.. index:: fix property/atom
.. index:: fix property/atom/kk

fix property/atom command
=========================

Accelerator Variants: *property/atom/kk*

Syntax
""""""

.. parsed-literal::

   fix ID group-ID property/atom name1 name2 ... keyword value ...

* ID, group-ID are documented in :doc:`fix <fix>` command
* property/atom = style name of this fix command
* name1,name2,... = *mol* or *q* or *rmass* or *i_name* or *d_name* or *i2_name* or *d2_name*

  .. parsed-literal::

       *mol* = molecule IDs
       *q* = charge
       *rmass* = per-atom mass
       *i_name* = new integer vector referenced by name
       *d_name* = new floating-point vector referenced by name
       *i2_name* = new integer array referenced by name
          i2_name arg = N = number of columns in the array
       *d2_name* = new floating-point array referenced by name
          d2_name arg = N = number of columns in the array

* zero of more keyword/value pairs may be appended
* keyword = *ghost*

  .. parsed-literal::

       *ghost* value = *no* or *yes* for whether ghost atom info in communicated

Examples
""""""""

.. code-block:: LAMMPS

   fix 1 all property/atom mol
   fix 1 all property/atom i_myflag1 i_myflag2
   fix 1 all property/atom d2_sxyz 3 ghost yes

Description
"""""""""""

Create one or more additional per-atom vectors or arrays to store
information about atoms and to use during a simulation.  The specified
*group-ID* is ignored by this fix.

The atom style used for a simulation defines a set of per-atom
properties, as explained on the :doc:`atom_style <atom_style>` and
:doc:`read_data <read_data>` doc pages.  The latter command defines
these properties for each atom in the system when a data file is read.
This fix augments the set of per-atom properties with new custom
ones. This can be useful in several scenarios.

If the atom style does not define molecule IDs, per-atom charge, or
per-atom mass, they can be added using the *mol*\ , *q* or *rmass*
keywords.  This could be useful to define "molecules" to use as rigid
bodies with the :doc:`fix rigid <fix_rigid>` command, or to carry
around an extra flag with atoms (stored as a molecule ID) that can be
used by various commands like :doc:`compute chunk/atom
<compute_chunk_atom>` to group atoms without having to use the group
command (which is limited to a total of 32 groups including *all*\ ).

Another application is to use the *rmass* flag in order to have
per-atom masses instead of per-type masses.  This could be used to
study isotope effects with partial isotope substitution. :ref:`See
below <isotopes>` for an example of simulating a mixture of light and
heavy water with the TIP4P water potential.

An alternative to using fix *property/atom* for these examples is to
use an atom style that does define molecule IDs or charge or per-atom
mass (indirectly via diameter and density) or to use a hybrid atom
style that combines two or more atom styles to provide the union of
all their atom properties. However, this has two practical drawbacks:
first, it typically necessitates changing the format of the Atoms
section in the data file and second, it may define additional
properties that are not needed such as bond lists, which incurs some
overhead when there are no bonds.

In the future, we may add additional existing per-atom properties to
fix property/atom, similar to *mol*\ , *q* or *rmass*\ , which
"turn-on" specific properties defined by some atom styles, so they can
be easily used by atom styles that do not define them.

More generally, the *i_name* and *d_name* options allow one or more
new custom per-atom vectors to be defined.  Likewise the *i2_name* and
*d2_name* options allow one or more custom per-atom arrays to be
defined.  The *i2_name* and *d2_name* options take an argument *N*
which specifies the number of columns in the per-atom array, i.e. the
number of attributes associated with each atom.  *N* >= 1 is required.

Each name must be unique and can use alphanumeric or underscore
characters.  These vectors and arrays can store whatever values you
decide are useful in your simulation.  As explained below there are
several ways to initialize, access, and output these values, via input
script commands, data files, and in new code you add to LAMMPS.

