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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4973 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-10-05 16:12:36 +00:00
parent ef5709a9a4
commit d2442ba5df
4 changed files with 38 additions and 4 deletions
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14
doc/create_box.html
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@ -59,6 +59,20 @@ non-zero, then both the x and y dimensions must be periodic.
Similarly, x and z must be periodic if xz is non-zero and y and z must Similarly, x and z must be periodic if xz is non-zero and y and z must
be periodic if yz is non-zero. be periodic if yz is non-zero.
</P> </P>
<P>IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
you should not make the lo/hi box dimensions (as defined in your
<A HREF = "region.html">region</A> command) radically smaller/larger than the extent
of the atoms you eventually plan to create, e.g. via the
<A HREF = "create_atoms.html">create_atoms</A> command. 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 when using "fixed" boundary conditions
(see the <A HREF = "boundary.html">boundary</A> command). When using "shrink-wrap"
boundary conditions (see the <A HREF = "boundary.html">boundary</A> command), a huge
(mostly empty) box may cause a parallel simulation to lose atoms the
first time that LAMMPS shrink-wraps the box around the atoms.
</P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>An <A HREF = "atom_style.html">atom_style</A> and <A HREF = "region.html">region</A> must have <P>An <A HREF = "atom_style.html">atom_style</A> and <A HREF = "region.html">region</A> must have

14
doc/create_box.txt
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@ -56,6 +56,20 @@ non-zero, then both the x and y dimensions must be periodic.
Similarly, x and z must be periodic if xz is non-zero and y and z must Similarly, x and z must be periodic if xz is non-zero and y and z must
be periodic if yz is non-zero. be periodic if yz is non-zero.
IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
you should not make the lo/hi box dimensions (as defined in your
"region"_region.html command) radically smaller/larger than the extent
of the atoms you eventually plan to create, e.g. via the
"create_atoms"_create_atoms.html command. 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 when using "fixed" boundary conditions
(see the "boundary"_boundary.html command). When using "shrink-wrap"
boundary conditions (see the "boundary"_boundary.html command), a huge
(mostly empty) box may cause a parallel simulation to lose atoms the
first time that LAMMPS shrink-wraps the box around the atoms.
[Restrictions:] [Restrictions:]
An "atom_style"_atom_style.html and "region"_region.html must have An "atom_style"_atom_style.html and "region"_region.html must have

7
doc/read_data.html
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@ -144,8 +144,11 @@ lo/hi values radically smaller/larger than the extent of the atoms.
For example, if your atoms extend from 0 to 50, you should not specify 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 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 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 (mostly empty) box will be sub-optimal for performance when using
parallel simulation to lose atoms the first time that LAMMPS "fixed" boundary conditions (see the <A HREF = "boundary.html">boundary</A>
command). When using "shrink-wrap" boundary conditions (see the
<A HREF = "boundary.html">boundary</A> command), a huge (mostly empty) box may cause
a parallel simulation to lose atoms the first time that LAMMPS
shrink-wraps the box around the atoms. shrink-wraps the box around the atoms.
</P> </P>
<P>The "extra bond per atom" setting should be used if new bonds will be <P>The "extra bond per atom" setting should be used if new bonds will be

7
doc/read_data.txt
View File

@ -141,8 +141,11 @@ lo/hi values radically smaller/larger than the extent of the atoms.
For example, if your atoms extend from 0 to 50, you should not specify 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 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 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 (mostly empty) box will be sub-optimal for performance when using
parallel simulation to lose atoms the first time that LAMMPS "fixed" boundary conditions (see the "boundary"_boundary.html
command). When using "shrink-wrap" boundary conditions (see the
"boundary"_boundary.html command), a huge (mostly empty) box may cause
a parallel simulation to lose atoms the first time that LAMMPS
shrink-wraps the box around the atoms. shrink-wraps the box around the atoms.
The "extra bond per atom" setting should be used if new bonds will be The "extra bond per atom" setting should be used if new bonds will be