From 3277e8b47b888ba600e1ea00435c95c20af61b17 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 20 May 2008 15:38:43 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1856 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/read_data.html | 25 +++++++++++++++---------- doc/read_data.txt | 25 +++++++++++++++---------- 2 files changed, 30 insertions(+), 20 deletions(-) diff --git a/doc/read_data.html b/doc/read_data.html index af7f7ec705..d508ddb60d 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -120,20 +120,25 @@ coords for atoms that appear in the file; the default of -0.5 0.5 is valid if all z coords are 0.0. For 2d triclinic simulations, the xz and yz tilt factors must be 0.0.

-

If the system is non-periodic (in a dimension), then all atoms in the -data file should have coordinates (in that dimension) between the lo -and hi values. Furthermore, if running in parallel, the lo/hi values -should be just a bit smaller/larger than the min/max extent of atoms. -For example, if your atoms extend from 0 to 50, you should not specify -the box bounds as -10000 and 10000. Since LAMMPS uses the specified -box size to layout the 3d grid of processors, this will be sub-optimal -and may cause a parallel simulation to lose atoms when LAMMPS -shrink-wraps the box to the atoms. -

If the system is periodic (in a dimension), then atom coordinates can be outside the bounds; they will be remapped (in a periodic sense) back inside the box.

+

IMPORTANT NOTE: If the system is non-periodic (in a dimension), then +all atoms in the data file must have coordinates (in that dimension) +that are greater than the lo value and less than the hi value. +Actually "greater than or equal to" is OK for the lo value, but they +must be "less than", not "less than or equal to" for the hi value. +Thus the lo/hi values you specify should be just a bit smaller/larger +than the min/max extent of atoms. However you do not want to make +these values much smaller/larger than the extent of the atoms. For +example, if your atoms extend from 0 to 50, you should not specify the +box bounds as -10000 and 10000. This is because LAMMPS uses the +specified box size to layout the 3d grid of processors. A huge +(mostly empty) box will be sub-optimal for performance and may cause a +parallel simulation to lose atoms if LAMMPS shrink-wraps the box +around the atoms. +

These are the section keywords for the body of the file. diff --git a/doc/read_data.txt b/doc/read_data.txt index b82d8f8964..d38e435ef5 100644 --- a/doc/read_data.txt +++ b/doc/read_data.txt @@ -115,20 +115,25 @@ coords for atoms that appear in the file; the default of -0.5 0.5 is valid if all z coords are 0.0. For 2d triclinic simulations, the xz and yz tilt factors must be 0.0. -If the system is non-periodic (in a dimension), then all atoms in the -data file should have coordinates (in that dimension) between the lo -and hi values. Furthermore, if running in parallel, the lo/hi values -should be just a bit smaller/larger than the min/max extent of atoms. -For example, if your atoms extend from 0 to 50, you should not specify -the box bounds as -10000 and 10000. Since LAMMPS uses the specified -box size to layout the 3d grid of processors, this will be sub-optimal -and may cause a parallel simulation to lose atoms when LAMMPS -shrink-wraps the box to the atoms. - If the system is periodic (in a dimension), then atom coordinates can be outside the bounds; they will be remapped (in a periodic sense) back inside the box. +IMPORTANT NOTE: If the system is non-periodic (in a dimension), then +all atoms in the data file must have coordinates (in that dimension) +that are greater than the lo value and less than the hi value. +Actually "greater than or equal to" is OK for the lo value, but they +must be "less than", not "less than or equal to" for the hi value. +Thus the lo/hi values you specify should be just a bit smaller/larger +than the min/max extent of atoms. However you do not want to make +these values much smaller/larger than the extent of the atoms. For +example, if your atoms extend from 0 to 50, you should not specify the +box bounds as -10000 and 10000. This is because LAMMPS uses the +specified box size to layout the 3d grid of processors. A huge +(mostly empty) box will be sub-optimal for performance and may cause a +parallel simulation to lose atoms if LAMMPS shrink-wraps the box +around the atoms. + :line These are the section keywords for the body of the file.