[AMBER-Developers] Fun with ntx, irest, and init

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 11 Jan 2011 17:49:06 -0500

Hi All,

In my efforts to add reading and writing of a new Netcdf restart
format to sander I've had to work closely with the variables ntx,
irest, and init and had some general comments/questions regarding

ntx is used all over the place. In getcor() ntx 1, 5, and 7 are
probably the values everyone uses (5 and 7 seem to have identical
behavior). ntx=2 reads unformatted coordinates, ntx=3 reads
unformatted coords and forces, and ntx=4 reads unformatted coords and
velocities. If ntx=6 the code follows ntx=4, then will attempt to read
box coords using rfree(); however rfree() seems to expect the file to
be formatted while the coord file has been opened unformatted, so ntx
6 is effectively broken (and by the time getcor() has been called the
box info has been read by the ewald routines anyway). Should ntx=6 be

Also, I was thinking of making ntx=8 netcdf restart coord, and ntx=9
netcdf restart coords and velocities. ntx is open, but there is one
reference to ntx=9 in ew_box.f (in firstbox() subroutine) that seems
to consider ntx=9 a formatted restart. However, I can't find any other
references to ntx=9. Does anyone have any more info, or any reason why
I shouldn't use 8 and 9?

Init is set based on irest (irest=0 is init=3 and irest=1 is init=4)
and appears to be used solely in runmd.f as far as I can tell. Is the
reason init is used instead of irest just a case of "If it ain't broke
don't fix it" or is there something else I am missing?

Lastly, are there any objections to me putting this netcdf restart
format into the git tree?


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Received on Tue Jan 11 2011 - 15:00:04 PST
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