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-
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 @@ -164,11 +164,15 @@ 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) diff --git a/doc/dump.txt b/doc/dump.txt index ce43aafdc9..d0c052b01c 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -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)