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Bug #452

eneconv error with -dt: missing energy sums

Added by Teemu Murtola over 9 years ago. Updated over 9 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

If one tries to use eneconv -dt with git master (tested with 4.0.99-dev-20100621-d101dcc) to remove some frames from an .edr file, one gets a lot of warnings about missing energy sums, but only for every second frame or so. gmxdump on the original .edr file shows that all sums are present in the file for all frames, so this seems like a bug in eneconv. This also affects the output: the sums are not accumulated over the skipped frames as they should. If -dt is not used, no warnings occur.

I'll attach a .tpr file generated from spc216.gro that runs for 1000 steps and writes energies every 100 frames. Running that, and then running
eneconv -f ener.edr -dt 1
outputs (initial parts skipped):

Reading energy frame 0 time 0.000
Continue writing frames from t=0, step=0
Reading energy frame 2 time 0.400
WARNING: missing energy sums at time 0.400000
Reading energy frame 4 time 0.800
WARNING: missing energy sums at time 0.800000
Reading energy frame 7 time 1.400
WARNING: missing energy sums at time 1.400000
Reading energy frame 9 time 1.800
WARNING: missing energy sums at time 1.800000
Last energy frame read 10 time 2.000
Last step written from test.edr: t 2, step 1000

Last frame written was at step 1000, time 2.000000
Wrote 3 frames

gmxdump -e fixed.edr shows that for the last frame, the sums are identical as in the original .edr.

test.tpr (31 KB) test.tpr Simple .tpr file for reproducing the bug. Teemu Murtola, 06/22/2010 11:23 AM

History

#1 Updated by Teemu Murtola over 9 years ago

Created an attachment (id=479)
Simple .tpr file for reproducing the bug.

#2 Updated by Berk Hess over 9 years ago

I fixed it.

Berk

#3 Updated by Rossen Apostolov over 9 years ago

Thanks Berk, closing the bug.

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