forked from lijiext/lammps
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400 lines
16 KiB
HTML
<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>molecule command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>molecule ID file1 file2 ...
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</PRE>
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<UL><LI>ID = user-assigned name for the molecule template
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<LI>file1,file2,... = names of files containing molecule descriptions
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>molecule 1 mymol
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molecule 1 co2.txt h2o.txt
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molecule CO2 co2.txt
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</PRE>
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<P><B>Description:</B>
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</P>
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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 (or will in the future) include:
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</P>
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<UL><LI><A HREF = "fix_deposit.html">fix deposit</A>
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<LI><A HREF = "fix_pour.html">fix pour</A>
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<LI><A HREF = "fix_rigid.html">fix rigid/small</A>
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<LI><A HREF = "fix_shake.html">fix shake</A>
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<LI><A HREF = "fix_gcmc.html">fix gcmc</A> (not yet)
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<LI><A HREF = "create_atoms.html">create_atoms</A>
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<LI><A HREF = "atom_style.html">atom_style template</A>
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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.
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</P>
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<P>A single template can contain multiple molecules, listed one per file.
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Many 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 HREF = "atom_style.html">atom_style
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template</A> command allows multiple-molecule templates
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to define a system with more than one templated molecule.
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</P>
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<P>IMPORTANT NOTE: When using the <A HREF = "atom_style.html">atom_style template</A>
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command with a molecule template that contains multiple molecules, you
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should insure the atom types, bond types, angle_types, etc in all the
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molecules are consistent. E.g. if one molecule represents H2O and
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another CO2, then you probably do not want each molecule file to
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define 2 atom types and a single bond type, because they will conflict
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with each other when a mixture system of H2O and CO2 molecules is
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defined, e.g. by the <A HREF = "read_data.html">read_data</A> command. Rather the
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H2O molecule should define atom types 1 and 2, and bond type 1. And
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the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
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2 if a single oxygen type is desired), and bond type 2.
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</P>
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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 HREF = "read_data.html">read_data</A> commands, and is as follows.
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</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.
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</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.
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</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.
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</P>
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<UL><LI>N <I>atoms</I> = # of atoms N in molecule, default = 0
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<LI>Nb <I>bonds</I> = # of bonds Nb in molecule, default = 0
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<LI>Na <I>angles</I> = # of angles Na in molecule, default = 0
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<LI>Nd <I>dihedrals</I> = # of dihedrals Nd in molecule, default = 0
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<LI>Ni <I>impropers</I> = # of impropers Ni in molecule, default = 0
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<LI>Mtotal <I>mass</I> = total mass of molecule
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<LI>Xc Yc Zc <I>com</I> = coordinates of center-of-mass of molecule
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<LI>Ixx Iyy Izz Ixy Ixz Iyz <I>inertia</I> = 6 components of inertia tensor of molecule
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</UL>
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<P>For <I>mass</I>, <I>com</I>, and <I>inertia</I>, 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. You typically only need to
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specify these values for a rigid body consisting of overlapping
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finite-size particles.
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</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.
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</P>
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<P>These are the allowed section keywords for the body of the file.
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</P>
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<UL><LI><I>Coords, Types, Charges, Diameters, Masses</I> = atom-property sections
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<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topology sections
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<LI><I>Special Bond Counts, Special Bonds</I> = special neighbor info
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<LI><I>Shake Flags, Shake Atoms, Shake Bond Types</I> = SHAKE info
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</UL>
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<P>IMPORTANT NOTE: Whether a section is required depends on how the
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molecule template is used by other LAMMPS commands. For example, to
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add a molecule via the <A HREF = "fix_deposit.html">fix deposit</A> command, the
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Coords and Types sections are required. To add a rigid body via the
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<A HREF = "fix_pout.html">fix pour</A> command, the Bonds (Angles, etc) sections are
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not required, since the molecule will be treated as a rigid body.
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Some sections are optional. For example, the <A HREF = "fix_pour.html">fix pour</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.
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</P>
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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.
