>move</em> keyword allows one or more <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a> to be used to specify the x,y,z displacement
|
|
of the region, typically as a function of time. A variable is
|
|
specified as v_name, where name is the variable name. Any of the
|
|
three variables can be specified as NULL, in which case no
|
|
displacement is calculated in that dimension.</p>
|
|
<p>Note that equal-style variables can specify formulas with various
|
|
mathematical functions, and include <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a>
|
|
command keywords for the simulation box parameters and timestep and
|
|
elapsed time. Thus it is easy to specify a region displacement that
|
|
change as a function of time or spans consecutive runs in a continuous
|
|
fashion. For the latter, see the <em>start</em> and <em>stop</em> keywords of the
|
|
<a class="reference internal" href="run.html"><span class="doc">run</span></a> command and the <em>elaplong</em> keyword of <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> for details.</p>
|
|
<p>For example, these commands would displace a region from its initial
|
|
position, in the positive x direction, effectively at a constant
|
|
velocity:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">dx</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
|
|
<span class="n">region</span> <span class="mi">2</span> <span class="n">sphere</span> <span class="mf">10.0</span> <span class="mf">10.0</span> <span class="mf">0.0</span> <span class="mi">5</span> <span class="n">move</span> <span class="n">v_dx</span> <span class="n">NULL</span> <span class="n">NULL</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>Note that the initial displacemet is 0.0, though that is not required.</p>
|
|
<p>Either of these varaibles would “wiggle” the region back and forth in
|
|
the y direction:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">dy</span> <span class="n">equal</span> <span class="n">swiggle</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">5</span><span class="p">,</span><span class="mi">100</span><span class="p">)</span>
|
|
<span class="n">variable</span> <span class="n">dysame</span> <span class="n">equal</span> <span class="mi">5</span><span class="o">*</span><span class="n">sin</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">PI</span><span class="o">*</span><span class="n">elaplong</span><span class="o">*</span><span class="n">dt</span><span class="o">/</span><span class="mi">100</span><span class="p">)</span>
|
|
<span class="n">region</span> <span class="mi">2</span> <span class="n">sphere</span> <span class="mf">10.0</span> <span class="mf">10.0</span> <span class="mf">0.0</span> <span class="mi">5</span> <span class="n">move</span> <span class="n">NULL</span> <span class="n">v_dy</span> <span class="n">NULL</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>The <em>rotate</em> keyword rotates the region around a rotation axis <em>R</em> =
|
|
(Rx,Ry,Rz) that goes thru a point <em>P</em> = (Px,Py,Pz). The rotation
|
|
angle is calculated, presumably as a function of time, by a variable
|
|
specified as v_theta, where theta is the variable name. The variable
|
|
should generate its result in radians. The direction of rotation for
|
|
the region around the rotation axis is consistent with the right-hand
|
|
rule: if your right-hand thumb points along <em>R</em>, then your fingers
|
|
wrap around the axis in the direction of rotation.</p>
|
|
<p>The <em>move</em> and <em>rotate</em> keywords can be used together. In this case,
|
|
the displacement specified by the <em>move</em> keyword is applied to the <em>P</em>
|
|
point of the <em>rotate</em> keyword.</p>
|
|
<hr class="docutils" />
|
|
<p>Styles with a <em>kk</em> suffix are functionally the same as the
|
|
corresponding style without the suffix. They have been optimized to
|
|
run faster, depending on your available hardware, as discussed in
|
|
<a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual. The
|
|
accelerated styles take the same arguments and should produce the same
|
|
results, except for round-off and precision issues.</p>
|
|
<p>The code using the region (such as a fix or compute) must also be supported
|
|
by Kokkos or no acceleration will occur. Currently, only <em>block</em> style
|
|
regions are supported by Kokkos.</p>
|
|
<p>These accelerated styles are part of the Kokkos package. They are
|
|
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>You can specify the accelerated styles explicitly in your input script
|
|
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
|
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
|
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
|
|
more instructions on how to use the accelerated styles effectively.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>A prism cannot be of 0.0 thickness in any dimension; use a small z
|
|
thickness for 2d simulations. For 2d simulations, the xz and yz
|
|
parameters must be 0.0.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a>, <a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>,
|
|
<a class="reference internal" href="delete_atoms.html"><span class="doc">delete_atoms</span></a>, <a class="reference internal" href="group.html"><span class="doc">group</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults are side = in, units = lattice, and no move or
|
|
rotation.</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
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</div>
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<hr/>
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<p>
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</p>
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