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603 lines
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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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<div class="section" id="molecule-command">
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<span id="index-0"></span><h1>molecule command<a class="headerlink" href="#molecule-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>molecule ID file1 keyword values ... file2 keyword values ... fileN ...
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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 molecule template</li>
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<li>file1,file2,... = names of files containing molecule descriptions</li>
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<li>zero or more keyword/value pairs may be appended after each file</li>
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<li>keyword = <em>offset</em> or <em>toff</em> or <em>boff</em> or <em>aoff</em> or <em>doff</em> or <em>ioff</em> or <em>scale</em></li>
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</ul>
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<pre class="literal-block">
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<em>offset</em> values = Toff Boff Aoff Doff Ioff
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Toff = offset to add to atom types
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Boff = offset to add to bond types
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Aoff = offset to add to angle types
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Doff = offset to add to dihedral types
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Ioff = offset to add to improper types
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<em>toff</em> value = Toff
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Toff = offset to add to atom types
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<em>boff</em> value = Boff
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Boff = offset to add to bond types
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<em>aoff</em> value = Aoff
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Aoff = offset to add to angle types
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<em>doff</em> value = Doff
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Doff = offset to add to dihedral types
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<em>ioff</em> value = Ioff
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Ioff = offset to add to improper types
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<em>scale</em> value = sfactor
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sfactor = scale factor to apply to the size and mass of the molecule
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>molecule 1 mymol.txt
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molecule 1 co2.txt h2o.txt
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molecule CO2 co2.txt boff 3 aoff 2
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molecule 1 mymol.txt offset 6 9 18 23 14
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molecule objects file.1 scale 1.5 file.1 scale 2.0 file.2 scale 1.3
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Define a molecule template that can be used as part of other LAMMPS
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commands, typically to define a collection of particles as a bonded
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molecule or a rigid body. Commands that currently use molecule
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templates include:</p>
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<ul class="simple">
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<li><a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a></li>
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<li><a class="reference internal" href="fix_pour.html"><em>fix pour</em></a></li>
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<li><a class="reference internal" href="fix_rigid.html"><em>fix rigid/small</em></a></li>
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<li><a class="reference internal" href="fix_shake.html"><em>fix shake</em></a></li>
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<li><a class="reference internal" href="fix_gcmc.html"><em>fix gcmc</em></a></li>
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<li><a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a></li>
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<li><a class="reference internal" href="atom_style.html"><em>atom_style template</em></a></li>
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</ul>
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<p>The ID of a molecule template can only contain alphanumeric characters
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and underscores.</p>
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<p>A single template can contain multiple molecules, listed one per file.
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Some of the commands listed above currently use only the first
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molecule in the template, and will issue a warning if the template
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contains multiple molecules. The <a class="reference internal" href="atom_style.html"><em>atom_style template</em></a> command allows multiple-molecule templates
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to define a system with more than one templated molecule.</p>
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<p>Each filename can be followed by optional keywords which are applied
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only to the molecule in the file as used in this template. This is to
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make it easy to use the same molecule file in different molecule
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templates or in different simulations. You can specify the same file
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multiple times with different optional keywords.</p>
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<p>The <em>offset</em>, <em>toff</em>, <em>aoff</em>, <em>doff</em>, <em>ioff</em> keywords add the
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specified offset values to the atom types, bond types, angle types,
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dihedral types, and/or improper types as they are read from the
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molecule file. E.g. if <em>toff</em> = 2, and the file uses atom types
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1,2,3, then each created molecule will have atom types 3,4,5. For the
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<em>offset</em> keyword, all five offset values must be specified, but
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individual values will be ignored if the molecule template does not
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use that attribute (e.g. no bonds).</p>
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<p>The <em>scale</em> keyword scales the size of the molecule. This can be
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useful for modeling polydisperse granular rigid bodies. The scale
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factor is applied to each of these properties in the molecule file, if
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they are defined: the individual particle coordinates (Coords
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section), the individual mass of each particle (Masses section), the
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individual diameters of each particle (Diameters section), the total
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mass of the molecule (header keyword = mass), the center-of-mass of
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the molecule (header keyword = com), and the moments of inertia of the
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molecule (header keyword = inertia).</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 molecule command can be used to define molecules with bonds,
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angles, dihedrals, imporopers, or special bond lists of neighbors
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within a molecular topology, so that you can later add the molecules
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to your simulation, via one or more of the commands listed above. If
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such molecules do not already exist when LAMMPS creates the simulation
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box, via the <a class="reference internal" href="create_box.html"><em>create_box</em></a> or
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<a class="reference internal" href="read_data.html"><em>read_data</em></a> command, when you later add them you may
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overflow the pre-allocated data structures which store molecular
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topology information with each atom, and an error will be generated.