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</P>
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<HR>
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<P><I>Coords</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: ID x y z
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<LI>x,y,z = coordinate of atom
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</UL>
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<HR>
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<P><I>Types</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: ID type
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<LI>type = atom type of atom
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</UL>
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<HR>
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<P><I>Charges</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: ID q
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<LI>q = charge on atom
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</UL>
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<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</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.
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</P>
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<HR>
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<P><I>Diameters</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: ID diam
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<LI>diam = diameter of atom
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</UL>
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<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</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.
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</P>
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<HR>
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<P><I>Masses</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: ID mass
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<LI>mass = mass of atom
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</UL>
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<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</A> that
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support per-atom mass, as opposed to per-type mass. See the
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<A HREF = "mass.html">mass</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 HREF = "units.html">units</A> of mass/volume.
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</P>
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<HR>
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<P><I>Bonds</I> section:
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</P>
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<UL><LI>one line per bond
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<LI>line syntax: ID type atom1 atom2
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<LI>type = bond type (1-Nbondtype)
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<LI>atom1,atom2 = IDs of atoms in bond
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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.
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</P>
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<HR>
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<P><I>Angles</I> section:
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</P>
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<UL><LI>one line per angle
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<LI>line syntax: ID type atom1 atom2 atom3
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<LI>type = angle type (1-Nangletype)
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<LI>atom1,atom2,atom3 = IDs of atoms in angle
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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.
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</P>
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<HR>
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<P><I>Dihedrals</I> section:
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</P>
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<UL><LI>one line per dihedral
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<LI>line syntax: ID type atom1 atom2 atom3 atom4
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<LI>type = dihedral type (1-Ndihedraltype)
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<LI>atom1,atom2,atom3,atom4 = IDs of atoms in dihedral
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</UL>
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<P>The IDs for the four atoms in each dihedral should be values from 1 to
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Natoms, where Natoms = # of atoms in the molecule. The 4 atoms are
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ordered linearly within the dihedral.
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</P>
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<HR>
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<P><I>Impropers</I> section:
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</P>
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<UL><LI>one line per improper
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<LI>line syntax: ID type atom1 atom2 atom3 atom4
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<LI>type = improper type (1-Nimpropertype)
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<LI>atom1,atom2,atom3,atom4 = IDs of atoms in improper
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</UL>
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<P>The IDs for the four atoms in each improper should be values from 1 to
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Natoms, where Natoms = # of atoms in the molecule. The ordering of
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the 4 atoms determines the definition of the improper angle used in
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the formula for the defined <A HREF = "improper_style.html">improper style</A>. See
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the doc pages for individual styles for details.
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</P>
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<HR>
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<P><I>Special Bond Counts</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: ID N1 N2 N3
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<LI>N1 = # of 1-2 bonds
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<LI>N2 = # of 1-3 bonds
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<LI>N3 = # of 1-4 bonds
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</UL>
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<P>N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of
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this atom within the topology of the molecule. See the
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<A HREF = "special_bonds.html">special_bonds</A> doc page for more discussion of
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1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds
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section must also appear. If this section is not specied, the
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atoms in the molecule will have no special bonds.
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</P>
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<HR>
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<P><I>Special Bonds</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: ID a b c d ...
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<LI>a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds
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</UL>
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<P>A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3,
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1-4 neighbors of this atom. The IDs should be values from 1 to
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Natoms, where Natoms = # of atoms in the molecule. The first N1
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values should be the 1-2 neighbors, the next N2 should be the 1-3
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neighbors, the last N3 should be the 1-4 neighbors. No atom ID should
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appear more than once. See the <A HREF = "special_bonds.html">special_bonds</A> doc
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page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section
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appears, the Special Bond Counts section must also appear. If this
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section is not specied, the atoms in the molecule will have no special
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bonds.
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</P>
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<HR>
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<P><I>Shake Flags</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: ID flag
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<LI>flag = 0,1,2,3,4
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</UL>
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<P>This section is only needed when molecules created using the template
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will be constrained by SHAKE via the "fix shake" command. The other
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two Shake sections must also appear in the file, following this one.
