From 13335a703f9257b7f3c74b6f4918804db6222722 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 29 Jan 2014 15:19:21 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11372 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_ave_spatial.html | 4 ++++ doc/fix_ave_spatial.txt | 4 ++++ doc/fix_box_relax.html | 14 ++++++++++++++ doc/fix_box_relax.txt | 13 ++++++++++++- 4 files changed, 34 insertions(+), 1 deletion(-) diff --git a/doc/fix_ave_spatial.html b/doc/fix_ave_spatial.html index 477afc51c2..0e4245c82a 100644 --- a/doc/fix_ave_spatial.html +++ b/doc/fix_ave_spatial.html @@ -249,6 +249,10 @@ count of atoms in the bin. The printed value for the bin is Total-quantity / Total-count. In other words it is an average over the entire Nfreq timescale.

+

As described above, if the region keyword is used, the atom must be +in both the group and the specified geometric region in +order to contribute to bin averages. +

For a sample setting, the bin quantity is summed over atoms for only a single sample, as is the count, and a "average sample value" is computed, i.e. Sample-quantity / Sample-count. The printed value for diff --git a/doc/fix_ave_spatial.txt b/doc/fix_ave_spatial.txt index 3c251c4a04..ecba9b19cb 100644 --- a/doc/fix_ave_spatial.txt +++ b/doc/fix_ave_spatial.txt @@ -234,6 +234,10 @@ count of atoms in the bin. The printed value for the bin is Total-quantity / Total-count. In other words it is an average over the entire {Nfreq} timescale. +As described above, if the {region} keyword is used, the atom must be +in both the group and the specified geometric "region"_region.html in +order to contribute to bin averages. + For a {sample} setting, the bin quantity is summed over atoms for only a single sample, as is the count, and a "average sample value" is computed, i.e. Sample-quantity / Sample-count. The printed value for diff --git a/doc/fix_box_relax.html b/doc/fix_box_relax.html index d6884195dd..28813ca161 100644 --- a/doc/fix_box_relax.html +++ b/doc/fix_box_relax.html @@ -122,6 +122,20 @@ the large volume of communication needed to acquire ghost atoms around a processor's irregular-shaped sub-domain. For extreme values of tilt, LAMMPS may also lose atoms and generate an error.

+

IMPORTANT NOTE: Performing a minimization with this fix is not a +mathematically well-defined minimization problem. This is because the +objective function being minimized changes if the box size/shape +changes. In practice this means the minimizer can get "stuck" before +you have reached the desired tolerance. The solution to this is to +restart the minmizer from the new adjusted box size/shape, since that +creates a new objective function valid for the new box size/shape. +Repeat as necessary until the box size/shape has reached its new +equilibrium. +

+
+ +
+

The couple keyword allows two or three of the diagonal components of diff --git a/doc/fix_box_relax.txt b/doc/fix_box_relax.txt index a1575ce477..93f5ae50bd 100644 --- a/doc/fix_box_relax.txt +++ b/doc/fix_box_relax.txt @@ -28,7 +28,6 @@ keyword = {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} {fixedpoint} values = x y z x,y,z = perform relaxation dilation/contraction around this point (distance units) :pre - :ule [Examples:] @@ -118,6 +117,18 @@ the large volume of communication needed to acquire ghost atoms around a processor's irregular-shaped sub-domain. For extreme values of tilt, LAMMPS may also lose atoms and generate an error. +IMPORTANT NOTE: Performing a minimization with this fix is not a +mathematically well-defined minimization problem. This is because the +objective function being minimized changes if the box size/shape +changes. In practice this means the minimizer can get "stuck" before +you have reached the desired tolerance. The solution to this is to +restart the minmizer from the new adjusted box size/shape, since that +creates a new objective function valid for the new box size/shape. +Repeat as necessary until the box size/shape has reached its new +equilibrium. + +:line +:line :line The {couple} keyword allows two or three of the diagonal components of