From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Mon Jul 20 2009 - 07:12:04 CDT
How does the harmonic position "constraints" module (with "consref" and
"conRef") deal with periodic conditions that use "WrapAll on"?
Conceptionally, let us assume we have an ion very close to the box
boundary, focusing on one dimension only:
- box boundaries are $x-$a and $x, where $x and $a are positive floats
- an ion has position $x-$eps, to which it is weakly harmonically
"constrained" with 0<$eps<<$a.
Now, let us assume, having ended a first run, whose final restart file
is such that the ion is at $x-$a+$eps, the opposite side of the box.
The next run has to use the original "consRef" file with the ion
reference set to $x-$eps (see *note in the bottom).
In which direction does the "constraints" module "pull" the ion? Is it
smart enough to pull it into the negative direction, or will it pull it
into the positive direction?
*note: I know that I could simply change my "consRef" file to the last
restart file, but that would complicate the way my wrapper code works.
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