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

17
doc/fix_store_force.html
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@ -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 <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>. indent</A>.
</P> </P>
<P>IMPORTANT NOTE: The order in which the various fixes, including this <P>IMPORTANT NOTE: The order in which various fixes are applied which
one, which operate at the same point during the timestep is the same operate at the same point during the timestep, is the same as the
as the order they are specified in the input script. Thus normally, order they are specified in the input script. Thus normally, if you
if you want to store per-atom forces due to force field interactions, want to store per-atom forces due to force field interactions, before
before constraints are applied, you should list this fix first, before constraints are applied, you should list this fix first within that
other fixes that apply constraints. However, if you wish to include set of fixes, i.e. before other fixes that apply constraints.
certain constraints (e.g. fix shake) in the stored force, then it However, if you wish to include certain constraints (e.g. fix shake)
could be specified after some fixes and before others. in the stored force, then it could be specified after some fixes and
before others.
</P> </P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B> <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P> </P>