.. index:: molecule

molecule command
================

Syntax
""""""

.. code-block:: LAMMPS

   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*

  .. parsed-literal::

       *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
""""""""

.. code-block:: LAMMPS

   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:

* :doc:`fix deposit <fix_deposit>`
* :doc:`fix pour <fix_pour>`
* :doc:`fix rigid/small <fix_rigid>`
* :doc:`fix shake <fix_shake>`
* :doc:`fix gcmc <fix_gcmc>`
* :doc:`fix bond/react <fix_bond_react>`
* :doc:`create_atoms <create_atoms>`
* :doc:`atom_style template <atom_style>`

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 :doc:`atom_style template
<atom_style>` 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 :doc:`labelmap <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 :doc:`create_box <create_box>` command or the
   :doc:`read_data <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 :doc:`create_box <create_box>` command and
   the :doc:`read_data <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 :doc:`read_data <read_data>`
commands.  Here is a simple example for a TIP3P water molecule:

.. code-block::

   # 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).

.. list-table::
      :header-rows: 1
      :widths: 20 13 42 15

      * - 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 :doc:`labelmap
<labelmap>` command or in data files read by the :doc:`read_data
<read_data>` command which have sections for Atom Type Labels, Bond
Type Labels, Angle Type Labels, etc.  See the :doc:`Howto type labels
<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 :doc:`special_bonds
<special_bonds>` command for more details.  One reason to list the
special bond info explicitly is for the :doc:`thermalized Drude
oscillator model <Howto_drude>` 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 :doc:`fix deposit <fix_deposit>` command, the Coords and
   Types sections are required.  To add a rigid body via the :doc:`fix
   pour <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 :doc:`fix pour <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 :doc:`atom styles <atom_style>` 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 :doc:`atom styles <atom_style>` 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.

----------

.. versionadded:: 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 :doc:`atom styles <atom_style>` 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 :doc:`atom styles <atom_style>` that
support per-atom mass, as opposed to per-type mass.  See the
:doc:`mass <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
:doc:`units <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 :doc:`improper style <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
:doc:`special_bonds <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 :doc:`special_bonds <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 :doc:`fix shake <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 :doc:`fix shake <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 :doc:`labelmap <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 :doc:`fix shake <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 :doc:`Howto body <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 :doc:`Howto body <Howto_body>` page for a further description of
the file format.

----------

Restrictions
""""""""""""

None

Related commands
""""""""""""""""

:doc:`fix deposit <fix_deposit>`, :doc:`fix pour <fix_pour>`,
:doc:`fix gcmc <fix_gcmc>`

Default
"""""""

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