From c32e4b0b0b5ecb227890ba3df9c8594ae02080ce Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 22 Dec 2009 01:14:57 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3614 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/compute_rdf.html | 18 +++++++++--------- doc/compute_rdf.txt | 18 +++++++++--------- doc/fix_store_force.html | 17 +++++++++-------- 3 files changed, 27 insertions(+), 26 deletions(-) diff --git a/doc/compute_rdf.html b/doc/compute_rdf.html index 8ae0cd920c..be0f413202 100644 --- a/doc/compute_rdf.html +++ b/doc/compute_rdf.html @@ -75,15 +75,15 @@ a specific histogram if the following criteria are met:
  • the type of the J atom matches jtypeN (one or a range of types)
  • the I,J interaction is included in the neighbor list -

    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 -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 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 diff --git a/doc/compute_rdf.txt b/doc/compute_rdf.txt index 3cac027908..23f746e0f6 100644 --- a/doc/compute_rdf.txt +++ b/doc/compute_rdf.txt @@ -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} diff --git a/doc/fix_store_force.html b/doc/fix_store_force.html index c0a05e912e..1b5caf7fc3 100644 --- a/doc/fix_store_force.html +++ b/doc/fix_store_force.html @@ -41,14 +41,15 @@ potentially modify the force on each atom. Examples of such fixes are fix shake, fix wall, and fix indent.

    -

    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. +

    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.

    Restart, fix_modify, output, run start/stop, minimize info: