Re: [AMBER-Developers] namelist

From: case <>
Date: Wed, 17 Mar 2010 18:09:34 -0400

On Wed, Mar 17, 2010, Carlos Simmerling wrote:

> does anyone know if there is a way to know if a user specified a variable in
> the mdin namelist? I'm wondering about making it bullet proof- make sure a
> user doesn't set something that they should not.

Well, you can check to see if the variable has changed from its default value,
which can only happen if the user set it. Here's some pseudo-code:

! set defaults
gbalphaSB = 5.2d0
read (5,cntrl)

if (igb .eq. 8) then
   if (gbalphaSB .ne. 5.2d0) then
      ! print warning/error message, exit if this is fatal
      ! and/or reset the value back to its default, etc.

This won't catch the fact that the user might have set gbalphaSB to its
default value, but that shouldn't do any harm.

> or should I assume that if I say in the manual that a
> variable is ignored unless you run a certain type of calculation, that it's
> ok to silently ignore a user's request to change the value?

We certainly don't trap all irrelevant variables at present, so I wouldn't
feel bad if you add some new "silently ignore" situations.

[I'm not sure if the above is what you are thinking about or not....]

Once the dust settles from Amber11, a good task for someone (!?!) would be
to add more organization and more intelligence to the parts of mdread.f that
try to find bad input. We could have a "expert" mode that would prevent lots
of changes to the defaults unless it were set. There's a little bit of this
in the manual, where users are warned about changing parameters that are not
in bold-face, but I think few people either know about that, or try to follow


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Received on Wed Mar 17 2010 - 15:30:02 PDT
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