[AMBER-Developers] Ptraj Trajectory File Abstraction

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 25 Jan 2010 12:31:39 -0500

Hi All,

Just a quick note to let you know I have begun to implement the file
abstraction stuff I talked about at the meeting. I have tested the code with
intel 11.1 compilers (serial/parallel both w/wo netcdf). The changes should
be almost invisible to everyone, but they do represent a major rewrite of a
significant portion of some important code. That being the case please
report any bugs or problems you find to me ASAP so I can zap them.

FYI the code may print out messages like:

WARNING in safe_close(): Attempting to close a NULL FILE and buffer!

or some other warning related to file closing. These warnings are harmless
and result from the transition from the file stack to the new abstraction.
Specifically ptraj now makes sure that all files are closed and all memory
freed after a stop (either the trajectories have been read through or an
error has occurred), which in some cases means it tries to close an already
closed file. This is in the process of being cleaned up.

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Received on Mon Jan 25 2010 - 10:00:02 PST
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