lammps/doc/molecule.txt

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:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)

:line

molecule command :h3

[Syntax:]

molecule ID file :pre

ID = user-assigned name or template ID for the molecule
file = name of file containing molecule description :ul

[Examples:]

molecule 1 mymol
molecule CO2 co2.txt :pre

[Description:]

Define a molecule that can be used as part of other LAMMPS commands,
typically to define a collection of particles as a bonded molecule or
a rigid body.  Commands that use molecule definitions include (or will
include) "fix deposit"_fix_deposit.html, "fix pour"_fix_pour.html, and
"fix gcmc"_fix_gcmc.html.

The ID of a molecule can only contain alphanumeric characters and
underscores.

The format of the molecule description file is similar to
the data file read by the "read_data"_read_data.html commands,
and is as follows.

A molecule file has a header and a body.  The header appears first.
The first line of the header is always skipped; it typically contains
a description of the file.  Then lines are read one at a time.  Lines
can have a trailing comment starting with '#' that is ignored.  If the
line is blank (only whitespace after comment is deleted), it is
skipped.  If the line contains a header keyword, the corresponding
value(s) is read from the line.  If it doesn't contain a header
keyword, the line begins the body of the file.

The body of the file contains zero or more sections.  The first line
of a section has only a keyword.  The next line is skipped.  The
remaining lines of the section contain values.  The number of lines
depends on the section keyword as described below.  Zero or more blank
lines can be used between sections.  Sections can appear in any order,
with a few exceptions as noted below.

These are the recognized header keywords.  Header lines can come in
any order.  The value(s) are read from the beginning of the line.
Thus the keyword {atoms} should be in a line like "10 atoms"; the
keyword {ylo yhi} should be in a line like "-10.0 10.0 ylo yhi"; the
keyword {xy xz yz} should be in a line like "0.0 5.0 6.0 xy xz yz".
All these settings have a default value of 0, except the lo/hi box
size defaults are -0.5 and 0.5.  A line need only appear if the value
is different than the default.

{atoms} = # of atoms in molecule
{bonds} = # of bonds in molecule
{angles} = # of angles in molecule
{dihedrals} = # of dihedrals in molecule
{impropers} = # of impropers in molecule :ul

These are the allowed section keywords for the body of the file.

{Coords, Types, Charges, Diameters, Masses} = atom-property sections 
{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections 
{Special Bond Counts, Special Bonds} = special neighbor info :ul

IMPORTANT NOTE: Whether a section is required depends on how the
molecule definition is used by other LAMMPS commands.  For example, to
add a molecule via the "fix deposit"_fix_deposit.html command, the
Coords and Types sections are required.  To add a rigid body via the
"fix pour"_fix_pout.html command, the Bonds (Angles, etc) sections are
not required, since the molecule will be treated as a rigid body.
Some sections are optional.  For example, the "fix pour"_fix_pour.html
command can add finite-size granular particles.  If the Diameters
section is not specified, added particles will have a default diameter
of 1.0.  See the doc pages for LAMMPS commands that use read-in
molecules for more details.

Each section is listed below in alphabetic order.  The format of each
section is described including the number of lines it must contain and
rules (if any) for whether it can appear in the data file.  In each
case the ID is ignored; it is simply included for readability as a
number from 1 to Nlines for the section, indicating which atom (or
bond, etc) the entry applies to.  The lines must be listed in order
from 1 to Nlines.

:line

{Coords} section:

one line per atom
line syntax: ID x y z
x,y,z = coordinate of atom :ul

:line

{Types} section:

one line per atom
line syntax: ID type
type = atom type of atom :ul

:line

{Charges} section:

one line per atom
line syntax: ID q
q = charge on atom :ul

This section is only allowed for "atom styles"_atom_style.html that
support charge.  If not listed, the default charge on each atom in the
molecule is 0.0.

:line

{Diameters} section:

one line per atom
line syntax: ID diam
diam = diameter of atom :ul

This section is only allowed for "atom styles"_atom_style.html that
support finite-size spherical particles, e.g. atom_style sphere.  If
not listed, the default diameter of each atom in the molecule is 1.0.

:line

{Masses} section:

one line per atom
line syntax: ID mass
mass = mass of atom :ul

This section is only allowed for "atom styles"_atom_style.html that
support per-atom mass, as opposed to per-type mass.  See the
"mass"_mass.html command for details.  If not listed, the default mass
for each atom is derived from its volume (see Diameters section) and a
default density of 1.0, in "units"_units.html of mass/volume.

:line

{Bonds} section:

one line per bond
line syntax: ID type atom1 atom2
type = bond type (1-Nbondtype)
atom1,atom2 = IDs of atoms in bond :ul

The IDs for the two atoms in each bond should be values
from 1 to Natoms, where Natoms = # of atoms in the molecule.

:line

{Angles} section:

one line per angle
line syntax: ID type atom1 atom2 atom3
type = angle type (1-Nangletype)
atom1,atom2,atom3 = IDs of atoms in angle :ul

The IDs for the three atoms in each angle should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule.  The 3 atoms are
ordered linearly within the angle.  Thus the central atom (around
which the angle is computed) is the atom2 in the list.

:line

{Dihedrals} section:

one line per dihedral
line syntax: ID type atom1 atom2 atom3 atom4
type = dihedral type (1-Ndihedraltype)
atom1,atom2,atom3,atom4 = IDs of atoms in dihedral :ul

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.

:line

{Impropers} section:

one line per improper
line syntax: ID type atom1 atom2 atom3 atom4
type = improper type (1-Nimpropertype)
atom1,atom2,atom3,atom4 = IDs of atoms in improper :ul

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 "improper style"_improper_style.html.  See
the doc pages for individual styles for details.

:line

{Special Bond Counts} section:

one line per atom
line syntax: ID N1 N2 N3
N1 = # of 1-2 bonds
N2 = # of 1-3 bonds
N3 = # of 1-4 bonds :ul

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
"special_bonds"_special_bonds.html 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.

:line

{Special Bonds} section:

one line per atom
line syntax: ID a b c d ...
a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds :ul

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 "special_bonds"_special_bonds.html 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.

:line

[Restrictions:] none

[Related commands:]

"fix deposit"_fix_deposit.html, "fix pour"_fix_pour.html,
"fix_gcmc"_fix_gcmc.html

[Default:] none