[Wien] Initialization issue with core leak out of sphere And RMT Sums Greater than NN-DIST

Ghosh SUDDHASATTWA ssghosh at igcar.gov.in
Mon Dec 5 12:59:13 CET 2011


As Dr. Blaha said, 
Since it is a rhombohedral system, you have to use the lattice parameters
for hexagonal setting and atomic positions in rhombohedral coordinates
Your cif file is in hexagonal setting (pl see it is R-3m:h) 
Convert it into R-3m:r using Bilbao server programs 

Cheers 




-----Original Message-----
From: wien-bounces at zeus.theochem.tuwien.ac.at
[mailto:wien-bounces at zeus.theochem.tuwien.ac.at] On Behalf Of Qiwen YAO
Sent: Monday, December 05, 2011 4:58 PM
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] Initialization issue with core leak out of sphere And
RMT Sums Greater than NN-DIST

Dear Ghosh, Peter and Sharat ,

Thank for your responds, particularly Ghosh's detailed respond allows me to
go further.

Now, I put the lufe2o4.cif  file in the directory and deleted the old struct
file in the working directory, went to the StructGen in w2web, it indeed
sees a file lufe2o4.cif there, so I highlighted the cif file (by clicking on
the round circle next to the file name - the black dot stays there afterward
- means that the file has been selected. I then clicked on "Use selected
CIF/TXT file" - but nothing happened- except that the page was sort of
refreshed and the cif file has been dis-selected, so
 I repeated the operation again - by selected the file, and click on the
button "Use selected CIF/TXT file" - and the same thing happened - I was not
directed to a new (supposedly structural ) page. Does this mean that my
w2web isn't installed properly or, is there anything I didn't do correctly? 

Or is there something wrong with the cif file?

Thank you,
Wen

Here below is the cif file - in case you want to look at it:

#####################################################
############################################################################
##
#
#
# Fe-Lu-O          # LuFe2O4                                       # 1405830
#
#
#
############################################################################
##
#
#
#                           Pearson's Crystal Data
#
#      Crystal Structure Database for Inorganic Compounds (on CD-ROM)
#
#                              Release 2010/11
#
#                  Editors: Pierre Villars and Karin Cenzual
#
#
#
#   Copyright (c) ASM International & Material Phases Data System (MPDS),
#
# Switzerland & National Institute for Materials Science (NIMS), Japan, 2010
#
#  (Data generated pre-2002: Copyright (c) ASM International & MPDS & NIMS;
#
#             post-2001: Copyright (c) ASM International & MPDS)
#
#                   All rights reserved. Version 2010.06
#
#
#
#   This copy of Pearson's Crystal Data is licensed to:
#
#   Hiroko Nakajima, National Institute for Materials Science
#
#
#
############################################################################
##

data_1405830
_audit_creation_date                     2011-12-05
_audit_creation_method
;
Pearson's Crystal Data browser
;
#_database_code_PCD                      1405830

# Entry summary

_chemical_formula_structural             LuFe2O4
_chemical_formula_sum                    Fe2LuO4
_chemical_name_mineral                   ?
_chemical_compound_source                ?
_chemical_name_structure_type            (Eu0.5Yb0.5)Fe2O4,hR21,166
_chemical_formula_weight                 350.7
_chemical_melting_point                  ?

# Bibliographic data

_publ_section_title                      'Structures of LuFeCoO4 and
LuFe2O4'
_journal_coden_ASTM                      ACSCEE
_journal_year                            1990
_journal_volume                          46
_journal_page_first                      1917
_journal_page_last                       1918
_journal_language                        English
loop_
 _publ_author_name
 _publ_author_address
'Isobe M.'
;
National Institute of Research in Inorganic Materials
?
Tsukuba / Ibaraki
Japan
;
'Kimizuka N.'
;
National Institute of Research in Inorganic Materials
?
Tsukuba / Ibaraki
Japan
;
'Ilda J.'
;
National Institute of Research in Inorganic Materials
?
Tsukuba / Ibaraki
Japan
;
'Takekawa S.'
;
National Institute of Research in Inorganic Materials
?
Tsukuba / Ibaraki
Japan
;

