molecule command — LAMMPS documentation

\(\renewcommand{\AA}{\text{Å}}\)

# molecule command

## Syntax

    molecule ID file1 keyword values ... file2 keyword values ... fileN ...

- ID = user-assigned name for the molecule template

- file1,file2,… = names of files containing molecule descriptions

- zero or more keyword/value pairs may be appended after each file

- keyword = offset or toff or boff or aoff or doff or ioff or scale

      offset values = Toff Boff Aoff Doff Ioff
        Toff = offset to add to atom types
        Boff = offset to add to bond types
        Aoff = offset to add to angle types
        Doff = offset to add to dihedral types
        Ioff = offset to add to improper types
      toff value = Toff
        Toff = offset to add to atom types
      boff value = Boff
        Boff = offset to add to bond types
      aoff value = Aoff
        Aoff = offset to add to angle types
      doff value = Doff
        Doff = offset to add to dihedral types
      ioff value = Ioff
        Ioff = offset to add to improper types
      scale value = sfactor
        sfactor = scale factor to apply to the size and mass of the molecule

## Examples

    molecule 1 mymol.txt
    molecule 1 co2.txt h2o.txt
    molecule CO2 co2.txt boff 3 aoff 2
    molecule 1 mymol.txt offset 6 9 18 23 14
    molecule objects file.1 scale 1.5 file.1 scale 2.0 file.2 scale 1.3

## Description

Define a molecule template 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 currently use molecule templates include:

- fix deposit

- fix pour

- fix rigid/small

- fix shake

- fix gcmc

- fix bond/react

- create_atoms

- atom_style template

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

A single template can contain multiple molecules, listed one per file. Some of the commands listed above currently use only the first molecule in the template, and will issue a warning if the template contains multiple molecules. The atom_style template command allows multiple-molecule templates to define a system with more than one templated molecule.

Each filename can be followed by optional keywords which are applied only to the molecule in the file as used in this template. This is to make it easy to use the same molecule file in different molecule templates or in different simulations. You can specify the same file multiple times with different optional keywords.

The offset, toff, boff, aoff, doff, ioff keywords add the specified offset values to the atom types, bond types, angle types, dihedral types, and/or improper types as they are read from the molecule file. E.g. if toff = 2, and the file uses atom types 1,2,3, then each created molecule will have atom types 3,4,5. For the offset keyword, all five offset values must be specified, but individual values will be ignored if the molecule template does not use that attribute (e.g. no bonds).

Note

Offsets are ignored on lines using type labels, as the type labels will determine the actual types directly depending on the current labelmap settings.

The scale keyword scales the size of the molecule. This can be useful for modeling polydisperse granular rigid bodies. The scale factor is applied to each of these properties in the molecule file, if they are defined: the individual particle coordinates (Coords section), the individual mass of each particle (Masses section), the individual diameters of each particle (Diameters section), the total mass of the molecule (header keyword = mass), the center-of-mass of the molecule (header keyword = com), and the moments of inertia of the molecule (header keyword = inertia).

Note

The molecule command can be used to define molecules with bonds, angles, dihedrals, impropers, or special bond lists of neighbors within a molecular topology, so that you can later add the molecules to your simulation, via one or more of the commands listed above. Since this topology-related information requires that suitable storage is reserved when LAMMPS creates the simulation box (e.g. when using the create_box command or the read_data command) suitable space has to be reserved so you do not overflow those pre-allocated data structures when adding molecules later. Both the create_box command and the read_data command have “extra” options which ensure space is allocated for storing topology info for molecules that are added later.

## Format of a molecule file

The format of an individual molecule file looks similar but is different than that of a data file read by the read_data commands. Here is a simple example for a TIP3P water molecule:

    # Water molecule. TIP3P geometry
    # header section:
    3 atoms
    2 bonds
    1 angles

    # body section:
    Coords

    1    0.00000  -0.06556   0.00000
    2    0.75695   0.52032   0.00000
    3   -0.75695   0.52032   0.00000

    Types

    1        1   # O
    2        2   # H
    3        2   # H

    Charges

    1       -0.834
    2        0.417
    3        0.417

    Bonds

    1   1      1      2
    2   1      1      3

    Angles

    1   1      2      1      3

A molecule file has a header and a body. The header appears first. The first line of the header and thus of the molecule file is always skipped; it typically contains a description of the file or a comment from the software that created the file.

Then lines are read one line at a time. Lines can have a trailing comment starting with ‘#’ that is ignored. There must be at least one blank between any valid content and the comment. If the line is blank (i.e. contains only white-space after comments are deleted), it is skipped. If the line contains a header keyword, the corresponding value(s) is/are read from the line. A line that is not blank and does not contains a header keyword 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 numeric value(s) are read from the beginning of the line. The keyword should appear at the end of the line. All these settings have default values, as explained below. A line need only appear if the value(s) are different than the default, except when defining a body particle, which requires setting the number of atoms to 1, and setting the inertia in a specific section (see below).