This is effectively a simple way to add per-atom properties to a model
without needing to write code for a new :doc:`atom style <atom_style>`
that defines the properties.  Note however that implementing a new
atom style allows new atom properties to be more tightly and
seamlessly integrated with the rest of the code.

The new atom properties encode values that migrate with atoms to new
processors and are written to restart files.  If you want the new
properties to also be defined for ghost atoms, then use the *ghost*
keyword with a value of *yes*\ .  This will invoke extra communication
when ghost atoms are created (at every re-neighboring) to insure the
new properties are also defined for the ghost atoms.

.. admonition:: Properties on ghost atoms
   :class: note

   If you use the *mol*\ , *q* or *rmass* names, you most likely want
   to set *ghost* yes, since these properties are stored with ghost
   atoms if you use an :doc:`atom_style <atom_style>` that defines
   them.  Many LAMMPS operations that use molecule IDs or charge, such
   as neighbor lists and pair styles, will expect ghost atoms to have
   these values.  LAMMPS will issue a warning it you define those
   vectors but do not set *ghost* yes.

.. admonition:: Limitations on ghost atom properties
   :class: note

   The specified properties for ghost atoms are not updated every
   timestep, but only once every few steps when neighbor lists are
   re-built.  Thus the *ghost* keyword is suitable for static
   properties, like molecule IDs, but not for dynamic properties that
   change every step.  For the latter, the code you add to LAMMPS to
   change the properties will also need to communicate their new
   values to/from ghost atoms, an operation that can be invoked from
   within a :doc:`pair style <pair_style>` or :doc:`fix <fix>` or
   :doc:`compute <compute>` that you write.

----------

This fix is one of a small number that can be defined in an input
script before the simulation box is created or atoms are defined.
This is so it can be used with the :doc:`read_data <read_data>`
command as described next.

Per-atom properties that are defined by the :doc:`atom style
<atom_style>` are initialized when atoms are created, e.g. by the
:doc:`read_data <read_data>` or :doc:`create_atoms <create_atoms>`
commands.  The per-atom properties defined by this fix are not.  So
you need to initialize them explicitly.  One way to do this is
:doc:`read_data <read_data>` command, using its *fix* keyword and
passing it the fix-ID of this fix.

Thus these commands:

.. code-block:: LAMMPS

   fix prop all property/atom mol d_flag
   read_data data.txt fix prop NULL Molecules

would allow a data file to have a section like this:

.. parsed-literal::

   Molecules

   1 4 1.5
   2 4 3.0
   3 10 1.0
   4 10 1.0
   5 10 1.0
   ...
   N 763 4.5

where N is the number of atoms, the first field on each line is the
atom-ID, the next two are a molecule-ID and a floating point value
that will be stored in a new property called "flag".  If a per-atom
array was specified in the fix property/atom command then the *N*
values for that array must be specified consecutively for that
property on each line.  Note that the order of values on each line
corresponds to the order of custom names in the fix property/atom
command.

Note that the the lines of per-atom properties can be listed in any
order.  Also note that all the per-atom properties specified by the
fix ID (prop in this case) must be included on each line in the
specified data file section (Molecules in this case).

Another way of initializing the new properties is via the :doc:`set
<set>` command.  For example, if you wanted molecules defined for
every set of 10 atoms, based on their atom-IDs, these commands could
be used:

.. code-block:: LAMMPS

   fix prop all property/atom mol
   variable cluster atom ((id-1)/10)+1
   set atom * mol v_cluster

The :doc:`atom-style variable <variable>` will create values for atoms
with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9.  When the
:doc:`set <set>` commands assigns them to the molecule ID for each
atom, they will be truncated to an integer value, so atoms 31-40 will
all be assigned a molecule ID of 4.

Note that :doc:`atomfile-style variables <variable>` can also be used
in place of atom-style variables, which means in this case that the
molecule IDs could be read-in from a separate file and assigned by the
:doc:`set <set>` command.  This allows you to initialize new per-atom
properties in a completely general fashion.

