Skip to content
Snippets Groups Projects
Commit b245332f authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@908 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 36fbdf75
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
doc/compute_attribute_atom.html 0 → 100644
+ 72
− 0
View file @ b245332f
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute attribute/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID attribute/atom style
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>attribute/atom = style name of this compute command
<LI>style = <I>x</I> or <I>y</I> or <I>z</I> or <I>xu</I> or <I>yu</I> or <I>zu</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>fx</I> or <I>fy</I> or <I>fz</I> or <I>xyz</I> or <I>v</I> or <I>f</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all attribute/atom vy
compute mine all attribute/atom xyz
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates (or simply stores) one or more
attributes for each atom in a group. This is useful for input to the
<A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command to do spatial averaging
by layers or to the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command to
perform time-averaging of per-atom quantities. The attribute values
can also be output directly by the <A HREF = "dump.html">dump custom</A> command,
but it has keywords that output these quantities without the need to
define an additional compute.
</P>
<P>The styles <I>x</I>, <I>y</I>, <I>z</I>, <I>xu</I>, <I>yu</I>, <I>zu</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>,
<I>fy</I>, and <I>fz</I> each store a single scalar value per atom.
</P>
<P>The <I>x</I>, <I>y</I>, <I>z</I> keywords store atom coordinate in the appropriate
distance <A HREF = "units.html">units</A> (Angstroms, sigma, etc) and will always be
inside (or slightly outside) the simulation box. Use <I>xu</I>, <I>yu</I>, <I>zu</I>
if you want the coordinates "unwrapped" by the image flags for each
atom. Unwrapped means that if the atom has passed thru a periodic
boundary one or more times, the value is printed for what the
coordinate would be if it had not been wrapped back into the periodic
box. Note that using <I>xu</I>, <I>yu</I>, <I>zu</I> means that the coordinate
values may be far outside the simulation box.
</P>
<P>Note that if you want to compute the time-averaged position of an atom
coordinate that could pass thru a periodic boundary (e.g. via the <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command), you probably want to use <I>xu</I>
instead of <I>x</I>.
</P>
<P>The styles <I>xyz</I>, <I>v</I>, and <I>f</I> each store a vector of 3 quantities per
atom.
</P>
<P>Note that the various commands that reference this compute use a
different syntax for accessing scalar versus vector values, e.g. c_ID
versus c_ID<B>2</B>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>, <A HREF = "dump.html">dump custom</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
doc/compute_attribute_atom.txt 0 → 100644
+ 67
− 0
View file @ b245332f
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute attribute/atom command :h3
[Syntax:]
compute ID group-ID attribute/atom style :pre
ID, group-ID are documented in "compute"_compute.html command
attribute/atom = style name of this compute command
style = {x} or {y} or {z} or {xu} or {yu} or {zu} or {vx} or {vy} or {vz} or {fx} or {fy} or {fz} or {xyz} or {v} or {f} :ul
[Examples:]
compute 1 all attribute/atom vy
compute mine all attribute/atom xyz :pre
[Description:]
Define a computation that calculates (or simply stores) one or more
attributes for each atom in a group. This is useful for input to the
"fix ave/spatial"_fix_ave_spatial.html command to do spatial averaging
by layers or to the "fix ave/atom"_fix_ave_atom.html command to
perform time-averaging of per-atom quantities. The attribute values
can also be output directly by the "dump custom"_dump.html command,
but it has keywords that output these quantities without the need to
define an additional compute.
The styles {x}, {y}, {z}, {xu}, {yu}, {zu}, {vx}, {vy}, {vz}, {fx},
{fy}, and {fz} each store a single scalar value per atom.
The {x}, {y}, {z} keywords store atom coordinate in the appropriate
distance "units"_units.html (Angstroms, sigma, etc) and will always be
inside (or slightly outside) the simulation box. Use {xu}, {yu}, {zu}
if you want the coordinates "unwrapped" by the image flags for each
atom. Unwrapped means that if the atom has passed thru a periodic
boundary one or more times, the value is printed for what the
coordinate would be if it had not been wrapped back into the periodic
box. Note that using {xu}, {yu}, {zu} means that the coordinate
values may be far outside the simulation box.
Note that if you want to compute the time-averaged position of an atom
coordinate that could pass thru a periodic boundary (e.g. via the "fix
ave/atom"_fix_ave_atom.html command), you probably want to use {xu}
instead of {x}.
The styles {xyz}, {v}, and {f} each store a vector of 3 quantities per
atom.
Note that the various commands that reference this compute use a
different syntax for accessing scalar versus vector values, e.g. c_ID
versus c_ID[2].
[Restrictions:] none
[Related commands:]
"fix ave/atom"_fix_ave_atom.html, "fix
ave/spatial"_fix_ave_spatial.html, "dump custom"_dump.html
[Default:] none
doc/compute_sum_atom.html 0 → 100644
+ 49
− 0
View file @ b245332f
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute sum/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID sum/atom compute-ID1 compute-ID2 ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>sum/atom = style name of this compute command
<LI>compute-ID1, 2, ... = IDs of computes that calculate per-atom quantities
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all sum/atom atomKE atomEpair atomEbond
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that sums the results of two or more other
computes for each atom in a group. This is useful for summing atom
properties such as pairwise energy, bond energy, kinetic energy, etc.
The resulting values can be accessed by any command that uses per-atom
computes, e.g. the <A HREF = "dump.html">dump custom</A> command or <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command or <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command.