Number(s) | Keyword | Meaning | Default Value
--- | --- | --- | ---
N | atoms | # of atoms N in molecule | 0
Nb | bonds | # of bonds Nb in molecule | 0
Na | angles | # of angles Na in molecule | 0
Nd | dihedrals | # of dihedrals Nd in molecule | 0
Ni | impropers | # of impropers Ni in molecule | 0
Nf | fragments | # of fragments Nf in molecule | 0
Ninteger Ndouble | body | # of integer and floating-point values in body particle | 0
Mtotal | mass | total mass of molecule | computed
Xc Yc Zc | com | coordinates of center-of-mass of molecule | computed
Ixx Iyy Izz Ixy Ixz Iyz | inertia | 6 components of inertia tensor of molecule | computed

For mass, com, and inertia, the default is for LAMMPS to calculate this quantity itself if needed, assuming the molecules consist of a set of point particles or finite-size particles (with a non-zero diameter) that do not overlap. If finite-size particles in the molecule do overlap, LAMMPS will not account for the overlap effects when calculating any of these 3 quantities, so you should pre-compute them yourself and list the values in the file.

The mass and center-of-mass coordinates (Xc,Yc,Zc) are self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally.

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

- Coords, Types, Molecules, Fragments, Charges, Diameters, Dipoles, Masses = atom-property sections

- Bonds, Angles, Dihedrals, Impropers = molecular topology sections

- Special Bond Counts, Special Bonds = special neighbor info

- Shake Flags, Shake Atoms, Shake Bond Types = SHAKE info

- Body Integers, Body Doubles = body-property sections

For the Types, Bonds, Angles, Dihedrals, and Impropers sections, each atom/bond/angle/etc type can be specified either as a number (numeric type) or as an alphanumeric type label. The latter is only allowed if type labels have been defined, either by the labelmap command or in data files read by the read_data command which have sections for Atom Type Labels, Bond Type Labels, Angle Type Labels, etc. See the Howto type labels doc page for the allowed syntax of type labels and a general discussion of how type labels can be used. When using type labels, any values specified as offset are ignored.

If a Bonds section is specified then the Special Bond Counts and Special Bonds sections can also be used, if desired, to explicitly list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see details below). This is optional since if these sections are not included, LAMMPS will auto-generate this information. Note that LAMMPS uses this info to properly exclude or weight bonded pairwise interactions between bonded atoms. See the special_bonds command for more details. One reason to list the special bond info explicitly is for the thermalized Drude oscillator model which treats the bonds between nuclear cores and Drude electrons in a different manner.

Note

Whether a section is required depends on how the molecule template is used by other LAMMPS commands. For example, to add a molecule via the fix deposit command, the Coords and Types sections are required. To add a rigid body via the fix pour 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 command can be used to add “molecules” which are clusters of finite-size granular particles. If the Diameters section is not specified, each particle in the molecule will have a default diameter of 1.0. See the doc pages for LAMMPS commands that use molecule templates 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. For per- atom sections, entries should be numbered from 1 to Natoms (where Natoms is the number of atoms in the template), indicating which atom (or bond, etc) the entry applies to. Per-atom sections need to include a setting for every atom, but the atoms can be listed in any order.

Coords section:

- one line per atom

- line syntax: ID x y z

- x,y,z = coordinate of atom

Types section:

- one line per atom

- line syntax: ID type

- type = atom type of atom (1-Natomtype, or type label)

Molecules section:

- one line per atom

- line syntax: ID molecule-ID

- molecule-ID = molecule ID of atom

Fragments section:

- one line per fragment

- line syntax: ID a b c d …

- a,b,c,d,… = IDs of atoms in fragment

The ID of a fragment can only contain alphanumeric characters and underscores. The atom IDs should be values from 1 to Natoms, where Natoms = # of atoms in the molecule.

Charges section:

- one line per atom

- line syntax: ID q

- q = charge on atom

This section is only allowed for atom styles that support charge. If this section is not included, the default charge on each atom in the molecule is 0.0.

Diameters section:

- one line per atom

- line syntax: ID diam

- diam = diameter of atom

This section is only allowed for atom styles 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.

Added in version 7Feb2024.

Dipoles section:

- one line per atom

- line syntax: ID mux muy muz

- mux,muy,muz = x-, y-, and z-component of point dipole vector of atom

This section is only allowed for atom styles that support particles with point dipoles, e.g. atom_style dipole. If not listed, the default dipole component of each atom in the molecule is set to 0.0.