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Both the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command and the data files read
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by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command have “extra” options which
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insure space is allocated for storing topology info for molecules that
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are added later.</p>
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</div>
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<p>The format of an individual molecule file is similar to the data file
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read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> commands, and is as follows.</p>
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<p>A molecule file has a header and a body. The header appears first.
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The first line of the header is always skipped; it typically contains
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a description of the file. Then lines are read one at a time. Lines
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can have a trailing comment starting with ‘#’ that is ignored. If the
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line is blank (only whitespace after comment is deleted), it is
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skipped. If the line contains a header keyword, the corresponding
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value(s) is read from the line. If it doesn’t contain a header
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keyword, the line begins the body of the file.</p>
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<p>The body of the file contains zero or more sections. The first line
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of a section has only a keyword. The next line is skipped. The
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remaining lines of the section contain values. The number of lines
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depends on the section keyword as described below. Zero or more blank
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lines can be used between sections. Sections can appear in any order,
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with a few exceptions as noted below.</p>
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<p>These are the recognized header keywords. Header lines can come in
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any order. The numeric value(s) are read from the beginning of the
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line. The keyword should appear at the end of the line. All these
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settings have default values, as explained below. A line need only
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appear if the value(s) are different than the default.</p>
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<ul class="simple">
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<li>N <em>atoms</em> = # of atoms N in molecule, default = 0</li>
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<li>Nb <em>bonds</em> = # of bonds Nb in molecule, default = 0</li>
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<li>Na <em>angles</em> = # of angles Na in molecule, default = 0</li>
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<li>Nd <em>dihedrals</em> = # of dihedrals Nd in molecule, default = 0</li>
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<li>Ni <em>impropers</em> = # of impropers Ni in molecule, default = 0</li>
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<li>Mtotal <em>mass</em> = total mass of molecule</li>
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<li>Xc Yc Zc <em>com</em> = coordinates of center-of-mass of molecule</li>
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<li>Ixx Iyy Izz Ixy Ixz Iyz <em>inertia</em> = 6 components of inertia tensor of molecule</li>
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</ul>
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<p>For <em>mass</em>, <em>com</em>, and <em>inertia</em>, the default is for LAMMPS to
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calculate this quantity itself if needed, assuming the molecules
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consists of a set of point particles or finite-size particles (with a
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non-zero diameter) that do not overlap. If finite-size particles in
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the molecule do overlap, LAMMPS will not account for the overlap
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effects when calculating any of these 3 quantities, so you should
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pre-compute them yourself and list the values in the file.</p>
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<p>The mass and center-of-mass coordinates (Xc,Yc,Zc) are
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self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
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should be the values consistent with the current orientation of the
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rigid body around its center of mass. The values are with respect to
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the simulation box XYZ axes, not with respect to the prinicpal axes of
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the rigid body itself. LAMMPS performs the latter calculation
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internally.</p>
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<p>These are the allowed section keywords for the body of the file.</p>
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<ul class="simple">
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<li><em>Coords, Types, Charges, Diameters, Masses</em> = atom-property sections</li>
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<li><em>Bonds, Angles, Dihedrals, Impropers</em> = molecular topology sections</li>
