From b245332f41e777df0d82b2288f3950fe22261264 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 27 Sep 2007 23:28:06 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@908
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/compute_attribute_atom.html | 72 +++++++++++++++++++++++++++++
doc/compute_attribute_atom.txt | 67 +++++++++++++++++++++++++++
doc/compute_sum_atom.html | 49 ++++++++++++++++++++
doc/compute_sum_atom.txt | 44 ++++++++++++++++++
doc/fix_ave_atom.html | 82 +++++++++++++++++++++++++++++++++
doc/fix_ave_atom.txt | 77 +++++++++++++++++++++++++++++++
6 files changed, 391 insertions(+)
create mode 100644 doc/compute_attribute_atom.html
create mode 100644 doc/compute_attribute_atom.txt
create mode 100644 doc/compute_sum_atom.html
create mode 100644 doc/compute_sum_atom.txt
create mode 100644 doc/fix_ave_atom.html
create mode 100644 doc/fix_ave_atom.txt
diff --git a/doc/compute_attribute_atom.html b/doc/compute_attribute_atom.html
new file mode 100644
index 0000000000..85cfea24a5
--- /dev/null
+++ b/doc/compute_attribute_atom.html
@@ -0,0 +1,72 @@
+<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>
diff --git a/doc/compute_attribute_atom.txt b/doc/compute_attribute_atom.txt
new file mode 100644
index 0000000000..1b4a03c291
--- /dev/null
+++ b/doc/compute_attribute_atom.txt
@@ -0,0 +1,67 @@
+"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
diff --git a/doc/compute_sum_atom.html b/doc/compute_sum_atom.html
new file mode 100644
index 0000000000..517a0e6000
--- /dev/null
+++ b/doc/compute_sum_atom.html
@@ -0,0 +1,49 @@
+<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>
diff --git a/doc/compute_sum_atom.txt b/doc/compute_sum_atom.txt
new file mode 100644
index 0000000000..9caf64cf5b
--- /dev/null
+++ b/doc/compute_sum_atom.txt
@@ -0,0 +1,44 @@
+"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
diff --git a/doc/fix_ave_atom.html b/doc/fix_ave_atom.html
new file mode 100644
index 0000000000..eb9ebd7682
--- /dev/null
+++ b/doc/fix_ave_atom.html
@@ -0,0 +1,82 @@
+<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>
diff --git a/doc/fix_ave_atom.txt b/doc/fix_ave_atom.txt
new file mode 100644
index 0000000000..1cab82da6a
--- /dev/null
+++ b/doc/fix_ave_atom.txt
@@ -0,0 +1,77 @@
+"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
--
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