Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/_sources/fix_ave_atom.txt
9cf43f2a0b7flammm-master

Last Change
Raw File

fix_ave_atom.txt
View Options

.. index:: fix ave/atom
fix ave/atom command
====================
Syntax
""""""
.. parsed-literal::
fix ID group-ID ave/atom Nevery Nrepeat Nfreq value1 value2 ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* ave/atom = style name of this fix command
* Nevery = use input values every this many timesteps
* Nrepeat = # of times to use input values for calculating averages
* Nfreq = calculate averages every this many timesteps
one or more input values can be listed
* value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name
.. parsed-literal::
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
v_name = per-atom vector calculated by an atom-style variable with name
Examples
""""""""
.. parsed-literal::
fix 1 all ave/atom 1 100 100 vx vy vz
fix 1 all ave/atom 10 20 1000 c_my_stress[1]
Description
"""""""""""
Use one or more per-atom vectors as inputs every few timesteps, and
average them atom by atom over longer timescales. The resulting
per-atom averages can be used by other :ref:`output commands <howto_15>` such as the :doc:`fix ave/spatial <fix_ave_spatial>` or :doc:`dump custom <dump>` commands.
The group specified with the command means only atoms within the group
have their averages computed. Results are set to 0.0 for atoms not in
the group.
Each input value can be an atom attribute (position, velocity, force
component) or can be the result of a :doc:`compute <compute>` or
:doc:`fix <fix>` or the evaluation of an atom-style
:doc:`variable <variable>`. In the latter cases, the compute, fix, or
variable must produce a per-atom vector, not a global quantity or
local quantity. If you wish to time-average global quantities from a
compute, fix, or variable, then see the :doc:`fix ave/time <fix_ave_time>` command.
:doc:`Computes <compute>` that produce per-atom vectors or arrays are
those which have the word *atom* in their style name. See the doc
pages for individual :doc:`fixes <fix>` to determine which ones produce
per-atom vectors or arrays. :doc:`Variables <variable>` of style *atom*
are the only ones that can be used with this fix since they produce
per-atom vectors.
Each per-atom value of each input vector is averaged independently.
----------
The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
timesteps the input values will be used in order to contribute to the
average. The final averaged quantities are generated on timesteps
that are a multiple of *Nfreq*. The average is over *Nrepeat*
quantities, computed in the preceding portion of the simulation every
*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and
*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the timesteps
contributing to the average value cannot overlap,
i.e. Nrepeat*Nevery can not exceed Nfreq.
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc.
----------
The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
an input value from that compute.
.. note::
The x,y,z attributes are values that are re-wrapped inside the
periodic box whenever an atom crosses a periodic boundary. Thus if
you time average an atom that spends half its time on either side of
the periodic box, you will get a value in the middle of the box. If
this is not what you want, consider averaging unwrapped coordinates,
which can be provided by the :doc:`compute property/atom <compute_property_atom>` command via its xu,yu,zu
attributes.
If a value begins with "c_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the compute is used. If a
bracketed term containing an index I is appended, the Ith column of
the per-atom array calculated by the compute is used. Users can also
write code for their own compute styles and :doc:`add them to LAMMPS <Section_modify>`.
If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the fix is used. If a
bracketed term containing an index I is appended, the Ith column of
the per-atom array calculated by the fix is used. Note that some
fixes only produce their values on certain timesteps, which must be
compatible with *Nevery*, else an error will result. Users can also
write code for their own fix styles and :doc:`add them to LAMMPS <Section_modify>`.
If a value begins with "v_", a variable name must follow which has
been previously defined in the input script as an :doc:`atom-style variable <variable>` Variables of style *atom* can reference
thermodynamic keywords, or invoke other computes, fixes, or variables
when they are evaluated, so this is a very general means of generating
per-atom quantities to time average.
----------
Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global scalar or vector quantities are
stored by this fix for access by various :ref:`output commands <howto_15>`.
This fix produces a per-atom vector or array which can be accessed by
various :ref:`output commands <howto_15>`. A vector is
produced if only a single quantity is averaged by this fix. If two or
more quantities are averaged, then an array of values is produced.
The per-atom values can only be accessed on timesteps that are
multiples of *Nfreq* since that is when averaging is performed.
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:`compute <compute>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/spatial <fix_ave_spatial>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`variable <variable>`,
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
c4science · Help