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doc/compute_attribute_atom.html

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<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

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"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

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<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

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"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

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<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>

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