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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3614 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2009-12-22 01:14:57 +00:00
parent 2aa5636d76
commit c32e4b0b0b
3 changed files with 27 additions and 26 deletions
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18
doc/compute_rdf.html
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@ -75,15 +75,15 @@ a specific histogram if the following criteria are met:
<LI>the type of the J atom matches jtypeN (one or a range of types)
<LI>the I,J interaction is included in the neighbor list
</UL>
<P>The last point is relevant for molecular systems with bonds, because
if two atoms I,J are involved in 1-2, 1-3, 1-4 interactions within the
molecular topology, their pairwise interaction may be turned off, and
thus they will not appear in the neighbor list, and will not
contribute to g(r). More specifically, this is true of I,J pairs with
a weighting factor of 0.0; pairs with a non-zero weighting factor are
included. The weighting factors for 1-2, 1-3, and 1-4 pairwise
interactions are set by the <A HREF = "special_bonds.html">special_bonds</A>
command.
<P>IMPORTANT NOTE: The last point is relevant for molecular systems with
bonds, because if two atoms I,J are involved in 1-2, 1-3, 1-4
interactions within the molecular topology, their pairwise interaction
may be turned off, and thus they will not appear in the neighbor list,
and will not contribute to g(r). More specifically, this is true of
I,J pairs with a weighting factor of 0.0; pairs with a non-zero
weighting factor are included. The weighting factors for 1-2, 1-3,
and 1-4 pairwise interactions are set by the
<A HREF = "special_bonds.html">special_bonds</A> command.
</P>
<P>It is OK if a particular pairwise distance is included in more than
one individual histogram, due to the way the <I>itypeN</I> and <I>jtypeN</I>

18
doc/compute_rdf.txt
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@ -72,15 +72,15 @@ the type of the I atom matches itypeN (one or a range of types)
the type of the J atom matches jtypeN (one or a range of types)
the I,J interaction is included in the neighbor list :ul
The last point is relevant for molecular systems with bonds, because
if two atoms I,J are involved in 1-2, 1-3, 1-4 interactions within the
molecular topology, their pairwise interaction may be turned off, and
thus they will not appear in the neighbor list, and will not
contribute to g(r). More specifically, this is true of I,J pairs with
a weighting factor of 0.0; pairs with a non-zero weighting factor are
included. The weighting factors for 1-2, 1-3, and 1-4 pairwise
interactions are set by the "special_bonds"_special_bonds.html
command.
IMPORTANT NOTE: The last point is relevant for molecular systems with
bonds, because if two atoms I,J are involved in 1-2, 1-3, 1-4
interactions within the molecular topology, their pairwise interaction
may be turned off, and thus they will not appear in the neighbor list,
and will not contribute to g(r). More specifically, this is true of
I,J pairs with a weighting factor of 0.0; pairs with a non-zero
weighting factor are included. The weighting factors for 1-2, 1-3,
and 1-4 pairwise interactions are set by the
"special_bonds"_special_bonds.html command.
It is OK if a particular pairwise distance is included in more than
one individual histogram, due to the way the {itypeN} and {jtypeN}

17
doc/fix_store_force.html
View File

@ -41,14 +41,15 @@ potentially modify the force on each atom. Examples of such fixes are
<A HREF = "fix_shake.html">fix shake</A>, <A HREF = "fix_wall.html">fix wall</A>, and <A HREF = "fix_indent.html">fix
indent</A>.
</P>
<P>IMPORTANT NOTE: The order in which the various fixes, including this
one, which operate at the same point during the timestep is the same
as the order they are specified in the input script. Thus normally,
if you want to store per-atom forces due to force field interactions,
before constraints are applied, you should list this fix first, before
other fixes that apply constraints. However, if you wish to include
certain constraints (e.g. fix shake) in the stored force, then it
could be specified after some fixes and before others.
<P>IMPORTANT NOTE: The order in which various fixes are applied which
operate at the same point during the timestep, is the same as the
order they are specified in the input script. Thus normally, if you
want to store per-atom forces due to force field interactions, before
constraints are applied, you should list this fix first within that
set of fixes, i.e. before other fixes that apply constraints.
However, if you wish to include certain constraints (e.g. fix shake)
in the stored force, then it could be specified after some fixes and
before others.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>