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<li><em>Special Bond Counts, Special Bonds</em> = special neighbor info</li>
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<li><em>Shake Flags, Shake Atoms, Shake Bond Types</em> = SHAKE info</li>
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</ul>
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<p>If a Bonds section is specified then the Special Bond Counts and
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Special Bonds sections can also be used, if desired, to explicitly
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list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
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details below). This is optional since if these sections are not
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included, LAMMPS will auto-generate this information. Note that
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LAMMPS uses this info to properly exclude or weight bonded pairwise
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interactions between bonded atoms. See the
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<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command for more details. One
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reason to list the special bond info explicitly is for the
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<a class="reference internal" href="tutorial_drude.html"><em>thermalized Drude oscillator model</em></a> which treats
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the bonds between nuclear cores and Drude electrons in a different
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manner.</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">Whether a section is required depends on how the molecule
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template is used by other LAMMPS commands. For example, to add a
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molecule via the <a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a> command, the Coords
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and Types sections are required. To add a rigid body via the <code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">pour</span></code> command, the Bonds (Angles, etc) sections are not
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required, since the molecule will be treated as a rigid body. Some
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sections are optional. For example, the <a class="reference internal" href="fix_pour.html"><em>fix pour</em></a>
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command can be used to add “molecules” which are clusters of
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finite-size granular particles. If the Diameters section is not
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specified, each particle in the molecule will have a default diameter
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of 1.0. See the doc pages for LAMMPS commands that use molecule
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templates for more details.</p>
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</div>
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<p>Each section is listed below in alphabetic order. The format of each
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section is described including the number of lines it must contain and
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rules (if any) for whether it can appear in the data file. In each
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case the ID is ignored; it is simply included for readability, and
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should be a number from 1 to Nlines for the section, indicating which
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atom (or bond, etc) the entry applies to. The lines are assumed to be
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listed in order from 1 to Nlines, but LAMMPS does not check for this.</p>
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<hr class="docutils" />
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<p><em>Coords</em> section:</p>
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<ul class="simple">
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<li>one line per atom</li>
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<li>line syntax: ID x y z</li>
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<li>x,y,z = coordinate of atom</li>
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</ul>
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<hr class="docutils" />
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<p><em>Types</em> section:</p>
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<ul class="simple">
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<li>one line per atom</li>
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<li>line syntax: ID type</li>
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<li>type = atom type of atom</li>
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</ul>
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<hr class="docutils" />
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<p><em>Charges</em> section:</p>
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<ul class="simple">
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<li>one line per atom</li>
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<li>line syntax: ID q</li>
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<li>q = charge on atom</li>
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</ul>
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<p>This section is only allowed for <a class="reference internal" href="atom_style.html"><em>atom styles</em></a> that
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support charge. If this section is not included, the default charge
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on each atom in the molecule is 0.0.</p>
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<hr class="docutils" />
