.. index:: molecule

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

Syntax
""""""

.. parsed-literal::

   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*\ , *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, 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
   insure space is allocated for storing topology info for molecules that
   are added later.

The format of an individual molecule file is similar but
(not identical) to the data file read by the :doc:`read_data <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 white-space 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 does not 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
* Nf *fragments* = # of fragments 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, Molecules, Fragments, 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
: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.  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

----------

*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.

----------

*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)
* 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 :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>` 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 :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>` 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
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>` 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 second 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 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>` doc page for a further description
of SHAKE clusters.

----------

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

This command must come after the simulation box is define by a
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
:doc:`create_box <create_box>` command.

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.
