forked from lijiext/lammps
650 lines
38 KiB
HTML
650 lines
38 KiB
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<title>create_atoms 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 current"><a class="current reference internal" href="#">create_atoms 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-l3"><a class="reference internal" href="#description">Description</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"><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="include.html">include command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="jump.html">jump 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="lattice.html">lattice command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="log.html">log command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="mass.html">mass 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="min_style.html">min_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="minimize.html">minimize command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="molecule.html">molecule 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="neighbor.html">neighbor command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="newton.html">newton 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="package.html">package 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="pair_style.html">pair_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_write.html">pair_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="partition.html">partition command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="prd.html">prd command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="print.html">print 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="python.html">python command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="quit.html">quit command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="read_data.html">read_data 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="fixes.html">Fixes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</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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<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</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_atoms type style args keyword values ...
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</pre>
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<ul>
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<li><p class="first">type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)</p>
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</li>
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<li><p class="first">style = <em>box</em> or <em>region</em> or <em>single</em> or <em>random</em></p>
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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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</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>mol</em> or <em>basis</em> or <em>remap</em> or <em>var</em> or <em>set</em> or <em>units</em></p>
|
|
<pre class="literal-block">
|
|
<em>mol</em> value = template-ID seed
|
|
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command
|
|
seed = random # seed (positive integer)
|
|
<em>basis</em> values = M itype
|
|
M = which basis atom
|
|
itype = atom type (1-N) to assign to this basis atom
|
|
<em>remap</em> value = <em>yes</em> or <em>no</em>
|
|
<em>var</em> value = name = variable name to evaluate for test of atom creation
|
|
<em>set</em> values = dim name
|
|
dim = <em>x</em> or <em>y</em> or <em>z</em>
|
|
name = name of variable to set with x, y, or z atom position
|
|
<em>rotate</em> values = Rx Ry Rz theta
|
|
Rx,Ry,Rz = rotation vector for single molecule
|
|
theta = rotation angle for single molecule (degrees)
|
|
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
|
<em>lattice</em> = the geometry is defined in lattice units
|
|
<em>box</em> = the geometry is defined in simulation box units
|
|
</pre>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<pre class="literal-block">
|
|
create_atoms 1 box
|
|
create_atoms 3 region regsphere basis 2 3
|
|
create_atoms 3 single 0 0 5
|
|
create_atoms 1 box var v set x xpos set y ypos
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>This command creates atoms (or molecules) on a lattice, or a single
|
|
atom (or molecule), or a random collection of atoms (or molecules), as
|
|
an alternative to reading in their coordinates explicitly via a
|
|
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
|
|
command. A simulation box must already exist, which is typically
|
|
created via the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command. Before using
|
|
this command, a lattice must also be defined using the
|
|
<a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command, unless you specify the <em>single</em> style
|
|
with units = box or the <em>random</em> style. For the remainder of this doc
|
|
page, a created atom or molecule is referred to as a “particle”.</p>
|
|
<p>If created particles are individual atoms, they are assigned the
|
|
specified atom <em>type</em>, though this can be altered via the <em>basis</em>
|
|
keyword as discussed below. If molecules are being created, the type
|
|
of each atom in the created molecule is specified in the file read by
|
|
the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command, and those values are added to
|
|
the specified atom <em>type</em>. E.g. if <em>type</em> = 2, and the file specifies
|
|
atom types 1,2,3, then each created molecule will have atom types
|
|
3,4,5.</p>
|
|
<p>For the <em>box</em> style, the create_atoms command fills the entire
|
|
simulation box with particles on the lattice. If your simulation box
|
|
is periodic, you should insure its size is a multiple of the lattice
|
|
spacings, to avoid unwanted atom overlaps at the box boundaries. If
|
|
your box is periodic and a multiple of the lattice spacing in a
|
|
particular dimension, LAMMPS is careful to put exactly one particle at
|
|
the boundary (on either side of the box), not zero or two.</p>
|
|
<p>For the <em>region</em> style, a geometric volume is filled with particles on
|
|
the lattice. This volume what is inside the simulation box and is
|
|
also consistent with the region volume. See the <a class="reference internal" href="region.html"><span class="doc">region</span></a>
|
|
command for details. Note that a region can be specified so that its
|
|
“volume” is either inside or outside a geometric boundary. Also note
|
|
that if your region is the same size as a periodic simulation box (in
|
|
some dimension), LAMMPS does not implement the same logic described
|
|
above as for the <em>box</em> style, to insure exactly one particle at
|
|
periodic boundaries. if this is what you desire, you should either
|
|
use the <em>box</em> style, or tweak the region size to get precisely the
|
|
particles you want.</p>
|
|
<p>For the <em>single</em> style, a single particle is added to the system at
|
|
the specified coordinates. This can be useful for debugging purposes
|
|
or to create a tiny system with a handful of particles at specified
|
|
positions.</p>
|
|
<p>For the <em>random</em> style, N particles are added to the system at
|
|
randomly generated coordinates, which can be useful for generating an
|
|
amorphous system. The particles are created one by one using the
|
|
speficied random number <em>seed</em>, resulting in the same set of particles
|
|
coordinates, independent of how many processors are being used in the
|
|
simulation. If the <em>region-ID</em> argument is specified as NULL, then
|
|
the created particles will be anywhere in the simulation box. If a
|
|
<em>region-ID</em> is specified, a geometric volume is filled which is both
|
|
inside the simulation box and is also consistent with the region
|
|
volume. See the <a class="reference internal" href="region.html"><span class="doc">region</span></a> command for details. Note that
|
|
a region can be specified so that its “volume” is either inside or
|
|
outside a geometric boundary.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">Particles generated by the <em>random</em> style will typically be
|
|
highly overlapped which will cause many interatomic potentials to
|
|
compute large energies and forces. Thus you should either perform an
|
|
<a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a> or run dynamics with <a class="reference internal" href="fix_nve_limit.html"><span class="doc">fix nve/limit</span></a> to equilibrate such a system, before
|
|
running normal dynamics.</p>
|
|
</div>
|
|
<p>Note that this command adds particles to those that already exist.
