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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2687 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2009-03-19 14:34:23 +00:00
parent fecaf12b5f
commit a750dd2a47
4 changed files with 54 additions and 28 deletions
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15
doc/Manual.html
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@ -54,6 +54,21 @@ it gives quick access to documentation for all LAMMPS commands.
<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
<A HREF = "http://www.easysw.com/htmldoc">htmldoc</A>
</P>
<P>IMPORTANT NOTE: If you are reading these HTML doc pages on the LAMMPS
WWW site, then they describe the most current, fully-patched version
of LAMMPS, which has changed after the date listed above. These
additions are described on <A HREF = "http://lammps.sandia.gov/bug.html">this
page</A>. If you are reading these
HTML doc pages from the doc directory of the tarball you downloaded,
then they will describe that tarball, whether it was the original
version for the date listed above, or an upgraded tarball including
features up to the date you downloaded it, again as described on <A HREF = "http://lammps.sandia.gov/bug.html">this
page</A>. When the tarball unpacks, it
will contain the date that corresponds to which version you
downloaded. The PDF file described above is not regenerated for every
patch, so it always corresponds to the original version with the date
listed above.
</P>
<OL><LI><A HREF = "Section_intro.html">Introduction</A>
<UL> 1.1 <A HREF = "Section_intro.html#1_1">What is LAMMPS</A>

15
doc/Manual.txt
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@ -51,6 +51,21 @@ it gives quick access to documentation for all LAMMPS commands.
"PDF file"_Manual.pdf of the entire manual, generated by
"htmldoc"_http://www.easysw.com/htmldoc
IMPORTANT NOTE: If you are reading these HTML doc pages on the LAMMPS
WWW site, then they describe the most current, fully-patched version
of LAMMPS, which has changed after the date listed above. These
additions are described on "this
page"_http://lammps.sandia.gov/bug.html. If you are reading these
HTML doc pages from the doc directory of the tarball you downloaded,
then they will describe that tarball, whether it was the original
version for the date listed above, or an upgraded tarball including
features up to the date you downloaded it, again as described on "this
page"_http://lammps.sandia.gov/bug.html. When the tarball unpacks, it
will contain the date that corresponds to which version you
downloaded. The PDF file described above is not regenerated for every
patch, so it always corresponds to the original version with the date
listed above.
"Introduction"_Section_intro.html :olb,l
1.1 "What is LAMMPS"_1_1 :ulb,b
1.2 "LAMMPS features"_1_2 :b

26
doc/fix_rigid.html
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@ -56,9 +56,18 @@ means that each timestep the total force and torque on each rigid body
is computed and the coordinates and velocities of the atoms in each
body are updated so that they move as a rigid body. This can be
useful for freezing one or more portions of a large biomolecule, or
for simulating a system of colloidal particles. See the Restrictions
section if you simply want to hold a group of atoms motionless or have
them move with constant velocity.
for simulating a system of colloidal particles.
</P>
<P>IMPORTANT NOTE: This fix is overkill if you just want to hold group of
atoms stationary of have them move with a constant velocity. A
simpler way to hold atoms stationary is to not include those atoms in
your time integration fix. E.g. use "fix 1 mobile nve" instead of
"fix 1 all nve", where "mobile" is the group of atoms that you want to
move. You can move atoms with a constant velocity by assigning them
an initial velocity (via the <A HREF = "velocity.html">velocity</A> command),
setting the force on them to 0.0 (via the <A HREF = "fix_setforce.html">fix
setforce</A> command), and integrating them as usual
(e.g. via the <A HREF = "fix_nve.html">fix nve</A> command).
</P>
<P>IMPORTANT NOTE: This fix updates the positions and velocities of the
rigid atoms with a constant-energy time integration, so you should not
@ -195,17 +204,6 @@ boundary, the input data file must define the image flags for each
atom correctly, so that LAMMPS can "unwrap" the atoms into a valid
rigid body.
</P>
<P>This fix is overkill if you just want to hold group of atoms
stationary of have them move with a constant velocity. A simpler way
to hold atoms stationary is to not include those atoms in your time
integration fix. E.g. use "fix 1 mobile nve" instead of "fix 1 all
nve", where "mobile" is the group of atoms that you want to move. You
can move atoms with a constant velocity by assigning them an initial
velocity (via the <A HREF = "velocity.html">velocity</A> command), setting the force
on them to 0.0 (via the <A HREF = "fix_setforce.html">fix setforce</A> command), and
integrating them as usual (e.g. via the <A HREF = "fix_nve.html">fix nve</A>
command).
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "delete_bonds.html">delete_bonds</A>, <A HREF = "neigh_modify.html">neigh_modify</A>

26
doc/fix_rigid.txt
View File

@ -47,9 +47,18 @@ means that each timestep the total force and torque on each rigid body
is computed and the coordinates and velocities of the atoms in each
body are updated so that they move as a rigid body. This can be
useful for freezing one or more portions of a large biomolecule, or
for simulating a system of colloidal particles. See the Restrictions
section if you simply want to hold a group of atoms motionless or have
them move with constant velocity.
for simulating a system of colloidal particles.
IMPORTANT NOTE: This fix is overkill if you just want to hold group of
atoms stationary of have them move with a constant velocity. A
simpler way to hold atoms stationary is to not include those atoms in
your time integration fix. E.g. use "fix 1 mobile nve" instead of
"fix 1 all nve", where "mobile" is the group of atoms that you want to
move. You can move atoms with a constant velocity by assigning them
an initial velocity (via the "velocity"_velocity.html command),
setting the force on them to 0.0 (via the "fix
setforce"_fix_setforce.html command), and integrating them as usual
(e.g. via the "fix nve"_fix_nve.html command).
IMPORTANT NOTE: This fix updates the positions and velocities of the
rigid atoms with a constant-energy time integration, so you should not
@ -186,17 +195,6 @@ boundary, the input data file must define the image flags for each
atom correctly, so that LAMMPS can "unwrap" the atoms into a valid
rigid body.
This fix is overkill if you just want to hold group of atoms
stationary of have them move with a constant velocity. A simpler way
to hold atoms stationary is to not include those atoms in your time
integration fix. E.g. use "fix 1 mobile nve" instead of "fix 1 all
nve", where "mobile" is the group of atoms that you want to move. You
can move atoms with a constant velocity by assigning them an initial
velocity (via the "velocity"_velocity.html command), setting the force
on them to 0.0 (via the "fix setforce"_fix_setforce.html command), and
integrating them as usual (e.g. via the "fix nve"_fix_nve.html
command).
[Related commands:]
"delete_bonds"_delete_bonds.html, "neigh_modify"_neigh_modify.html