forked from lijiext/lammps
263 lines
8.8 KiB
Plaintext
263 lines
8.8 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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molecule command :h3
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[Syntax:]
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molecule ID file :pre
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ID = user-assigned name for the molecule template
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file = name of file containing molecule description :ul
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[Examples:]
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molecule 1 mymol
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molecule CO2 co2.txt :pre
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[Description:]
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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 use molecule templates
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include (or will include) "fix deposit"_fix_deposit.html, "fix
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pour"_fix_pour.html, and "fix gcmc"_fix_gcmc.html.
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The ID of a molecule template can only contain alphanumeric characters
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and underscores.
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The format of the molecule file is similar to the data file read by
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the "read_data"_read_data.html commands, and is as follows.
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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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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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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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N {atoms} = # of atoms N in molecule, default = 0
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Nb {bonds} = # of bonds Nb in molecule, default = 0
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Na {angles} = # of angles Na in molecule, default = 0
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Nd {dihedrals} = # of dihedrals Nd in molecule, default = 0
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Ni {impropers} = # of impropers Ni in molecule, default = 0
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Mtotal {mass} = total mass of molecule
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Xc Yc Zc {com} = coordinates of center-of-mass of molecule
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Ixx Iyy Izz Ixy Ixz Iyz {inertia} = 6 components of inertia tensor of molecule :ul
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For {mass}, {com}, and {inertia}, 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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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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These are the allowed section keywords for the body of the file.
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{Coords, Types, Charges, Diameters, Masses} = atom-property sections
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{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
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{Special Bond Counts, Special Bonds} = special neighbor info :ul
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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 "fix deposit"_fix_deposit.html command, the
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Coords and Types sections are required. To add a rigid body via the
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"fix pour"_fix_pout.html 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 "fix pour"_fix_pour.html
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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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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 as a
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number from 1 to Nlines for the section, indicating which atom (or
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bond, etc) the entry applies to. The lines are assumed to be listed
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in order from 1 to Nlines.
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:line
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{Coords} section:
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one line per atom
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line syntax: ID x y z
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x,y,z = coordinate of atom :ul
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:line
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{Types} section:
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one line per atom
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line syntax: ID type
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type = atom type of atom :ul
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:line
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{Charges} section:
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one line per atom
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line syntax: ID q
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q = charge on atom :ul
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This section is only allowed for "atom styles"_atom_style.html that
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support charge. If not listed, the default charge on each atom in the
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molecule is 0.0.
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:line
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{Diameters} section:
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one line per atom
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line syntax: ID diam
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diam = diameter of atom :ul
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This section is only allowed for "atom styles"_atom_style.html 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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:line
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{Masses} section:
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one line per atom
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line syntax: ID mass
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mass = mass of atom :ul
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This section is only allowed for "atom styles"_atom_style.html that
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support per-atom mass, as opposed to per-type mass. See the
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"mass"_mass.html command for details. If not listed, the default mass
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for each atom is derived from its volume (see Diameters section) and a
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default density of 1.0, in "units"_units.html of mass/volume.
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:line
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{Bonds} section:
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one line per bond
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line syntax: ID type atom1 atom2
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type = bond type (1-Nbondtype)
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atom1,atom2 = IDs of atoms in bond :ul
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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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:line
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{Angles} section:
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one line per angle
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line syntax: ID type atom1 atom2 atom3
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type = angle type (1-Nangletype)
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atom1,atom2,atom3 = IDs of atoms in angle :ul
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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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:line
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{Dihedrals} section:
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one line per dihedral
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line syntax: ID type atom1 atom2 atom3 atom4
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type = dihedral type (1-Ndihedraltype)
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atom1,atom2,atom3,atom4 = IDs of atoms in dihedral :ul
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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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:line
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{Impropers} section:
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one line per improper
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line syntax: ID type atom1 atom2 atom3 atom4
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type = improper type (1-Nimpropertype)
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atom1,atom2,atom3,atom4 = IDs of atoms in improper :ul
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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 "improper style"_improper_style.html. See
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the doc pages for individual styles for details.
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:line
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{Special Bond Counts} section:
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one line per atom
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line syntax: ID N1 N2 N3
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N1 = # of 1-2 bonds
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N2 = # of 1-3 bonds
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N3 = # of 1-4 bonds :ul
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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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"special_bonds"_special_bonds.html 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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:line
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{Special Bonds} section:
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one line per atom
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line syntax: ID a b c d ...
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a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds :ul
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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 "special_bonds"_special_bonds.html 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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:line
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[Restrictions:] none
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[Related commands:]
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"fix deposit"_fix_deposit.html, "fix pour"_fix_pour.html,
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"fix_gcmc"_fix_gcmc.html
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[Default:] none
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