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</P>
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<P>The meaning of the flag for each atom is as follows. See the <A HREF = "fix_shake.html">fix
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shake</A> doc page for a further description of SHAKE
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clusters.
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</P>
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<UL><LI>0 = not part of a SHAKE cluster
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<LI>1 = part of a SHAKE angle cluster (two bonds and the angle they form)
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<LI>2 = part of a 2-atom SHAKE cluster with a single bond
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<LI>3 = part of a 3-atom SHAKE cluster with two bonds
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<LI>4 = part of a 4-atom SHAKE cluster with three bonds
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</UL>
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<HR>
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<P><I>Shake Atoms</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: ID a b c d
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<LI>a,b,c,d = IDs of atoms in cluster
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</UL>
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<P>This section is only needed when molecules created using the template
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will be constrained by SHAKE via the "fix shake" command. The other
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two Shake sections must also appear in the file.
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</P>
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<P>The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms
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in the SHAKE cluster that this atom belongs to. The number of values
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that must appear is determined by the shake flag for the atom (see the
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Shake Flags section above). All atoms in a particular cluster should
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list their a,b,c,d values identically.
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</P>
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<P>If flag = 0, no a,b,c,d values are listed on the line, just the
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(ignored) ID.
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</P>
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<P>If flag = 1, a,b,c are listed, where a = ID of central atom in the
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angle, and b,c the other two atoms in the angle.
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</P>
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<P>If flag = 2, a,b are listed, where a = ID of atom in bond with the the
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lowest ID, and b = ID of atom in bond with the highest ID.
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</P>
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<P>If flag = 3, a,b,c are listed, where a = ID of central atom,
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and b,c = IDs of other two atoms bonded to the central atom.
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</P>
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<P>If flag = 4, a,b,c,d are listed, where a = ID of central atom,
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and b,c,d = IDs of other three atoms bonded to the central atom.
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</P>
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<P>See the <A HREF = "fix_shake.html">fix shake</A> doc page for a further description
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of SHAKE clusters.
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</P>
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<HR>
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<P><I>Shake Bond Types</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: ID a b c
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<LI>a,b,c = bond types (or angle type) of bonds (or angle) in cluster
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</UL>
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<P>This section is only needed when molecules created using the template
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will be constrained by SHAKE via the "fix shake" command. The other
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two Shake sections must also appear in the file.
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</P>
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<P>The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
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in the SHAKE cluster that this atom belongs to. The number of values
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that must appear is determined by the shake flag for the atom (see the
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Shake Flags section above). All atoms in a particular cluster should
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list their a,b,c values identically.
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</P>
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<P>If flag = 0, no a,b,c values are listed on the line, just the
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(ignored) ID.
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</P>
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<P>If flag = 1, a,b,c are listed, where a = bondtype of the bond between
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the central atom and the first non-central atom (value b in the Shake
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Atoms section), b = bondtype of the bond between the central atom and
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the 2nd non-central atom (value c in the Shake Atoms section), and c =
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the angle type (1 to Nangletypes) of the angle between the 3 atoms.
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</P>
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<P>If flag = 2, only a is listed, where a = bondtype of the bond between
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the 2 atoms in the cluster.
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</P>
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<P>If flag = 3, a,b are listed, where a = bondtype of the bond between
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the central atom and the first non-central atom (value b in the Shake
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Atoms section), and b = bondtype of the bond between the central atom
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and the 2nd non-central atom (value c in the Shake Atoms section).
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</P>
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<P>If flag = 4, a,b,c are listed, where a = bondtype of the bond between
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the central atom and the first non-central atom (value b in the Shake
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Atoms section), b = bondtype of the bond between the central atom and
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the 2nd non-central atom (value c in the Shake Atoms section), and c =
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bondtype of the bond between the central atom and the 3rd non-central
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atom (value d in the Shake Atoms section).
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</P>
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<P>See the <A HREF = "fix_shake.html">fix shake</A> doc page for a further description
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of SHAKE clusters.
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</P>
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<HR>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_deposit.html">fix deposit</A>, <A HREF = "fix_pour.html">fix pour</A>,
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<A HREF = "fix_gcmc.html">fix_gcmc</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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