</P>
<P>The result of this compute depends on the results generated by the
other computes that it invokes. E.g. if the other computes each
generate a scalar value per atom, so will this compute. If the other
computes each generate a vector of values per atom, so will this
compute. In the latter case, all the other computes must generate
vectors of the same size.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>
doc/compute_sum_atom.txt 0 → 100644
+ 44
− 0
View file @ b245332f
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute sum/atom command :h3
[Syntax:]
compute ID group-ID sum/atom compute-ID1 compute-ID2 ... :pre
ID, group-ID are documented in "compute"_compute.html command
sum/atom = style name of this compute command
compute-ID1, 2, ... = IDs of computes that calculate per-atom quantities :ul
[Examples:]
compute 1 all sum/atom atomKE atomEpair atomEbond :pre
[Description:]
Define a computation that sums the results of two or more other
computes for each atom in a group. This is useful for summing atom
properties such as pairwise energy, bond energy, kinetic energy, etc.
The resulting values can be accessed by any command that uses per-atom
computes, e.g. the "dump custom"_dump.html command or "fix
ave/spatial"_fix_ave_spatial.html command or "fix
ave/atom"_fix_ave_atom.html command.
The result of this compute depends on the results generated by the
other computes that it invokes. E.g. if the other computes each
generate a scalar value per atom, so will this compute. If the other
computes each generate a vector of values per atom, so will this
compute. In the latter case, all the other computes must generate
vectors of the same size.
[Restrictions:] none
[Related commands:] none
[Default:] none
doc/fix_ave_atom.html 0 → 100644
+ 82
− 0
View file @ b245332f
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix ave/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID ave/atom Nevery Nrepeat Nfreq compute-ID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>ave/atom = style name of this fix command
<LI>Nevery = calculate property every this many timesteps
<LI>Nrepeat = # of times to repeat the Nevery calculation before averaging
<LI>Nfreq = timestep frequency at which the average value is calculated
<LI>compute-ID = ID of per-atom compute that performs the calculation
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all ave/atom 1 100 100 myVx
fix 1 all ave/atom 10 20 1000 my_epair
</PRE>
<P><B>Description:</B>
</P>
<P>Calculate one or more time-averaged per-atom quantities every few
timesteps. The results of this calculation can be spatially averaged
via the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command or output
to a file via the <A HREF = "dump.html">dump custom</A> command.
</P>
<P>The <I>compute-ID</I> specifies a <A HREF = "compute.html">compute</A> which calculates
the desired property. It must be a per-atom compute (one with the
word "atom" in its style name) that calculates one or more values for
each atom, as opposed to a global compute. The compute must be
previously defined in the input script. Users can also write code for
their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
</P>
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify how the
property will be time-averaged. The final averaged value(s) are
computed every <I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I>
values, computed in the preceeding portion of the simulation every
<I>Nevery</I> timesteps. Thus 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 at timestep 100. Similary for timesteps
190,192,194,196,198,200 at timestep 200, etc.
</P>
<P>If this fix is referenced by a <A HREF = "dump.html">dump custom</A> or <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command, the time-averaged values
can only be accessed every <I>Nfreq</I> timesteps.
</P>
<P>If the compute calculates a single or multiple values per atom, then
fix ave/atom will also calculate one or multiple time-averaged
quantities per atom. This makes a difference in how the quantities
are referenced in a <A HREF = "dump.html">dump custom</A> command, e.g. c_ID versus
c_ID[2].
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>, <A HREF = "dump.html">dump
custom</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
doc/fix_ave_atom.txt 0 → 100644
+ 77
− 0
View file @ b245332f
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix ave/atom command :h3
[Syntax:]
fix ID group-ID ave/atom Nevery Nrepeat Nfreq compute-ID :pre
ID, group-ID are documented in "fix"_fix.html command
ave/atom = style name of this fix command
Nevery = calculate property every this many timesteps
Nrepeat = # of times to repeat the Nevery calculation before averaging
Nfreq = timestep frequency at which the average value is calculated
compute-ID = ID of per-atom compute that performs the calculation :ul
[Examples:]
fix 1 all ave/atom 1 100 100 myVx
fix 1 all ave/atom 10 20 1000 my_epair :pre
[Description:]
Calculate one or more time-averaged per-atom quantities every few
timesteps. The results of this calculation can be spatially averaged
via the "fix ave/spatial"_fix_ave_spatial.html command or output
to a file via the "dump custom"_dump.html command.
The {compute-ID} specifies a "compute"_compute.html which calculates
the desired property. It must be a per-atom compute (one with the
word "atom" in its style name) that calculates one or more values for
each atom, as opposed to a global compute. The compute must be
previously defined in the input script. Users can also write code for
their own compute styles and "add them to LAMMPS"_Section_modify.html.
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify how the
property will be time-averaged. The final averaged value(s) are
computed every {Nfreq} timesteps. The average is over {Nrepeat}
values, computed in the preceeding portion of the simulation every
{Nevery} timesteps. Thus 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 at timestep 100. Similary for timesteps
190,192,194,196,198,200 at timestep 200, etc.
If this fix is referenced by a "dump custom"_dump.html or "fix
ave/spatial"_fix_ave_spatial.html command, the time-averaged values
can only be accessed every {Nfreq} timesteps.
If the compute calculates a single or multiple values per atom, then
fix ave/atom will also calculate one or multiple time-averaged
quantities per atom. This makes a difference in how the quantities
are referenced in a "dump custom"_dump.html command, e.g. c_ID versus
c_ID\[2\].
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
"compute"_compute.html, "fix ave/spatial"_fix_ave_spatial.html, "dump
custom"_dump.html
[Default:] none
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment