mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@908 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
36fbdf7502
commit
b245332f41
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|||
<HTML>
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<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>
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</CENTER>
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<HR>
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<H3>compute attribute/atom command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID attribute/atom style
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>attribute/atom = style name of this compute command
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<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>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute 1 all attribute/atom vy
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compute mine all attribute/atom xyz
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Define a computation that calculates (or simply stores) one or more
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attributes for each atom in a group. This is useful for input to the
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<A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command to do spatial averaging
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by layers or to the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command to
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perform time-averaging of per-atom quantities. The attribute values
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can also be output directly by the <A HREF = "dump.html">dump custom</A> command,
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but it has keywords that output these quantities without the need to
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define an additional compute.
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</P>
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<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>,
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<I>fy</I>, and <I>fz</I> each store a single scalar value per atom.
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</P>
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<P>The <I>x</I>, <I>y</I>, <I>z</I> keywords store atom coordinate in the appropriate
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distance <A HREF = "units.html">units</A> (Angstroms, sigma, etc) and will always be
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inside (or slightly outside) the simulation box. Use <I>xu</I>, <I>yu</I>, <I>zu</I>
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if you want the coordinates "unwrapped" by the image flags for each
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atom. Unwrapped means that if the atom has passed thru a periodic
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boundary one or more times, the value is printed for what the
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coordinate would be if it had not been wrapped back into the periodic
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box. Note that using <I>xu</I>, <I>yu</I>, <I>zu</I> means that the coordinate
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values may be far outside the simulation box.
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</P>
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<P>Note that if you want to compute the time-averaged position of an atom
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coordinate that could pass thru a periodic boundary (e.g. via the <A HREF = "fix_ave_atom.html">fix
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ave/atom</A> command), you probably want to use <I>xu</I>
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instead of <I>x</I>.
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</P>
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<P>The styles <I>xyz</I>, <I>v</I>, and <I>f</I> each store a vector of 3 quantities per
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atom.
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</P>
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<P>Note that the various commands that reference this compute use a
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different syntax for accessing scalar versus vector values, e.g. c_ID
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versus c_ID<B>2</B>.
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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix
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ave/spatial</A>, <A HREF = "dump.html">dump custom</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute attribute/atom command :h3
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[Syntax:]
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compute ID group-ID attribute/atom style :pre
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ID, group-ID are documented in "compute"_compute.html command
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attribute/atom = style name of this compute command
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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
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[Examples:]
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compute 1 all attribute/atom vy
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compute mine all attribute/atom xyz :pre
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[Description:]
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Define a computation that calculates (or simply stores) one or more
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attributes for each atom in a group. This is useful for input to the
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"fix ave/spatial"_fix_ave_spatial.html command to do spatial averaging
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by layers or to the "fix ave/atom"_fix_ave_atom.html command to
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perform time-averaging of per-atom quantities. The attribute values
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can also be output directly by the "dump custom"_dump.html command,
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but it has keywords that output these quantities without the need to
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define an additional compute.
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The styles {x}, {y}, {z}, {xu}, {yu}, {zu}, {vx}, {vy}, {vz}, {fx},
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{fy}, and {fz} each store a single scalar value per atom.
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The {x}, {y}, {z} keywords store atom coordinate in the appropriate
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distance "units"_units.html (Angstroms, sigma, etc) and will always be
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inside (or slightly outside) the simulation box. Use {xu}, {yu}, {zu}
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if you want the coordinates "unwrapped" by the image flags for each
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atom. Unwrapped means that if the atom has passed thru a periodic
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boundary one or more times, the value is printed for what the
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coordinate would be if it had not been wrapped back into the periodic
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box. Note that using {xu}, {yu}, {zu} means that the coordinate
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values may be far outside the simulation box.
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Note that if you want to compute the time-averaged position of an atom
|
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coordinate that could pass thru a periodic boundary (e.g. via the "fix
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ave/atom"_fix_ave_atom.html command), you probably want to use {xu}
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instead of {x}.
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The styles {xyz}, {v}, and {f} each store a vector of 3 quantities per
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atom.
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Note that the various commands that reference this compute use a
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different syntax for accessing scalar versus vector values, e.g. c_ID
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versus c_ID[2].
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[Restrictions:] none
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[Related commands:]
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"fix ave/atom"_fix_ave_atom.html, "fix
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ave/spatial"_fix_ave_spatial.html, "dump custom"_dump.html
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[Default:] none
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@ -0,0 +1,49 @@
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<HTML>
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<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>
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</CENTER>
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<HR>
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<H3>compute sum/atom command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID sum/atom compute-ID1 compute-ID2 ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>sum/atom = style name of this compute command
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<LI>compute-ID1, 2, ... = IDs of computes that calculate per-atom quantities
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute 1 all sum/atom atomKE atomEpair atomEbond
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Define a computation that sums the results of two or more other
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computes for each atom in a group. This is useful for summing atom
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properties such as pairwise energy, bond energy, kinetic energy, etc.
