forked from lijiext/lammps
483 lines
28 KiB
HTML
483 lines
28 KiB
HTML
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<title>create_box command — LAMMPS documentation</title>
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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_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_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 class="toctree-l2"><a class="reference internal" href="angle_coeff.html">angle_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_style.html">angle_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atom_modify.html">atom_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atom_style.html">atom_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="balance.html">balance command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_coeff.html">bond_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_style.html">bond_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_write.html">bond_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="boundary.html">boundary command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="box.html">box command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="change_box.html">change_box command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="clear.html">clear command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_modify.html">comm_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_style.html">comm_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute.html">compute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_modify.html">compute_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_atoms.html">create_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_bonds.html">create_bonds command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">create_box command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l2"><a class="reference internal" href="delete_atoms.html">delete_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="delete_bonds.html">delete_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dielectric.html">dielectric command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dihedral_style.html">dihedral_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dimension.html">dimension command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="displace_atoms.html">displace_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html">dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-custom-vtk-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">custom/vtk</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-h5md-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">h5md</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-image-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">image</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-movie-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">movie</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-molfile-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">molfile</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_custom_vtk.html">dump custom/vtk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_h5md.html">dump h5md command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_image.html">dump image command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_image.html#dump-movie-command">dump movie command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_modify.html">dump_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_molfile.html">dump molfile command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="echo.html">echo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix.html">fix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_modify.html">fix_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group.html">group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group2ndx.html">group2ndx command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group2ndx.html#ndx2group-command">ndx2group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="if.html">if command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_coeff.html">improper_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_style.html">improper_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_modify.html">kspace_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_style.html">kspace_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="label.html">label command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_modify.html">min_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neb.html">neb command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neigh_modify.html">neigh_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="next.html">next command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_coeff.html">pair_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_modify.html">pair_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="processors.html">processors command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_dump.html">read_dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_restart.html">read_restart command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="region.html">region command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="replicate.html">replicate command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="rerun.html">rerun command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="reset_timestep.html">reset_timestep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="restart.html">restart command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="run.html">run command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="run_style.html">run_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="set.html">set command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="shell.html">shell command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="special_bonds.html">special_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="suffix.html">suffix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="tad.html">tad command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="temper.html">temper command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo.html">thermo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_modify.html">thermo_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_style.html">thermo_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timer.html">timer command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timestep.html">timestep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="uncompute.html">uncompute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="undump.html">undump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="unfix.html">unfix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="units.html">units command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="variable.html">variable command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="velocity.html">velocity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_coeff.html">write_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_dump.html">write_dump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_restart.html">write_restart command</a></li>
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<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
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<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
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<div class="section" id="create-box-command">
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<span id="index-0"></span><h1>create_box command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<pre class="literal-block">
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create_box N region-ID keyword value ...
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</pre>
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<ul>
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<li><p class="first">N = # of atom types to use in this simulation</p>
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</li>
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<li><p class="first">region-ID = ID of region to use as simulation domain</p>
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</li>
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<li><p class="first">zero or more keyword/value pairs may be appended</p>
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</li>
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<li><p class="first">keyword = <em>bond/types</em> or <em>angle/types</em> or <em>dihedral/types</em> or <em>improper/types</em> or <em>extra/bond/per/atom</em> or <em>extra/angle/per/atom</em> or <em>extra/dihedral/per/atom</em> or <em>extra/improper/per/atom</em></p>
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<pre class="literal-block">
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<em>bond/types</em> value = # of bond types
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<em>angle/types</em> value = # of angle types
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<em>dihedral/types</em> value = # of dihedral types
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<em>improper/types</em> value = # of improper types
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<em>extra/bond/per/atom</em> value = # of bonds per atom
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<em>extra/angle/per/atom</em> value = # of angles per atom
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<em>extra/dihedral/per/atom</em> value = # of dihedrals per atom
|
|
<em>extra/improper/per/atom</em> value = # of impropers per atom
|
|
<em>extra/special/per/atom</em> value = # of special neighbors per atom
|
|
</pre>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<pre class="literal-block">
|
|
create_box 2 mybox
|
|
create_box 2 mybox bond/types 2 extra/bond/per/atom 1
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>This command creates a simulation box based on the specified region.
|
|
Thus a <a class="reference internal" href="region.html"><span class="doc">region</span></a> command must first be used to define a
|
|
geometric domain. It also partitions the simulation box into a
|
|
regular 3d grid of rectangular bricks, one per processor, based on the
|
|
number of processors being used and the settings of the
|
|
<a class="reference internal" href="processors.html"><span class="doc">processors</span></a> command. The partitioning can later be
|
|
changed by the <a class="reference internal" href="balance.html"><span class="doc">balance</span></a> or <a class="reference internal" href="fix_balance.html"><span class="doc">fix balance</span></a> commands.</p>
|
|
<p>The argument N is the number of atom types that will be used in the
|
|
simulation.</p>
|
|
<p>If the region is not of style <em>prism</em>, then LAMMPS encloses the region
|
|
(block, sphere, etc) with an axis-aligned orthogonal bounding box
|
|
which becomes the simulation domain.</p>
|
|
<p>If the region is of style <em>prism</em>, LAMMPS creates a non-orthogonal
|
|
simulation domain shaped as a parallelepiped with triclinic symmetry.
