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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1194 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2007-11-30 21:58:15 +00:00
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4
doc/Section_commands.txt
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@ -388,7 +388,6 @@ of each style or click on the style itself for a full description:
"efield"_fix_efield.html,
"enforce2d"_fix_enforce2d.html,
"freeze"_fix_freeze.html,
"gran/diag"_fix_gran_diag.html,
"gravity"_fix_gravity.html,
"gyration"_fix_gyration.html,
"heat"_fix_heat.html,
@ -441,10 +440,9 @@ description:
"attribute/atom"_compute_attribute_atom.html,
"centro/atom"_compute_centro_atom.html,
"coord/atom"_compute_coord_atom.html,
"ebond/atom"_compute_ebond_atom.html,
"epair/atom"_compute_epair_atom.html,
"ke/atom"_compute_ke_atom.html,
"pe"_compute_pe.html,
"pe/atom"_compute_pe_atom.html,
"pressure"_compute_pressure.html,
"rotate/dipole"_compute_rotate_dipole.html,
"rotate/gran"_compute_rotate_gran.html,

3
doc/compute.txt
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@ -90,10 +90,9 @@ defined in LAMMPS:
"attribute/atom"_compute_attribute_atom.html - attribute (x,v,f,etc) of each atom
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
"coord/atom"_compute_coord_atom.html - coordination number for each atom
"ebond/atom"_compute_ebond_atom.html - bond energy for each atom
"epair/atom"_compute_epair_atom.html - pairwise energy for each atom
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
"pe"_compute_pe.html - potential energy
"pe"_compute_pe.html - potential energy for each atom
"pressure"_compute_pressure.html - total pressure and pressure tensor
"rotate/dipole"_compute_rotate_dipole.html - rotational energy of dipolar atoms
"rotate/gran"_compute_rotate_gran.html - rotational energy of granular atoms

51
doc/compute_ebond_atom.html
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@ -1,51 +0,0 @@
<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 ebond/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID ebond/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>ebond/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all ebond/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that computes the per-atom bond energy for each
atom in a group.
</P>
<P>The bond energy for each atom is computed by looping over the atoms it
is bonded to and computing the bond energy associated with the defined
<A HREF = "bond_style.html">bond_style</A> command for each I-J bond (divided by 2).
Thus the sum of per-atom bond energy for all atoms should give the
total bond energy of the system.
</P>
<P>If two atoms are bonded and only one of them is in the compute group,
the energy of the bond is included in the per-atom energy of the atom
in the group.
</P>
<P>Computation of per-atom bond energy requires a loop thru the bond list
and inter-processor communication, so it can be inefficient to
compute/dump this quantity too frequently or to have multiple
compute/dump commands, each of a <I>ebond/atom</I> style.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>

46
doc/compute_ebond_atom.txt
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@ -1,46 +0,0 @@
"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 ebond/atom command :h3
[Syntax:]
compute ID group-ID ebond/atom :pre
ID, group-ID are documented in "compute"_compute.html command
ebond/atom = style name of this compute command :ul
[Examples:]
compute 1 all ebond/atom :pre
[Description:]
Define a computation that computes the per-atom bond energy for each
atom in a group.
The bond energy for each atom is computed by looping over the atoms it
is bonded to and computing the bond energy associated with the defined
"bond_style"_bond_style.html command for each I-J bond (divided by 2).
Thus the sum of per-atom bond energy for all atoms should give the
total bond energy of the system.
If two atoms are bonded and only one of them is in the compute group,
the energy of the bond is included in the per-atom energy of the atom
in the group.
Computation of per-atom bond energy requires a loop thru the bond list
and inter-processor communication, so it can be inefficient to
compute/dump this quantity too frequently or to have multiple
compute/dump commands, each of a {ebond/atom} style.
[Restrictions:] none
[Related commands:] none
[Default:] none

58
doc/compute_epair_atom.html
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@ -1,58 +0,0 @@
<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 epair/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID epair/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>epair/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all epair/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that computes the per-atom pairwise energy for
each atom in a group.
</P>
<P>The pairwise energy for each atom is computed by looping over its
neighbors and computing the energy associated with the defined
<A HREF = "pair_style.html">pair_style</A> command for each I,J pair (divided by 2).
Thus the sum of per-atom energy for all atoms should give the total
pairwise energy of the system.
</P>
<P>If two atoms interact and only one of them is in the compute group,
the energy of the pairwise interaction is included in the per-atom
energy of the atom in the group.
</P>
<P>For force fields that include a contribution to the pairwise energy
that is computed as part of dihedral terms (i.e. 1-4 interactions),
this contribution is NOT included in the per-atom pairwise energy.
</P>
<P>Computation of per-atom pairwise energy requires a loop thru the
neighbor list and inter-processor communication, so it can be
inefficient to compute/dump this quantity too frequently or to have
multiple compute/dump commands, each of a <I>epair/atom</I> style.
</P>
<P><B>Restrictions:</B>
</P>
<P>Some pair potentials do not allow the calculation of per-atom energy
via this command. An error will be generated if this is the case.
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>

