From 39c25bd61aebfc1d3996e6364b2dfd0d0a9c69d0 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Sat, 8 Aug 2009 18:43:01 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3020 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_indent.html | 18 ++++++++++-------- doc/fix_indent.txt | 18 ++++++++++-------- 2 files changed, 20 insertions(+), 16 deletions(-) diff --git a/doc/fix_indent.html b/doc/fix_indent.html index f401c4d71b..06e1506dc6 100644 --- a/doc/fix_indent.html +++ b/doc/fix_indent.html @@ -72,11 +72,16 @@ must set one of those 3 keywords.

on each atom where k is the specified force constant, r is the distance from the atom to the center of the indenter, and R is the radius of the indenter. The force is repulsive and F(r) = 0 for r > -R. +R. The calculation of distance to the indenter center accounts +for periodic boundaries, which means the indenter can effectively +straddle one or more periodic boundaries.

A cylindrical indenter exerts the same force, except that r is the distance from the atom to the center axis of the cylinder. The -cylinder extends infinitely along its axis. +cylinder extends infinitely along its axis. The calculation of +distance to the indenter axis accounts for periodic boundaries, which +means the indenter can effectively straddle one or more periodic +boundaries.

A planar indenter is really an axis-aligned infinite-extent wall exerting the same force on atoms in the system, where R is the @@ -93,7 +98,9 @@ the spherical (or cylindrical or planar) indenter will move during the simulation, based on its initial position (x,y,z) and the specified (vx,vy,vz). Note that if you do multiple runs, the initial position of the indenter (x,y,z) does not change, so it will continue to move -at the specified velocity. +at the specified velocity. For periodic systems and spherical or +cylindrical indenters, the new position of the center or axis is +wrapped back into the periodic box as needed.

If the rstart keyword is specified, then the radius of the indenter is a time-dependent quantity. This only applies to spherical or @@ -121,11 +128,6 @@ choice affects not only the indenter's physical geometry, but also its velocity and force constant since they are defined in terms of distance as well.

-

IMPORTANT NOTE: For spherical and cylindrical indenters, you should -insure the indenter's extent does not overlap a periodic boundary, -either for a fixed indenter, or one that moves. No check for such -overlaps is performed by the code. -

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

No information about this fix is written to binary restart diff --git a/doc/fix_indent.txt b/doc/fix_indent.txt index cdf40865d7..46d38acea1 100644 --- a/doc/fix_indent.txt +++ b/doc/fix_indent.txt @@ -63,11 +63,16 @@ F(r) = - k (r - R)^2 :pre on each atom where {k} is the specified force constant, {r} is the distance from the atom to the center of the indenter, and {R} is the radius of the indenter. The force is repulsive and F(r) = 0 for {r} > -{R}. +{R}. The calculation of distance to the indenter center accounts +for periodic boundaries, which means the indenter can effectively +straddle one or more periodic boundaries. A cylindrical indenter exerts the same force, except that {r} is the distance from the atom to the center axis of the cylinder. The -cylinder extends infinitely along its axis. +cylinder extends infinitely along its axis. The calculation of +distance to the indenter axis accounts for periodic boundaries, which +means the indenter can effectively straddle one or more periodic +boundaries. A planar indenter is really an axis-aligned infinite-extent wall exerting the same force on atoms in the system, where {R} is the @@ -84,7 +89,9 @@ the spherical (or cylindrical or planar) indenter will move during the simulation, based on its initial position (x,y,z) and the specified (vx,vy,vz). Note that if you do multiple runs, the initial position of the indenter (x,y,z) does not change, so it will continue to move -at the specified velocity. +at the specified velocity. For periodic systems and spherical or +cylindrical indenters, the new position of the center or axis is +wrapped back into the periodic box as needed. If the {rstart} keyword is specified, then the radius of the indenter is a time-dependent quantity. This only applies to spherical or @@ -112,11 +119,6 @@ choice affects not only the indenter's physical geometry, but also its velocity and force constant since they are defined in terms of distance as well. -IMPORTANT NOTE: For spherical and cylindrical indenters, you should -insure the indenter's extent does not overlap a periodic boundary, -either for a fixed indenter, or one that moves. No check for such -overlaps is performed by the code. - [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart