Re: [AMBER-Developers] namelist

From: Volodymyr Babin <>
Date: Wed, 17 Mar 2010 23:17:55 -0400 (EDT)

> However, IF a serious effort was to be undertaken then in addition to
> supporting expert and novice modes, we could go whole hog and create a
> whole new input structure which handles a complete project and is based on
> XML.

IMHO, XML shines for *documents*, (like, for example, prmtop) but
not for "control"; scripting language is good for "control", and if
it was not fortran, I would go this way.

> Please redirect your OOhhh my its computer science comments
> directly to /dev/null.

But think again, XML is for markup (structuring), while something
more like "control" is more natural for the mdin (lua interpreter?)

> The Columbus quan chem package has been down this road
> and created a readable, single input file, completely backward
> compatible Columbus Input Markup Language.
> I bet even u can read it:
> <ciml>
> <molecule>
> <description>
> CH2 (4s5p1d/5s1p)->(2s2p1d/3s1p) (1.09A, 80). Christiansen ecp. From
> argos.txt.
> </description>
> <symmetry> C2v </symmetry>
> <geometry>
> <units> bohr </units>
> C 0.0 0.0 0.0
> H 0.0 1.32401540 1.57790010
> H 0.0 -1.32401540 1.57790010
> </geometry>
> </molecule>
> <basis>

this definitely will work; but truly long-term strategy would be a
scripting language, using your example:

m = new molecule(XML that describes the molecule goes here);

integrator = new leapfrog();


OTOH, I am not suggesting doing anything like that to sander.



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Received on Wed Mar 17 2010 - 20:30:04 PDT
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