index out of bounds error with some values of bForwrev about alchemical-analysis HOT 5 CLOSED

Can you provide some sample data to reproduce this? We've not run into this
yet and a fix will be simpler if we can reproduce the problem.

On Wed, Jan 13, 2016 at 2:54 AM, MatteoA [email protected] wrote:

I find that when using certain values with the flag "-f", I get an index
out of bounds error because the array ts in the function dF_t() is one
element longer than expected I found this issue with -f values of 6 or 28
so far

I believe it has to do with the fact the array tf is defined with
numpyarange:
tf = numpyarange(0,1+increment,increment)

(max(nsnapshots)-1)+1 In some cases (like for 6 or 28) it seems that the
'stop' (1+increment) element is included in the array, later on resulting
in a ts array that is one element longer than expected, and with ts[-1]
having a time over the end time of the simulation I imagine it could be a
problem related to the representation of floating numbers, and possibly
replacing arange with linspace might be enough to solve the issue: tf =
numpylinspace(00, 10, n_tf)(max(nsnapshots)-1)+1

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#64.

David Mobley
Associate Professor
Department of Pharmaceutical Sciences
Department of Chemistry
3134B Natural Sciences I
University of California, Irvine
Irvine, CA 92697
[email protected]
work (949) 824-6383
cell (949) 385-2436

from alchemical-analysis.

Of course, here are the xvg files with the first 0.5ns of some data I was looking at:
https://www.dropbox.com/sh/1xngv1t3isx7a23/AACvL9zB6n12lbC78Ywpspy1a?dl=0

from alchemical-analysis.

Should be resolved by #72 . Can you check?

from alchemical-analysis.

Just checked, this seems resolved now indeed.

from alchemical-analysis.

Marking as closed.

from alchemical-analysis.