git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14950 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
163
doc/html/_sources/fix_ave_atom.txt
Normal file
163
doc/html/_sources/fix_ave_atom.txt
Normal file
@ -0,0 +1,163 @@
|
||||
.. 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
|
||||
Reference in New Issue
Block a user