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<p><em>Diameters</em> section:</p>
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<ul class="simple">
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<li>one line per atom</li>
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<li>line syntax: ID diam</li>
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<li>diam = diameter of atom</li>
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</ul>
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<p>This section is only allowed for <a class="reference internal" href="atom_style.html"><em>atom styles</em></a> that
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support finite-size spherical particles, e.g. atom_style sphere. If
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not listed, the default diameter of each atom in the molecule is 1.0.</p>
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<hr class="docutils" />
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<p><em>Masses</em> section:</p>
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<ul class="simple">
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<li>one line per atom</li>
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<li>line syntax: ID mass</li>
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<li>mass = mass of atom</li>
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</ul>
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<p>This section is only allowed for <a class="reference internal" href="atom_style.html"><em>atom styles</em></a> that
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support per-atom mass, as opposed to per-type mass. See the
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<a class="reference internal" href="mass.html"><em>mass</em></a> command for details. If this section is not
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included, the default mass for each atom is derived from its volume
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(see Diameters section) and a default density of 1.0, in
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<a class="reference internal" href="units.html"><em>units</em></a> of mass/volume.</p>
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<hr class="docutils" />
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<p><em>Bonds</em> section:</p>
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<ul class="simple">
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<li>one line per bond</li>
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<li>line syntax: ID type atom1 atom2</li>
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<li>type = bond type (1-Nbondtype)</li>
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<li>atom1,atom2 = IDs of atoms in bond</li>
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</ul>
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<p>The IDs for the two atoms in each bond should be values
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from 1 to Natoms, where Natoms = # of atoms in the molecule.</p>
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<hr class="docutils" />
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<p><em>Angles</em> section:</p>
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<ul class="simple">
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<li>one line per angle</li>
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<li>line syntax: ID type atom1 atom2 atom3</li>
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<li>type = angle type (1-Nangletype)</li>
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<li>atom1,atom2,atom3 = IDs of atoms in angle</li>
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</ul>
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<p>The IDs for the three atoms in each angle should be values from 1 to
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Natoms, where Natoms = # of atoms in the molecule. The 3 atoms are
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ordered linearly within the angle. Thus the central atom (around
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which the angle is computed) is the atom2 in the list.</p>
|
|
<hr class="docutils" />
|
|
<p><em>Dihedrals</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per dihedral</li>
|
|
<li>line syntax: ID type atom1 atom2 atom3 atom4</li>
|
|
<li>type = dihedral type (1-Ndihedraltype)</li>
|
|
<li>atom1,atom2,atom3,atom4 = IDs of atoms in dihedral</li>
|
|
</ul>
|
|
<p>The IDs for the four atoms in each dihedral should be values from 1 to
|
|
Natoms, where Natoms = # of atoms in the molecule. The 4 atoms are
|
|
ordered linearly within the dihedral.</p>
|
|
<hr class="docutils" />
|
|
<p><em>Impropers</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per improper</li>
|
|
<li>line syntax: ID type atom1 atom2 atom3 atom4</li>
|
|
<li>type = improper type (1-Nimpropertype)</li>
|
|
<li>atom1,atom2,atom3,atom4 = IDs of atoms in improper</li>
|
|
</ul>
|
|
<p>The IDs for the four atoms in each improper should be values from 1 to
|
|
Natoms, where Natoms = # of atoms in the molecule. The ordering of
|
|
the 4 atoms determines the definition of the improper angle used in
|
|
the formula for the defined <a class="reference internal" href="improper_style.html"><em>improper style</em></a>. See
|
|
the doc pages for individual styles for details.</p>
|
|
<hr class="docutils" />
|
|
<p><em>Special Bond Counts</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per atom</li>
|
|
<li>line syntax: ID N1 N2 N3</li>
|
|
<li>N1 = # of 1-2 bonds</li>
|
|
<li>N2 = # of 1-3 bonds</li>
|
|
<li>N3 = # of 1-4 bonds</li>
|
|
</ul>
|
|
<p>N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of
|
|
this atom within the topology of the molecule. See the
|
|
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> doc page for more discussion of
|
|
1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds
|
|
section must also appear. If this section is not specied, the
|
|
atoms in the molecule will have no special bonds.</p>
|
|
<hr class="docutils" />
|
|
<p><em>Special Bonds</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per atom</li>
|
|
