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document how using shrink-wrap boundaries can cause lost atoms in parallel

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Axel Kohlmeyer 2016-09-11 14:48:37 -04:00
parent d70e051ecd
commit a64eb330e3
1 changed files with 9 additions and 1 deletions
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10
doc/src/boundary.txt
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@ -54,7 +54,15 @@ allow for lost atoms.
For style {s}, the position of the face is set so as to encompass the For style {s}, the position of the face is set so as to encompass the
atoms in that dimension (shrink-wrapping), no matter how far they atoms in that dimension (shrink-wrapping), no matter how far they
move. move. Note that when the difference between the current box dimensions
and the shrink-wrap box dimensions is large, this can lead to lost
atoms at the beginning of a run when running in parallel. This is due
to the large change in the (global) box dimensions also causing
significant changes in the individual sub-domain sizes. If these
changes are farther than the communication cutoff, atoms will be lost.
This is best addressed by setting initial box dimensions to match the
shrink-wrapped dimensions more closely, by using {m} style boundaries
(see below).
For style {m}, shrink-wrapping occurs, but is bounded by the value For style {m}, shrink-wrapping occurs, but is bounded by the value
specified in the data or restart file or set by the specified in the data or restart file or set by the