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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5036 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2010-10-13 21:58:00 +00:00
parent 4c3d42e040
commit 8ba6841a32
2 changed files with 30 additions and 22 deletions
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26
doc/dump.html
View File

@ -139,19 +139,19 @@ this format.
<P>For post-processing purposes the <I>atom</I> and <I>custom</I> text files are
self-describing in the following sense.
</P>
<P>The simulation box bounds are included in each snapshot. For
orthogonal boxes this is formatted as:
<P>The dimensions of the simulation box are included in each snapshot.
For orthogonal simulation boxes this is formatted as:
</P>
<PRE>ITEM: BOX BOUNDS
xlo xhi
ylo yhi
zlo zhi
</PRE>
<P>where xlo,xhi are the bounds of the simulation box in the x-dimension,
and similarly for y and z.
<P>where xlo,xhi are the maximum extents of the simulation box in the
x-dimension, and similarly for y and z.
</P>
<P>For triclinic boxes (non-orthogonal), the tilt factors are also
included, as a 3rd value on each line:
<P>For triclinic simulation boxes (non-orthogonal), the tilt factors are
also included, as a 3rd value on each line:
</P>
<PRE>ITEM: BOX BOUNDS xy xz yz
xlo_bound xhi_bound xy
@ -164,11 +164,15 @@ relationship to other nomenclatures for triclinic geometries,
e.g. using 3 lattice constants <I>a</I>, <I>b</I>, and <I>c</I>, and 3 angles
<I>alpha</I>, <I>beta</I> and <I>gamma</I>.
</P>
<P>IMPORTANT NOTE: As noted above, for triclinic simulation boxes, the 6
box bounds (xlo,xhi,ylo,yhi,zlo,zhi) are actually written to the dump
file as a "bounding box" around the simulation domain, which means
they include the effect of any tilt, which is convenient for many
visualization programs. The bounding box is calculated as follows:
<P>IMPORTANT NOTE: As the notation above indicates, for triclinic
simulation boxes, the 6 box bounds written to the dump file
(xlo_bound,xhi_bound,ylo_bound,yhi_bound,zlo_bound,zhi_bound) are NOT
equivalent to the 6 extents (xlo,xhi,ylo,yhi,zlo,zhi) in the
orthogoonal case. Instead they are the extent in each dimension of
the smallest orthogonal "bounding box" that encapsulates the entire
tricilinc simulation box, including the effects of any tilt. This
bounding box is convenient for many visualization programs and is
calculated as follows:
</P>
<PRE>xlo_bound = MIN(xlo,xlo+xy,xlo+xz,xlo+xy+xz)
xhi_bound = MAX(xhi,xhi+xy,xhi+xz,xhi+xy+xz)

26
doc/dump.txt
View File

@ -129,19 +129,19 @@ this format.
For post-processing purposes the {atom} and {custom} text files are
self-describing in the following sense.
The simulation box bounds are included in each snapshot. For
orthogonal boxes this is formatted as:
The dimensions of the simulation box are included in each snapshot.
For orthogonal simulation boxes this is formatted as:
ITEM: BOX BOUNDS
xlo xhi
ylo yhi
zlo zhi :pre
where xlo,xhi are the bounds of the simulation box in the x-dimension,
and similarly for y and z.
where xlo,xhi are the maximum extents of the simulation box in the
x-dimension, and similarly for y and z.
For triclinic boxes (non-orthogonal), the tilt factors are also
included, as a 3rd value on each line:
For triclinic simulation boxes (non-orthogonal), the tilt factors are
also included, as a 3rd value on each line:
ITEM: BOX BOUNDS xy xz yz
xlo_bound xhi_bound xy
@ -154,11 +154,15 @@ relationship to other nomenclatures for triclinic geometries,
e.g. using 3 lattice constants {a}, {b}, and {c}, and 3 angles
{alpha}, {beta} and {gamma}.
IMPORTANT NOTE: As noted above, for triclinic simulation boxes, the 6
box bounds (xlo,xhi,ylo,yhi,zlo,zhi) are actually written to the dump
file as a "bounding box" around the simulation domain, which means
they include the effect of any tilt, which is convenient for many
visualization programs. The bounding box is calculated as follows:
IMPORTANT NOTE: As the notation above indicates, for triclinic
simulation boxes, the 6 box bounds written to the dump file
(xlo_bound,xhi_bound,ylo_bound,yhi_bound,zlo_bound,zhi_bound) are NOT
equivalent to the 6 extents (xlo,xhi,ylo,yhi,zlo,zhi) in the
orthogoonal case. Instead they are the extent in each dimension of
the smallest orthogonal "bounding box" that encapsulates the entire
tricilinc simulation box, including the effects of any tilt. This
bounding box is convenient for many visualization programs and is
calculated as follows:
xlo_bound = MIN(xlo,xlo+xy,xlo+xz,xlo+xy+xz)
xhi_bound = MAX(xhi,xhi+xy,xhi+xz,xhi+xy+xz)