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Re: [abinit-forum] How to get the xred?


Chronological Thread 
  • From: Quan Phung Manh <manhquank9@gmail.com>
  • To: forum@abinit.org
  • Subject: Re: [abinit-forum] How to get the xred?
  • Date: Mon, 1 Feb 2010 23:29:35 +0700
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Dear Haiou,

This is a real monocinic ZrO2. After converting the space group into P1, I got this

acell 5.2130 4.9670 5.3180 Angstrom
angdeg 90.0000 100.1600 90.0000       

xred
Zr    0.27580   0.04110   0.20820
O     0.07030   0.33590   0.34060
O     0.44230   0.75490   0.47890
Zr    0.72420   0.54110   0.29180
O     0.92970   0.83590   0.15940
O     0.55770   0.25490   0.02110
Zr    0.72420   0.95890   0.79180
O     0.92970   0.66410   0.65940
O     0.55770   0.24510   0.52110
Zr    0.27580   0.45890   0.70820
O     0.07030   0.16410   0.84060
O     0.44230   0.74510   0.97890

You can check this geometry by running Abinit and check if this system has space group P21/C

Best regards,

2010/2/1 haiou haiou <haiouwyj@gmail.com>
Dear Manh Quan, Martin and Hanyu
     Thank you all very much for your valuable help. I want to calculate Response Function of ZrO2.
     I got another .cif file of ZrO2 as following. For the monoclinic ZrO2, the xred can be set as
     xred   0.2758 0.0411 0.2082
            0.0703 0.3359 0.3406
            0.4423 0.7549 0.4789
     Is it right?



#------------------------------------------------------------------------------
#$Date: 2009-04-25 19:45:30 +0000 (Sat, 25 Apr 2009) $
#$Revision: 684 $
#$URL: svn://cod.ibt.lt/cod/cif/2/2300203.cif $

#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/. The original data for this entry
# were provided by IUCr Journals, http://journals.iucr.org/.
#
# The file may be used within the scientific community so long as
# proper attribution is given to the journal article from which the
# data were obtained.
#
data_2300203
loop_
_publ_author_name
'Wood, Ian G.'
'Vo\<cadlo, Lidunka'
'Dobson, David P.'
'Price, G. David'
'Fortes, A. D.'
'Cooper, Frances J.'
'Neale, J. W.'
'Walker, Andrew M.'
'Marshall, W. G.'
'Tucker, M. G.'
'Francis, D. J.'
'Stone, H. J.'
'McCammon, C. A.'
_publ_section_title
;
 Thermoelastic properties of magnesiow\"ustite,
 (Mg~1{-~<i>x</i>}Fe~<i>x~</i>)O: determination of the
 Anderson--Gr\"uneisen parameter by time-of-flight neutron powder
 diffraction at simultaneous high pressures and temperatures
;
_journal_issue                   5
_journal_name_full               'Journal of Applied Crystallography'
_journal_page_first              886
_journal_page_last               896
_journal_volume                  41
_journal_year                    2008

_chemical_formula_sum            'O2 Zr'
_chemical_formula_weight         123.22
_chemical_name_systematic        ' ?'
_space_group_IT_number           14
_symmetry_cell_setting           monoclinic
_symmetry_space_group_name_Hall  '-P 2ybc'
_symmetry_space_group_name_H-M   'P 1 21/c 1'
_cell_angle_alpha                90.0
_cell_angle_beta                 100.16(9)
_cell_angle_gamma                90.0

_cell_formula_units_Z            4
_cell_length_a                   5.213(5)
_cell_length_b                   4.967(6)
_cell_length_c                   5.318(5)
_cell_volume                     135.53223
_[local]_cod_data_source_file    ks5172.cif
_[local]_cod_data_source_block   PRL47388_ZRO2_phase_3
_[local]_cod_cif_authors_sg_H-M  P21/c
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 +x,+y,+z
2 -x,+y+1/2,-z+1/2
-1 -x,-y,-z
-2 +x,-y+1/2,+z+1/2
loop_
_atom_type_symbol
O
ZR
loop_
_atom_site_type_symbol

_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_thermal_displace_type
_atom_site_occupancy
ZR ZR1 0.2758 0.0411 0.2082 0.01 Uiso 1.0
O O2 0.0703 0.3359 0.3406 0.01 Uiso 1.0
O O3 0.4423 0.7549 0.4789 0.01 Uiso 1.0

2010/2/1 Quan Phung Manh <manhquank9@gmail.com>

Dear Haiou,
What do you intend to do? If you're looking for the structure of ZrO2, please try other .cif file. This .cif file was used in phase transition of ZrO2-YO1.5 and I think this is not the structure of ZrO2. ZrO2 crystal have FM-3M or P21-C symmetry group, not R3M (I found that) of your .cif file.

Best regards,

2010/1/31 haiou <haiouwyj@gmail.com>

hi, everyone
   I got a .cif file of ZrO2 as following. The atomic coordinates are at the

end of the file. As for ZrO2 there are three atoms, but only two atomic

coordinates are given in this .cif file. Can anybody tell me why? What is the

 coordinates of the third atom?
   Thank you for your kind help!

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

---
#$Date: 2009-11-18 14:56:34 +0000 (Wed, 18 Nov 2009) $
#$Revision: 858 $
#$URL: svn://cod.ibt.lt/cod/cif/2/2101234.cif $
#---------------------------------------------------------------------------

---
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/. The original data for this entry
# were provided by IUCr Journals, http://journals.iucr.org/.
#
# The file may be used within the scientific community so long as
# proper attribution is given to the journal article from which the
# data were obtained.
#
data_2101234
loop_
_publ_author_name
'Yashima, M.'
'Sasaki, S.'
'Kakihana, M.'
'Yamaguchi, Y.'
'Arashi, H.'
'Yoshimura, M.'
_publ_section_title
;
 Oxygen-induced structural change of the tetragonal phase around the
 tetragonal--cubic phase boundary in ZrO~2~--YO~1.5~ solid solutions
;
_journal_issue                   6
_journal_name_full               'Acta Crystallographica Section B'
_journal_page_first              663
_journal_page_last               672
_journal_volume                  50
_journal_year                    1994
_chemical_formula_moiety         'O2 Zr1'
_chemical_formula_sum            'O2 Zr'
_[local]_cod_chemical_formula_sum_orig 'O2 Zr1'
_symmetry_cell_setting           cubic
_symmetry_space_group_name_Hall  Fm3m
_symmetry_space_group_name_H-M   '-F 4 2 3'
_cell_angle_alpha                90.
_cell_angle_beta                 90.
_cell_angle_gamma                90.
_cell_formula_units_Z            4
_cell_length_a                   5.14335
_cell_length_b                   5.14335
_cell_length_c                   5.14335
_cell_volume                     51.83
_[local]_cod_data_source_file    oh0040.cif
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Zr .0 .0 .0
O .25 .25 .25



--
PHUNG, Manh Quan
Center for Computational Chemistry
Faculty of Chemistry - College of Science - VNU, Hanoi
Tel: 0439331898 - 01663922302

Samuel Goldwyn  - "I'm willing to admit that I may not always be right, but I am never wrong."




--
PHUNG, Manh Quan
Center for Computational Chemistry
Faculty of Chemistry - College of Science - VNU, Hanoi
Tel: 0439331898 - 01663922302

Stephen Leacock  - "I detest life-insurance agents: they always argue that I shall some day die, which is not so."


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