[Pw_forum] Re: Xcrysden error

[Axel Kohlmeyer]

On Sat, 14 Apr 2007, Eduardo Ariel Menendez P wrote:

EAM> 
EAM> Hi Tone,
EAM> 
EAM> I have just found that the computers at ICTP have defined the decimal
EAM> point as ',' instead of '.'. This may affect numerical operations.

aiiiih! 

another victim of NLS!
why-oh-why do people insist on this nonsense??

anyway, enough ranting. i can only _strongly_
recommend to use either (depending on your shell)
export LC_ALL=C
or
setenv LC_ALL C
whenever you do scientific work. this is only
a rather harmless example. not so long ago i
came across an example, where a simulation program
would give a completely wrong output depending on
whether one would do the calculation in the native
or the generic 'C' locale.

tone,
it might be a good idea to force LC_ALL=C inside of
xcrysden before executing any ancillary scripts or
executables (and the same would be true for PWGui).

EAM> 
EAM> In the case of the example CH3Rh111, I did
EAM> pwo2xsf.sh -ic CH3Rh111.out > CH3Rh111.xsf
EAM> 
EAM> Examining de file CH3Rh111.xsf I see this
EAM> PRIMVEC
EAM>    5,2917700000    0,0000000000    0,0000000000
EAM>    0,0000000000    0,0000000000    0,0000000000
EAM>    0,0000000000    0,0000000000   10,5835400000
EAM> 
EAM> They are numbers with decimal point ',' and the second lattice vector that
EAM> was (-.5000, .8660,.0000) in the .out file, is converted into (0,0,0)
EAM> 
EAM> I am afraid that I do not have control of the decimal point without root
EAM> priviledges (correct me if I can change it), and that I would have to

you don't need root priviledges to change this. just set LC_ALL to the 
proper value (i.e. C in this case). it might be a good idea for the 
scientific (sic!) computer section of ICTP (cc'd) to think about this 
in a more general way.

EAM> appeal to the UN Secratary to make the ICTP system manager to change this.
EAM> Is there any solution at the level of my local copy of xcrysden?

cheers,
   axel.


EAM> 
EAM> Thanks,
EAM> Eduardo
EAM> 
EAM> >
EAM> > Any kind of file-format is converted to XSF file. The xsf2xsf is some
EAM> > internal xcrysden's filter. Because the any-to-xsf conversion is always
EAM> > there, the xsf2xsf filter is always used. You have the problem with
EAM> > xsf2xsf (don't know why), so please try to see manually what is going
EAM> > on, i.e.:
EAM> >
EAM> > pwo2xsf.sh -lc my_pwscf_output_file.out > file.xsf
EAM> > $XCRYSDEN_TOPDIR/bin/xsf2xsf file.xsf output.xsf 3
EAM> >
EAM> > The first line converts pwscf output file to xsf file, and then you need
EAM> > to check what is going on with the xsf2xsf (2nd line).
EAM> >
EAM> > Regards, Tone
EAM> >
EAM> >
EAM> >
EAM> _______________________________________________
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EAM> http://www.democritos.it/mailman/listinfo/pw_forum
EAM> 

-- 
=======================================================================
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
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If you make something idiot-proof, the universe creates a better idiot.