|
|
This means it can be used to add particles to a system previously read
|
|
in from a data or restart file. Or the create_atoms command can be
|
|
used multiple times, to add multiple sets of particles to the
|
|
simulation. For example, grain boundaries can be created, by
|
|
interleaving create_atoms with <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> commands
|
|
specifying different orientations. By using the create_atoms command
|
|
in conjunction with the <a class="reference internal" href="delete_atoms.html"><span class="doc">delete_atoms</span></a> command,
|
|
reasonably complex geometries can be created, or a protein can be
|
|
solvated with a surrounding box of water molecules.</p>
|
|
<p>In all these cases, care should be taken to insure that new atoms do
|
|
not overlap existing atoms inappropriately, especially if molecules
|
|
are being added. The <a class="reference internal" href="delete_atoms.html"><span class="doc">delete_atoms</span></a> command can be
|
|
used to remove overlapping atoms or molecules.</p>
|
|
<hr class="docutils" />
|
|
<p>Individual atoms are inserted by this command, unless the <em>mol</em>
|
|
keyword is used. It specifies a <em>template-ID</em> previously defined
|
|
using the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command, which reads a file that
|
|
defines the molecule. The coordinates, atom types, charges, etc, as
|
|
well as any bond/angle/etc and special neighbor information for the
|
|
molecule can be specified in the molecule file. See the
|
|
<a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command for details. The only settings
|
|
required to be in this file are the coordinates and types of atoms in
|
|
the molecule.</p>
|
|
<p>Using a lattice to add molecules, e.g. via the <em>box</em> or <em>region</em> or
|
|
<em>single</em> styles, is exactly the same as adding atoms on lattice
|
|
points, except that entire molecules are added at each point, i.e. on
|
|
the point defined by each basis atom in the unit cell as it tiles the
|
|
simulation box or region. This is done by placing the geometric
|
|
center of the molecule at the lattice point, and giving the molecule a
|
|
random orientation about the point. The random <em>seed</em> specified with
|
|
the <em>mol</em> keyword is used for this operation, and the random numbers
|
|
generated by each processor are different. This means the coordinates
|
|
of individual atoms (in the molecules) will be different when running
|
|
on different numbers of processors, unlike when atoms are being
|
|
created in parallel.</p>
|
|
<p>Also note that because of the random rotations, it may be important to
|
|
use a lattice with a large enough spacing that adjacent molecules will
|
|
not overlap, regardless of their relative orientations.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">If the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command is used to create
|
|
the simulation box, followed by the create_atoms command with its
|
|
<em>mol</em> option for adding molecules, then you typically need to use the
|
|
optional keywords allowed by the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command
|
|
for extra bonds (angles,etc) or extra special neighbors. This is
|
|
because by default, the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command sets up a
|
|
non-molecular system which doesn’t allow molecules to be added.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>This is the meaning of the other allowed keywords.</p>
|
|
<p>The <em>basis</em> keyword is only used when atoms (not molecules) are being
|
|
created. It specifies an atom type that will be assigned to specific
|
|
basis atoms as they are created. See the <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a>
|
|
command for specifics on how basis atoms are defined for the unit cell
|
|
of the lattice. By default, all created atoms are assigned the
|
|
argument <em>type</em> as their atom type.</p>
|
|
<p>The <em>remap</em> keyword only applies to the <em>single</em> style. If it is set
|
|
to <em>yes</em>, then if the specified position is outside the simulation
|
|
box, it will mapped back into the box, assuming the relevant
|
|
dimensions are periodic. If it is set to <em>no</em>, no remapping is done
|
|
and no particle is created if its position is outside the box.</p>
|
|
<p>The <em>var</em> and <em>set</em> keywords can be used together to provide a
|
|
criterion for accepting or rejecting the addition of an individual
|
|
atom, based on its coordinates. The <em>name</em> specified for the <em>var</em>
|
|
keyword is the name of an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> which
|
|
should evaluate to a zero or non-zero value based on one or two or
|
|
three variables which will store the x, y, or z coordinates of an atom
|
|
(one variable per coordinate). If used, these other variables must be
|
|
<a class="reference internal" href="variable.html"><span class="doc">internal-style variables</span></a> defined in the input script;
|
|
