VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon May 25 2009 - 10:05:30 CDT

On Mon, 2009-05-25 at 00:04 -0700, Rob wrote:

> Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu) wrote:

> I want to read formatted data: the positions of all atoms in the
> unit cell; this also includes relaxation data (consecutive atom positions
> as the DFT code relaxes their positions), which results in a 'relaxation movie'.
> I also like to load unformatted data as the charge densities.

unformatted data is a PITA unless it uses some self-describing encoding.
abinit is fortran, right? then you have the additional (negative) fun
of having to deal with endianness and fortran recordlength indicators
or different size between different fortran compilers or even the same
compilers used with different flags. you can have a look at the
dcdplugin.c source for a fairly extensive example of how this is done.

> All this I have worked out for the VASP plugin; so I hope I can apply
> the same reasoning to the ABINIT plugin.

i don't remember seeing any binary i/o in them last time
i exorcised the non-portable c++-ism in them.

> > you don't have to compile VMD to compile the plugins. still
> > with over two years since the last release you don't want to
> > start working off an antiquated version of the code.
>
> I understand;
> meanwhile I have installed the beta3 release and I got the plugins
> from CVS. I hope that combination is alright!?!

yep. that should do. as i wrote before, it matters the most if you
want to include code that utilizes the new features. since it looks
like you don't, the main difference is that you should consider using
vmdcon_printf() with the proper priorities for output that should go
to the console. vmdcon will most likely not being enabled for 1.8.7
but it hope that it will be enabled for the next release.

thanks,
    axel.

> Rob.
>
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.