53
doc/compute_epair_atom.txt
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@ -1,53 +0,0 @@
"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 epair/atom command :h3
[Syntax:]
compute ID group-ID epair/atom :pre
ID, group-ID are documented in "compute"_compute.html command
epair/atom = style name of this compute command :ul
[Examples:]
compute 1 all epair/atom :pre
[Description:]
Define a computation that computes the per-atom pairwise energy for
each atom in a group.
The pairwise energy for each atom is computed by looping over its
neighbors and computing the energy associated with the defined
"pair_style"_pair_style.html command for each I,J pair (divided by 2).
Thus the sum of per-atom energy for all atoms should give the total
pairwise energy of the system.
If two atoms interact and only one of them is in the compute group,
the energy of the pairwise interaction is included in the per-atom
energy of the atom in the group.
For force fields that include a contribution to the pairwise energy
that is computed as part of dihedral terms (i.e. 1-4 interactions),
this contribution is NOT included in the per-atom pairwise energy.
Computation of per-atom pairwise energy requires a loop thru the
neighbor list and inter-processor communication, so it can be
inefficient to compute/dump this quantity too frequently or to have
multiple compute/dump commands, each of a {epair/atom} style.
[Restrictions:]
Some pair potentials do not allow the calculation of per-atom energy
via this command. An error will be generated if this is the case.
[Related commands:] none
[Default:] none

1
doc/fix.txt
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@ -91,7 +91,6 @@ Here is an alphabetic list of fix styles available in LAMMPS:
"efield"_fix_efield.html - impose electric field on system
"enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
"freeze"_fix_freeze.html - freeze atoms in a granular simulation
"gran/diag"_fix_gran_diag.html - compute granular diagnostics
"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
"gyration"_fix_gyration.html - compute radius of gyration
"heat"_fix_heat.html - add/subtract momentum-conserving heat

61
doc/fix_gran_diag.html
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@ -1,61 +0,0 @@
<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 gran/diag command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID gran/diag nevery file layer
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>gran/diag = style name of this fix command
<LI>nevery = compute diagnostics every this many timesteps
<LI>file = filename to store diagnostic info in
<LI>layer = bin size in z-dimension (3d) or y-dimension (2d)
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all gran/diag 1000 tmp 0.9
</PRE>
<P><B>Description:</B>
</P>
<P>Compute aggregate density, velocity, and stress diagnostics for a
group of granular atoms as a function of depth in the granular system.
"Depth" means the z-dimension for a 3d simulation, and the y-dimension
for a 2d simulation. The results are written to 3 files named
file.den, file.vel, and file.str. The bins begin at the bottom of the
system and extend upward with a thickness of <I>layer</I> for each bin.
The quantities written to the file are averaged over all atoms in the
bin.
</P>
<P><B>Restart, fix_modify, 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 global scalar or vector or per-atom
quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. 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>
</P>
<P>This fix is part of the "granular" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "atom_style.html">atom_style granular</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

56
doc/fix_gran_diag.txt
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@ -1,56 +0,0 @@
"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 gran/diag command :h3
[Syntax:]
fix ID group-ID gran/diag nevery file layer :pre
ID, group-ID are documented in "fix"_fix.html command
gran/diag = style name of this fix command
nevery = compute diagnostics every this many timesteps
file = filename to store diagnostic info in
layer = bin size in z-dimension (3d) or y-dimension (2d) :ul
[Examples:]
fix 1 all gran/diag 1000 tmp 0.9 :pre
[Description:]
Compute aggregate density, velocity, and stress diagnostics for a
group of granular atoms as a function of depth in the granular system.
"Depth" means the z-dimension for a 3d simulation, and the y-dimension
for a 2d simulation. The results are written to 3 files named
file.den, file.vel, and file.str. The bins begin at the bottom of the
system and extend upward with a thickness of {layer} for each bin.
The quantities written to the file are averaged over all atoms in the
bin.
[Restart, fix_modify, 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 global scalar or vector or per-atom
quantities are stored by this fix for access by various "output
commands"_Section_howto.html#4_15. 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:]
This fix is part of the "granular" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"atom_style granular"_atom_style.html
[Default:] none