----------

For new atom properties specified as *i_name*, *d_name*, *i2_name*, or
*d2_name*, the :doc:`dump custom <dump>` and :doc:`compute
property/atom <compute_property_atom>` commands can access their
values.  This means that the values can be used accessed by fixes like
:doc:`fix ave/atom <fix_ave_atom>`, accessed by other computes like
:doc:`compute reduce <compute_reduce>`, or used in :doc:`atom-style
variables <variable>`.

For example, these commands will output both the instantaneous and
time-averaged values of two new properties to a custom dump file:

.. code-block:: LAMMPS

   fix myprops all property/atom i_flag1 d_flag2
   compute 1 all property/atom i_flag1 d_flag2
   fix 1 all ave/atom 10 10 100 c_1[1] c_1[2]
   dump 1 all custom 100 tmp.dump id x y z i_flag1 d_flag2 f_1[1] f_1[2]

----------

If you wish to add new :doc:`pair styles <pair_style>`, :doc:`fixes
<fix>`, or :doc:`computes <compute>` that use the per-atom properties
defined by this fix, see the :doc:`Modify atom <Modify_atom>` doc page
which has details on how the custom properties of this fix can be
accessed from added classes.

----------

.. _isotopes:

Here is an example of using per-atom masses with TIP4P water to study
isotope effects. When setting up simulations with the :doc:`TIP4P pair
styles <Howto_tip4p>` for water, you have to provide exactly one atom
type each to identify the water oxygen and hydrogen atoms. Since the
atom mass is normally tied to the atom type, this makes it impossible
to study multiple isotopes in the same simulation.  With *fix
property/atom rmass* however, the per-type masses are replaced by
per-atom masses. Asumming you have a working input deck for regular
TIP4P water, where water oxygen is atom type 1 and water hydrogen is
atom type 2, the following lines of input script convert this to using
per-atom masses:

.. code-block:: LAMMPS

   fix Isotopes all property/atom rmass ghost yes
   set type 1 mass 15.9994
   set type 2 mass 1.008

When writing out the system data with the :doc:`write_data
<write_data>` command, there will be a new section named with the
fix-ID (i.e. *Isotopes* in this case). Alternatively, you can take an
existing data file and just add this *Isotopes* section with one line
per atom containing atom-ID and mass. Either way, the extended data
file can be read back with:

.. code-block:: LAMMPS

   fix Isotopes all property/atom rmass ghost yes
   read_data tip4p-isotopes.data fix Isotopes NULL Isotopes

Please note that the first *Isotopes* refers to the fix-ID and the
second to the name of the section. The following input script code
will now change the first 100 water molecules in this example to heavy
water:

.. code-block:: LAMMPS

   group hwat id 2:300:3
   group hwat id 3:300:3
   set group hwat mass 2.0141018

----------

.. include:: accel_styles.rst

----------

Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

This fix writes the per-atom values it stores to :doc:`binary restart
files <restart>`, so that the values can be restored when a simulation
is restarted.  See the :doc:`read_restart <read_restart>` command for
info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
uninterrupted fashion.

.. warning::

   When reading data from a restart file, this fix command has to be
   specified **exactly** the same was in the input script that created
   the restart file. LAMMPS will only check whether a fix is of the
   same style and has the same fix ID and in case of a match will then
   try to initialize the fix with the data stored in the binary
   restart file.  If the names and associated date types in the new
   fix property/atom command do not match the old one exactly, data
   can be corrupted or LAMMPS may crash.

None of the :doc:`fix_modify <fix_modify>` options are relevant to
this fix.  No global or per-atom quantities are stored by this fix for
access by various :doc:`output commands <Howto_output>`.  No parameter
of this fix can be used with the *start/stop* keywords of the
:doc:`run <run>` command.  This fix is not invoked during :doc:`energy
minimization <minimize>`.

Restrictions
""""""""""""
 none

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

:doc:`read_data <read_data>`, :doc:`set <set>`,
:doc:`compute property/atom <compute_property_atom>`

Default
"""""""

The default keyword value is ghost = no.