|
|
As defined by the <a class="reference internal" href="region.html"><span class="doc">region prism</span></a> command, the
|
|
parallelepiped has its “origin” at (xlo,ylo,zlo) and is defined by 3
|
|
edge vectors starting from the origin given by A = (xhi-xlo,0,0); B =
|
|
(xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). <em>Xy,xz,yz</em> can be 0.0 or
|
|
positive or negative values and are called “tilt factors” because they
|
|
are the amount of displacement applied to faces of an originally
|
|
orthogonal box to transform it into the parallelipiped.</p>
|
|
<p>By default, a <em>prism</em> region used with the create_box command must
|
|
have tilt factors (xy,xz,yz) that do not skew the box more than half
|
|
the distance of the parallel box length. For example, if xlo = 2 and
|
|
xhi = 12, then the x box length is 10 and the xy tilt factor must be
|
|
between -5 and 5. Similarly, both xz and yz must be between
|
|
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
|
|
since if the maximum tilt factor is 5 (as in this example), then
|
|
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
|
|
geometrically equivalent. If you wish to define a box with tilt
|
|
factors that exceed these limits, you can use the <a class="reference internal" href="box.html"><span class="doc">box tilt</span></a>
|
|
command, with a setting of <em>large</em>; a setting of <em>small</em> is the
|
|
default.</p>
|
|
<p>See <a class="reference internal" href="Section_howto.html#howto-12"><span class="std std-ref">Section 6.12</span></a> of the doc pages
|
|
for a geometric description of triclinic boxes, as defined by LAMMPS,
|
|
and how to transform these parameters to and from other commonly used
|
|
triclinic representations.</p>
|
|
<p>When a prism region is used, the simulation domain should normally be
|
|
periodic in the dimension that the tilt is applied to, which is given
|
|
by the second dimension of the tilt factor (e.g. y for xy tilt). This
|
|
is so that pairs of atoms interacting across that boundary will have
|
|
one of them shifted by the tilt factor. Periodicity is set by the
|
|
<a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command. For example, if the xy tilt factor
|
|
is non-zero, then the y dimension should be periodic. Similarly, the
|
|
z dimension should be periodic if xz or yz is non-zero. LAMMPS does
|
|
not require this periodicity, but you may lose atoms if this is not
|
|
the case.</p>
|
|
<p>Also note that if your simulation will tilt the box, e.g. via the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> command, the simulation box must be setup to
|
|
be triclinic, even if the tilt factors are initially 0.0. You can
|
|
also change an orthogonal box to a triclinic box or vice versa by
|
|
using the <a class="reference internal" href="change_box.html"><span class="doc">change box</span></a> command with its <em>ortho</em> and
|
|
<em>triclinic</em> options.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">If the system is non-periodic (in a dimension), then you should
|
|
not make the lo/hi box dimensions (as defined in your
|
|
<a class="reference internal" href="region.html"><span class="doc">region</span></a> command) radically smaller/larger than the extent
|
|
of the atoms you eventually plan to create, e.g. via the
|
|
<a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a> command. For example, if your atoms
|
|
extend from 0 to 50, you should not specify the box bounds as -10000
|
|
and 10000. This is because as described above, LAMMPS uses the
|
|
specified box size to layout the 3d grid of processors. A huge
|
|
(mostly empty) box will be sub-optimal for performance when using
|
|
“fixed” boundary conditions (see the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a>
|
|
command). When using “shrink-wrap” boundary conditions (see the
|
|
<a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command), a huge (mostly empty) box may cause
|
|
a parallel simulation to lose atoms the first time that LAMMPS
|
|
shrink-wraps the box around the atoms.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>The optional keywords can be used to create a system that allows for
|
|
bond (angle, dihedral, improper) interactions, or for molecules with
|
|
special 1-2,1-3,1-4 neighbors to be added later. These optional
|
|
keywords serve the same purpose as the analogous keywords that can be
|
|
used in a data file which are recognized by the
|
|
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command when it sets up a system.</p>
|
|
<p>Note that if these keywords are not used, then the create_box command
|
|
creates an atomic (non-molecular) simulation that does not allow bonds
|
|
between pairs of atoms to be defined, or a <a class="reference internal" href="bond_style.html"><span class="doc">bond potential</span></a> to be specified, or for molecules with
|
|
special neighbors to be added to the system by commands such as
|
|
<a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms mol</span></a>, <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a>
|
|
or <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>.</p>
|
|
<p>As an example, see the examples/deposit/in.deposit.molecule script,
|
|
which deposits molecules onto a substrate. Initially there are no
|
|
molecules in the system, but they are added later by the <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a> command. The create_box command in the
|
|
script uses the bond/types and extra/bond/per/atom keywords to allow
|
|
this. If the added molecule contained more than 1 special bond
|
|
(allowed by default), an extra/special/per/atom keyword would also
|
|
need to be specified.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>An <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> and <a class="reference internal" href="region.html"><span class="doc">region</span></a> must have
|
|
been previously defined to use this command.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>,
|
|
<a class="reference internal" href="region.html"><span class="doc">region</span></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
</div>
|
|
</div>
|
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|
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|
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</div>
|
|
</div>
|
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<footer>
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<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
|
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|
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<a href="delete_atoms.html" class="btn btn-neutral float-right" title="delete_atoms command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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<a href="create_bonds.html" class="btn btn-neutral" title="create_bonds command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
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</div>
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