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Re: [abinit-forum] xred


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  • From: Alain Jacques <ajs.jacques@gmail.com>
  • To: forum@abinit.org
  • Subject: Re: [abinit-forum] xred
  • Date: Sat, 28 Nov 2009 13:49:43 +0100
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Hello Sanjeev

Sanjeev Kumar Gupta wrote:
9c021210911280433n7be0acbdi4473cd27eecbeab1@mail.gmail.com" type="cite">Thank You very much sir for kind help.
Please clear me some of points.

1. What is .cif file? How to I get?
2. These input, Where i have to give to obtain xred?

.cif files are crystallographic information files as described in http://www.iucr.org/resources/cif - the workhorse of all crystallographers.
To answer your 2 questions, here is a short example - the cif file of the scandium hexagonal crystal adapted from Wyckoff:

#------------------------------------------------------------------------------
#$Date: 2008-03-10 08:25:41 +0000 (Mon, 10 Mar 2008) $
#$Revision: 255 $
#$URL: svn://cod.ibt.lt/cod/cif/9/9008514.cif $
#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/
#
# All data on this site have been placed in the public domain by the
# contributors.
#
data_9008514
loop_
_publ_author_name
'Wyckoff R W G'
_publ_section_title
;
 Second edition. Interscience Publishers, New York, New York
 Hexagonal closest packed, hcp, structure
;
_journal_name_full               'Crystal Structures'
_journal_page_first              7
_journal_page_last               83
_journal_volume                  1
_journal_year                    1963
_chemical_formula_sum            Sc
_chemical_name_mineral           Scandium
_symmetry_space_group_name_H-M   'P 63/m m c'
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                120
_cell_length_a                   3.3090
_cell_length_b                   3.3090
_cell_length_c                   5.2733
_cell_volume                     50.004
loop_
_symmetry_equiv_pos_as_xyz
x,y,z
-x,-x+y,1/2+z
x,x-y,1/2-z
-x+y,-x,1/2-z
x-y,x,1/2+z
-y,-x,z
y,x,-z
y,-x+y,-z
-y,x-y,z
x-y,-y,1/2+z
-x+y,y,1/2-z
x,y,1/2-z
-x,-y,1/2+z
x,x-y,z
-x,-x+y,-z
x-y,x,-z
-x+y,-x,z
y,x,1/2+z
-y,-x,1/2-z
-y,x-y,1/2-z
y,-x+y,1/2+z
-x+y,y,z
x-y,-y,-z
-x,-y,-z
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Sc 0.33333 0.66667 0.25000

#------------------------------------------------------------------------------

so, for 1. ... there are many sources of cif files, free or commercial - have a look on http://www.crystallography.net/
and for 2. ... for the reduced coordinates - look at the end of the file Sc 0.33333 0.66667 0.25000
And if you obtain data in other formats like pdb, there are several converter.


Kind regards,

Alain



9c021210911280433n7be0acbdi4473cd27eecbeab1@mail.gmail.com" type="cite">
Kind Regards
Sanjeev Gupta

2009/11/28 Josef Zwanziger <jzwanzig@gmail.com>
Well, xred is crystallographic data. From a .cif file, the space group number, Z, and the atom positions of the asymmetric unit (input as xred) will be enough for abinit to fill in the rest.

Sent from my iPod


On 2009-11-28, at 5:49, Sanjeev Kumar Gupta <skgupta.physics@gmail.com> wrote:

Dear Sir,

Can you tell me how I can obtain xred for any system? Is any scripts which can convert crystallographic data into abinit xred?

Thanks
Sanjeev GUPTA

--
S. K. Gupta
PhD Student,
Dept. of Physics, Bhavnagar University.
Bhavnagar, 364 022., Gujarat, India.






--
S. K. Gupta
PhD Student,
Dept. of Physics, Bhavnagar University.
Bhavnagar, 364 022., Gujarat, India.







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