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The resulting values can be accessed by any command that uses per-atom
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computes, e.g. the <A HREF = "dump.html">dump custom</A> command or <A HREF = "fix_ave_spatial.html">fix
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ave/spatial</A> command or <A HREF = "fix_ave_atom.html">fix
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ave/atom</A> command.
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</P>
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<P>The result of this compute depends on the results generated by the
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other computes that it invokes. E.g. if the other computes each
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generate a scalar value per atom, so will this compute. If the other
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computes each generate a vector of values per atom, so will this
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compute. In the latter case, all the other computes must generate
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vectors of the same size.
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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B> none
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute sum/atom command :h3
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[Syntax:]
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compute ID group-ID sum/atom compute-ID1 compute-ID2 ... :pre
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ID, group-ID are documented in "compute"_compute.html command
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sum/atom = style name of this compute command
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compute-ID1, 2, ... = IDs of computes that calculate per-atom quantities :ul
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[Examples:]
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compute 1 all sum/atom atomKE atomEpair atomEbond :pre
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[Description:]
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Define a computation that sums the results of two or more other
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computes for each atom in a group. This is useful for summing atom
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properties such as pairwise energy, bond energy, kinetic energy, etc.
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The resulting values can be accessed by any command that uses per-atom
|
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computes, e.g. the "dump custom"_dump.html command or "fix
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ave/spatial"_fix_ave_spatial.html command or "fix
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ave/atom"_fix_ave_atom.html command.
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The result of this compute depends on the results generated by the
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other computes that it invokes. E.g. if the other computes each
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generate a scalar value per atom, so will this compute. If the other
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computes each generate a vector of values per atom, so will this
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compute. In the latter case, all the other computes must generate
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vectors of the same size.
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[Restrictions:] none
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[Related commands:] none
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[Default:] none
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@ -0,0 +1,82 @@
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<HTML>
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<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>
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</CENTER>
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<HR>
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<H3>fix ave/atom command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID ave/atom Nevery Nrepeat Nfreq compute-ID
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>ave/atom = style name of this fix command
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<LI>Nevery = calculate property every this many timesteps
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<LI>Nrepeat = # of times to repeat the Nevery calculation before averaging
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<LI>Nfreq = timestep frequency at which the average value is calculated
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<LI>compute-ID = ID of per-atom compute that performs the calculation
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all ave/atom 1 100 100 myVx
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fix 1 all ave/atom 10 20 1000 my_epair
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Calculate one or more time-averaged per-atom quantities every few
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timesteps. The results of this calculation can be spatially averaged
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via the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command or output
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to a file via the <A HREF = "dump.html">dump custom</A> command.
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</P>
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<P>The <I>compute-ID</I> specifies a <A HREF = "compute.html">compute</A> which calculates
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the desired property. It must be a per-atom compute (one with the
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word "atom" in its style name) that calculates one or more values for
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each atom, as opposed to a global compute. The compute must be
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previously defined in the input script. Users can also write code for
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their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
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</P>
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<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify how the
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property will be time-averaged. The final averaged value(s) are
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computed every <I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I>
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values, computed in the preceeding portion of the simulation every
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<I>Nevery</I> timesteps. Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
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values on timesteps 90,92,94,96,98,100 will be used to compute the
|
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final average at timestep 100. Similary for timesteps
|
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190,192,194,196,198,200 at timestep 200, etc.
|
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</P>
|
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<P>If this fix is referenced by a <A HREF = "dump.html">dump custom</A> or <A HREF = "fix_ave_spatial.html">fix
|
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ave/spatial</A> command, the time-averaged values
|
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can only be accessed every <I>Nfreq</I> timesteps.
|
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</P>
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<P>If the compute calculates a single or multiple values per atom, then
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fix ave/atom will also calculate one or multiple time-averaged
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quantities per atom. This makes a difference in how the quantities
|
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are referenced in a <A HREF = "dump.html">dump custom</A> command, e.g. c_ID versus
|
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c_ID[2].
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</P>
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<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
|
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
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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
|
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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
|
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minimization</A>.
|
||||
</P>
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<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
|
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custom</A>
|
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</P>
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<P><B>Default:</B> none
|
||||
</P>
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</HTML>
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|
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@ -0,0 +1,77 @@
|
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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
|
||||
|
||||
fix ave/atom command :h3
|
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|
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[Syntax:]
|
||||
|
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fix ID group-ID ave/atom Nevery Nrepeat Nfreq compute-ID :pre
|
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|
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ID, group-ID are documented in "fix"_fix.html command
|
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ave/atom = style name of this fix command
|
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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
|
||||
Loading…
Reference in New Issue