<li>line syntax: ID a b c d ...</li>
|
|
<li>a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds</li>
|
|
</ul>
|
|
<p>A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3,
|
|
1-4 neighbors of this atom. The IDs should be values from 1 to
|
|
Natoms, where Natoms = # of atoms in the molecule. The first N1
|
|
values should be the 1-2 neighbors, the next N2 should be the 1-3
|
|
neighbors, the last N3 should be the 1-4 neighbors. No atom ID should
|
|
appear more than once. See the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> doc
|
|
page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section
|
|
appears, the Special Bond Counts section must also appear. If this
|
|
section is not specied, the atoms in the molecule will have no special
|
|
bonds.</p>
|
|
<hr class="docutils" />
|
|
<p><em>Shake Flags</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per atom</li>
|
|
<li>line syntax: ID flag</li>
|
|
<li>flag = 0,1,2,3,4</li>
|
|
</ul>
|
|
<p>This section is only needed when molecules created using the template
|
|
will be constrained by SHAKE via the “fix shake” command. The other
|
|
two Shake sections must also appear in the file, following this one.</p>
|
|
<p>The meaning of the flag for each atom is as follows. See the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> doc page for a further description of SHAKE
|
|
clusters.</p>
|
|
<ul class="simple">
|
|
<li>0 = not part of a SHAKE cluster</li>
|
|
<li>1 = part of a SHAKE angle cluster (two bonds and the angle they form)</li>
|
|
<li>2 = part of a 2-atom SHAKE cluster with a single bond</li>
|
|
<li>3 = part of a 3-atom SHAKE cluster with two bonds</li>
|
|
<li>4 = part of a 4-atom SHAKE cluster with three bonds</li>
|
|
</ul>
|
|
<hr class="docutils" />
|
|
<p><em>Shake Atoms</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per atom</li>
|
|
<li>line syntax: ID a b c d</li>
|
|
<li>a,b,c,d = IDs of atoms in cluster</li>
|
|
</ul>
|
|
<p>This section is only needed when molecules created using the template
|
|
will be constrained by SHAKE via the “fix shake” command. The other
|
|
two Shake sections must also appear in the file.</p>
|
|
<p>The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms
|
|
in the SHAKE cluster that this atom belongs to. The number of values
|
|
that must appear is determined by the shake flag for the atom (see the
|
|
Shake Flags section above). All atoms in a particular cluster should
|
|
list their a,b,c,d values identically.</p>
|
|
<p>If flag = 0, no a,b,c,d values are listed on the line, just the
|
|
(ignored) ID.</p>
|
|
<p>If flag = 1, a,b,c are listed, where a = ID of central atom in the
|
|
angle, and b,c the other two atoms in the angle.</p>
|
|
<p>If flag = 2, a,b are listed, where a = ID of atom in bond with the the
|
|
lowest ID, and b = ID of atom in bond with the highest ID.</p>
|
|
<p>If flag = 3, a,b,c are listed, where a = ID of central atom,
|
|
and b,c = IDs of other two atoms bonded to the central atom.</p>
|
|
<p>If flag = 4, a,b,c,d are listed, where a = ID of central atom,
|
|
and b,c,d = IDs of other three atoms bonded to the central atom.</p>
|
|
<p>See the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> doc page for a further description
|
|
of SHAKE clusters.</p>
|
|
<hr class="docutils" />
|
|
<p><em>Shake Bond Types</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per atom</li>
|
|
<li>line syntax: ID a b c</li>
|
|
<li>a,b,c = bond types (or angle type) of bonds (or angle) in cluster</li>
|
|
</ul>
|
|
<p>This section is only needed when molecules created using the template
|
|
will be constrained by SHAKE via the “fix shake” command. The other
|
|
two Shake sections must also appear in the file.</p>
|
|
<p>The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
|
|
in the SHAKE cluster that this atom belongs to. The number of values
|
|
that must appear is determined by the shake flag for the atom (see the
|
|
Shake Flags section above). All atoms in a particular cluster should
|
|
list their a,b,c values identically.</p>
|
|
<p>If flag = 0, no a,b,c values are listed on the line, just the
|
|
(ignored) ID.</p>
|
|
<p>If flag = 1, a,b,c are listed, where a = bondtype of the bond between
|
|
the central atom and the first non-central atom (value b in the Shake
|
|
Atoms section), b = bondtype of the bond between the central atom and
|
|
the 2nd non-central atom (value c in the Shake Atoms section), and c =
|
|
the angle type (1 to Nangletypes) of the angle between the 3 atoms.</p>
|
|
<p>If flag = 2, only a is listed, where a = bondtype of the bond between
|
|
the 2 atoms in the cluster.</p>
|
|
<p>If flag = 3, a,b are listed, where a = bondtype of the bond between
|
|
the central atom and the first non-central atom (value b in the Shake
|
|
Atoms section), and b = bondtype of the bond between the central atom
|
|
and the 2nd non-central atom (value c in the Shake Atoms section).</p>
|
|
<p>If flag = 4, a,b,c are listed, where a = bondtype of the bond between
|
|
the central atom and the first non-central atom (value b in the Shake
|
|
Atoms section), b = bondtype of the bond between the central atom and
|
|
the 2nd non-central atom (value c in the Shake Atoms section), and c =
|
|
bondtype of the bond between the central atom and the 3rd non-central
|
|
atom (value d in the Shake Atoms section).</p>
|
|
<p>See the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> doc page for a further description
|
|
of SHAKE clusters.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
|
<blockquote>
|
|
<div>none</div></blockquote>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p><a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a>, <a class="reference internal" href="fix_pour.html"><em>fix pour</em></a>,
|
|
<a class="reference internal" href="fix_gcmc.html"><em>fix gcmc</em></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
|
<p>The default keywords values are offset 0 0 0 0 0 and scale = 1.0.</p>
|
|
</div>
|
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</div>
|
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</div>
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<hr/>
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<p>
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