Masses section:

- one line per atom

- line syntax: ID mass

- mass = mass of atom

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

Bonds section:

- one line per bond

- line syntax: ID type atom1 atom2

- type = bond type (1-Nbondtype, or type label)

- atom1,atom2 = IDs of atoms in bond

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

Angles section:

- one line per angle

- line syntax: ID type atom1 atom2 atom3

- type = angle type (1-Nangletype, or type label)

- atom1,atom2,atom3 = IDs of atoms in angle

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

Dihedrals section:

- one line per dihedral

- line syntax: ID type atom1 atom2 atom3 atom4

- type = dihedral type (1-Ndihedraltype, or type label)

- atom1,atom2,atom3,atom4 = IDs of atoms in dihedral

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.

Impropers section:

- one line per improper

- line syntax: ID type atom1 atom2 atom3 atom4

- type = improper type (1-Nimpropertype, or type label)

- atom1,atom2,atom3,atom4 = IDs of atoms in improper

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. See the doc pages for individual styles for details.

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

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 page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds section must also appear.

As explained above, LAMMPS will auto-generate this information if this section is not specified. If specified, this section will override what would be auto-generated.

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

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 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.

As explained above, LAMMPS will auto-generate this information if this section is not specified. If specified, this section will override what would be auto-generated.

Shake Flags section:

- one line per atom

- line syntax: ID flag

- flag = 0,1,2,3,4

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.

The meaning of the flag for each atom is as follows. See the fix shake page for a further description of SHAKE clusters.

- 0 = not part of a SHAKE cluster

- 1 = part of a SHAKE angle cluster (two bonds and the angle they form)

- 2 = part of a 2-atom SHAKE cluster with a single bond

- 3 = part of a 3-atom SHAKE cluster with two bonds

- 4 = part of a 4-atom SHAKE cluster with three bonds

Shake Atoms section:

- one line per atom

- line syntax: ID a b c d

- a,b,c,d = IDs of atoms in cluster

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.

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.

If flag = 0, no a,b,c,d values are listed on the line, just the (ignored) ID.

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.

If flag = 2, a,b are listed, where a = ID of atom in bond with the lowest ID, and b = ID of atom in bond with the highest ID.

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.

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.

See the fix shake page for a further description of SHAKE clusters.

Shake Bond Types section:

- one line per atom

- line syntax: ID a b c

- a,b,c = bond types (or angle type) of bonds (or angle) in cluster

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.

The a,b,c values are bond types for all bonds in the SHAKE cluster that this atom belongs to. Bond types may be either numbers (from 1 to Nbondtypes) or bond type labels as defined by the labelmap command or a “Bond Type Labels” section of a data file.

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.

If flag = 0, no a,b,c values are listed on the line, just the (ignored) ID.

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 second non-central atom (value c in the Shake Atoms section), and c = the angle type (1 to Nangletypes, or angle type label) of the angle between the three atoms.

If flag = 2, only a is listed, where a = bondtype of the bond between the two atoms in the cluster.

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 second non-central atom (value c in the Shake Atoms section).

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 second non-central atom (value c in the Shake Atoms section), and c = bondtype of the bond between the central atom and the third non-central atom (value d in the Shake Atoms section).

See the fix shake page for a further description of SHAKE clusters.

Body Integers section:

- one line

- line syntax: N E F

- N = number of sub-particles or number or vertices

- E,F = number of edges and faces

This section is only needed when the molecule is a body particle. the other Body section must also appear in the file.

The total number of values that must appear is determined by the body style, and must be equal to the Ninteger value given in the body header.

For nparticle and rounded/polygon, only the number of sub-particles or vertices N is required, and Ninteger should have a value of 1.

For rounded/polyhedron, the number of edges E and faces F is required, and Ninteger should have a value of 3.

See the Howto body page for a further description of the file format.

Body Doubles section:

- first line

- line syntax: Ixx Iyy Izz Ixy Ixz Iyz

- Ixx Iyy Izz Ixy Ixz Iyz = 6 components of inertia tensor of body particle

- one line per sub-particle or vertex

- line syntax: x y z

- x, y, z = coordinates of sub-particle or vertex

- one line per edge

- line syntax: N1 N2

- N1, N2 = vertex indices

- one line per face

- line syntax: N1 N2 N3 N4

- N1, N2, N3, N4 = vertex indices

- last line

- line syntax: diam

- diam = rounded diameter that surrounds each vertex

This section is only needed when the molecule is a body particle. the other Body section must also appear in the file.

The total number of values that must appear is determined by the body style, and must be equal to the Ndouble value given in the body header. The 6 moments of inertia and the 3N coordinates of the sub-particles or vertices are required for all body styles.

For rounded/polygon, the E = 6 + 3*N + 1 edges are automatically determined from the vertices.

For rounded/polyhedron, the 2E vertex indices for the end points of the edges and 4F vertex indices defining the faces are required.

See the Howto body page for a further description of the file format.

## Restrictions

None

## Related commands

fix deposit, fix pour, fix gcmc

## Default

The default keywords values are offset 0 0 0 0 0 and scale = 1.0.