[Pw_forum] charge is wrong and system is non-metallic

[Axel Kohlmeyer]

On Wed, 28 Jan 2009, Jonas Baltrusaitis wrote:

JB> I deduce it from the error output (in fact it explicitly says that)
JB> 

it says "charge is wrong", but nothing about the system being 
metallic. ...and of course the GIGO principle applies to Q-E.

JB> Below is an output from the .cif file, obviously NH2 group is 
JB> symmetrical to one another. this somewhat brings me to another 
JB> question I asked earlier about how to use data in .cif files to 
JB> setup an pwscf input. I looked at the lecture notes on QE website 

there are cif parsers/readers/converters around, you just have 
to compile/install one of them and export to cartesian coordinates.

JB> how to use Wyckoff coordinates to setup an input but in this case it 
JB> wasn't useful

perhaps you didn't read it properly?

[...]

JB> loop_
JB> _symmetry_equiv_pos_as_xyz
JB>   'x,y,z'
JB>   '1/2-y,1/2-x,z'
JB>   'y,-x,-z'
JB>   '1/2-x,1/2+y,-z'
JB>   '-x,-y,z'
JB>   '1/2+y,1/2+x,z'
JB>   '-y,x,-z'
JB>   '1/2+x,1/2-y,-z'
JB> loop_

well, doesn't this block provide all you need?
i don't know CIF files very well, but with a little
bit of common sense once can deduce that you have to
apply the listed transformations to the coordinates 
below. then just remove the coordinates that map onto 
the same position (remember to consider PBC) and you 
should be done. can be done in a small script or with 
a piece of paper and a pencil in not too much time. 

[...]

JB> _atom_site_label
JB> _atom_site_fract_x
JB> _atom_site_fract_y
JB> _atom_site_fract_z
JB> C   0.00000   0.50000   0.32900
JB> O   0.00000   0.50000   0.59700
JB> N   0.14550   0.64550   0.17910
JB> H1   0.25610   0.75610   0.28550
JB> H2   0.14290   0.64290  -0.03700
JB> 


cheers,
  axel.

-- 
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Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
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