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Replicate bbox from Chris Knight

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Stan Moore
2017-11-06 11:31:43 -07:00
parent 39df9f5d94
commit e337db4059
2 changed files with 418 additions and 76 deletions
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doc/src/replicate.txt
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@ -10,9 +10,11 @@ replicate command :h3
[Syntax:]
replicate nx ny nz :pre
replicate nx ny nz {keyword} :pre
nx,ny,nz = replication factors in each dimension :ul
nx,ny,nz = replication factors in each dimension :ulb
optional {keyword} = {bbox} :l
{bbox} = only check atoms in replicas that overlap with a processor's subdomain :ule
[Examples:]
@ -43,6 +45,12 @@ file that crosses a periodic boundary should be between two atoms with
image flags that differ by 1. This will allow the bond to be
unwrapped appropriately.
The optional keyword {bbox} uses a bounding box to only check atoms
in replicas that overlap with a processor's subdomain when assigning
atoms to processors, and thus can result in substantial speedups for
calculations using a large number of processors. It does require
temporarily using more memory.
[Restrictions:]
A 2d simulation cannot be replicated in the z dimension.