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:

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, 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).

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, imporopers, 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. If such molecules do not already exist when LAMMPS creates the simulation box, via the create_box or read_data command, when you later add them you may overflow the pre-allocated data structures which store molecular topology information with each atom, and an error will be generated. Both the create_box command and the data files read by the read_data command have “extra” options which insure space is allocated for storing topology info for molecules that are added later.

The format of an individual molecule file is similar to the data file read by the read_data 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 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.

  • N atoms = # of atoms N in molecule, default = 0
  • Nb bonds = # of bonds Nb in molecule, default = 0
  • Na angles = # of angles Na in molecule, default = 0
  • Nd dihedrals = # of dihedrals Nd in molecule, default = 0
  • Ni impropers = # of impropers Ni in molecule, default = 0
  • Mtotal mass = total mass of molecule
  • Xc Yc Zc com = coordinates of center-of-mass of molecule
  • Ixx Iyy Izz Ixy Ixz Iyz inertia = 6 components of inertia tensor of molecule

For mass, com, and inertia, the default is for LAMMPS to calculate this quantity itself if needed, assuming the molecules consists 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, Charges, Diameters, 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

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. In each case the ID is ignored; it is simply included for readability, and should be a number from 1 to Nlines for the section, indicating which atom (or bond, etc) the entry applies to. The lines are assumed to be listed in order from 1 to Nlines, but LAMMPS does not check for this.


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

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.


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)
  • 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)
  • 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 3 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)
  • 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)
  • 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 doc 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 doc 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 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 doc 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 (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.

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 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.

If flag = 2, only a is listed, where a = bondtype of the bond between the 2 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 2nd 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 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).

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


Restrictions

none

Default

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