their initial numeric value can be anything. They must be
|
|
internal-style variables, because this command resets their values
|
|
directly. The <em>set</em> keyword is used to identify the names of these
|
|
other variables, one variable for the x-coordinate of a created atom,
|
|
one for y, and one for z.</p>
|
|
<p>When an atom is created, its x,y,z coordinates become the values for
|
|
any <em>set</em> variable that is defined. The <em>var</em> variable is then
|
|
evaluated. If the returned value is 0.0, the atom is not created. If
|
|
it is non-zero, the atom is created.</p>
|
|
<p>As an example, these commands can be used in a 2d simulation, to
|
|
create a sinusoidal surface. Note that the surface is “rough” due to
|
|
individual lattice points being “above” or “below” the mathematical
|
|
expression for the sinusoidal curve. If a finer lattice were used,
|
|
the sinusoid would appear to be “smoother”. Also note the use of the
|
|
“xlat” and “ylat” <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> keywords which
|
|
converts lattice spacings to distance. Click on the image for a
|
|
larger version.</p>
|
|
<pre class="literal-block">
|
|
variable x equal 100
|
|
variable y equal 25
|
|
lattice hex 0.8442
|
|
region box block 0 $x 0 $y -0.5 0.5
|
|
create_box 1 box
|
|
</pre>
|
|
<pre class="literal-block">
|
|
variable xx equal 0.0
|
|
variable yy equal 0.0
|
|
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"
|
|
create_atoms 1 box var v set x xx set y yy
|
|
</pre>
|
|
<a class=""
|
|
data-lightbox="group-default"
|
|
href="_images/sinusoid.jpg"
|
|
title=""
|
|
data-title=""
|
|
><img src="_images/sinusoid.jpg"
|
|
class="align-center"
|
|
width="25%"
|
|
height="auto"
|
|
alt=""/>
|
|
</a><p>The <em>rotate</em> keyword can be used with the <em>single</em> style, when adding
|
|
a single molecule to specify the orientation at which the molecule is
|
|
inserted. The axis of rotation is determined by the rotation vector
|
|
(Rx,Ry,Rz) that goes through the insertion point. The specified
|
|
<em>theta</em> determines the angle of rotation around that axis. Note that
|
|
the direction of rotation for the atoms around the rotation axis is
|
|
consistent with the right-hand rule: if your right-hand’s thumb points
|
|
along <em>R</em>, then your fingers wrap around the axis in the direction of
|
|
rotation.</p>
|
|
<p>The <em>units</em> keyword determines the meaning of the distance units used
|
|
to specify the coordinates of the one particle created by the <em>single</em>
|
|
style. A <em>box</em> value selects standard distance units as defined by
|
|
the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command, e.g. Angstroms for units = real or
|
|
metal. A <em>lattice</em> value means the distance units are in lattice
|
|
spacings.</p>
|
|
<hr class="docutils" />
|
|
<p>Atom IDs are assigned to created atoms in the following way. The
|
|
collection of created atoms are assigned consecutive IDs that start
|
|
immediately following the largest atom ID existing before the
|
|
create_atoms command was invoked. When a simulation is performed on
|
|
different numbers of processors, there is no guarantee a particular
|
|
created atom will be assigned the same ID. If molecules are being
|
|
created, molecule IDs are assigned to created molecules in a similar
|
|
fashion.</p>
|
|
<p>Aside from their ID, atom type, and xyz position, other properties of
|
|
created atoms are set to default values, depending on which quantities
|
|
are defined by the chosen <a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a>. See the <a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a> command for more details. See the
|
|
<a class="reference internal" href="set.html"><span class="doc">set</span></a> and <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></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"><span class="doc">molecule</span></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"><span class="doc">set</span></a> command can be used to override many of these
|
|
default settings.</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> 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</h2>
|
|
<p><a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a>, <a class="reference internal" href="region.html"><span class="doc">region</span></a>, <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>,
|
|
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</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>
|
|
</div>
|
|
</div>
|
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<a href="create_bonds.html" class="btn btn-neutral float-right" title="create_bonds command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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<a href="compute_modify.html" class="btn btn-neutral" title="compute_modify command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
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© Copyright 2013 Sandia Corporation.
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