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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1856 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2008-05-20 15:38:43 +00:00
parent e418e38df8
commit 3277e8b47b
2 changed files with 30 additions and 20 deletions
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25
doc/read_data.html
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@ -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 valid if all z coords are 0.0. For 2d triclinic simulations, the xz
and yz tilt factors must be 0.0. and yz tilt factors must be 0.0.
</P> </P>
<P>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.
</P>
<P>If the system is periodic (in a dimension), then atom coordinates can <P>If the system is periodic (in a dimension), then atom coordinates can
be outside the bounds; they will be remapped (in a periodic sense) be outside the bounds; they will be remapped (in a periodic sense)
back inside the box. back inside the box.
</P> </P>
<P>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.
</P>
<HR> <HR>
<P>These are the section keywords for the body of the file. <P>These are the section keywords for the body of the file.

25
doc/read_data.txt
View File

@ -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 valid if all z coords are 0.0. For 2d triclinic simulations, the xz
and yz tilt factors must be 0.0. 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 If the system is periodic (in a dimension), then atom coordinates can
be outside the bounds; they will be remapped (in a periodic sense) be outside the bounds; they will be remapped (in a periodic sense)
back inside the box. 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 :line
These are the section keywords for the body of the file. These are the section keywords for the body of the file.