# Standardized crystallographic data

_cell_length_a                           3.4406
_cell_length_b                           3.4406
_cell_length_c                           25.28
_cell_angle_alpha                        90
_cell_angle_beta                         90
_cell_angle_gamma                        120
_cell_volume                             259.2
_cell_formula_units_Z                    3
_symmetry_Int_Tables_number              166
_symmetry_space_group_name_H-M           'R-3m h'
loop_
 _symmetry_equiv_pos_site_id
 _symmetry_equiv_pos_as_xyz
 1 'x, y, z'
 2 '-x+y, -x, z'
 3 '-x+y, y, z'
 4 '-x, -x+y, -z'
 5 '-x, -y, -z'
 6 '-y, -x, z'
 7 '-y, x-y, z'
 8 'x, x-y, z'
 9 'x-y, -y, -z'
 10 'x-y, x, -z'
 11 'y, -x+y, -z'
 12 'y, x, -z'
 13 '0.66667+x, 0.33333+y, 0.33333+z'
 14 '0.66667-x+y, 0.33333-x, 0.33333+z'
 15 '0.66667-x+y, 0.33333+y, 0.33333+z'
 16 '0.66667-x, 0.33333-x+y, 0.33333-z'
 17 '0.66667-x, 0.33333-y, 0.33333-z'
 18 '0.66667-y, 0.33333-x, 0.33333+z'
 19 '0.66667-y, 0.33333+x-y, 0.33333+z'
 20 '0.66667+x, 0.33333+x-y, 0.33333+z'
 21 '0.66667+x-y, 0.33333-y, 0.33333-z'
 22 '0.66667+x-y, 0.33333+x, 0.33333-z'
 23 '0.66667+y, 0.33333-x+y, 0.33333-z'
 24 '0.66667+y, 0.33333+x, 0.33333-z'
 25 '0.33333+x, 0.66667+y, 0.66667+z'
 26 '0.33333-x+y, 0.66667-x, 0.66667+z'
 27 '0.33333-x+y, 0.66667+y, 0.66667+z'
 28 '0.33333-x, 0.66667-x+y, 0.66667-z'
 29 '0.33333-x, 0.66667-y, 0.66667-z'
 30 '0.33333-y, 0.66667-x, 0.66667+z'
 31 '0.33333-y, 0.66667+x-y, 0.66667+z'
 32 '0.33333+x, 0.66667+x-y, 0.66667+z'
 33 '0.33333+x-y, 0.66667-y, 0.66667-z'
 34 '0.33333+x-y, 0.66667+x, 0.66667-z'
 35 '0.33333+y, 0.66667-x+y, 0.66667-z'
 36 '0.33333+y, 0.66667+x, 0.66667-z'
loop_
 _atom_type_symbol
 _atom_type_oxidation_number
 O 0
 Fe 0
 Lu 0
loop_
 _atom_site_label
 _atom_site_type_symbol
 _atom_site_Wyckoff_symbol
 _atom_site_symmetry_multiplicity
 _atom_site_fract_x
 _atom_site_fract_y
 _atom_site_fract_z
 _atom_site_occupancy
 O1 O c 6 0 0 0.1281 1
 Fe Fe c 6 0 0 0.21518 1
 O2 O c 6 0 0 0.2926 1
 Lu Lu a 3 0 0 0 1


_exptl_crystal_colour                    ?
_exptl_crystal_density_meas              ?
_cell_measurement_temperature            295
_cell_measurement_radiation              'X-rays, Mo Ka'
_cell_measurement_wavelength             0.71073
_cell_measurement_reflns_used            18
_diffrn_ambient_temperature              295
_diffrn_measurement_device               'automatic diffractometer'
_diffrn_measurement_device_type          'Enraf-Nonius CAD4'
_diffrn_radiation_type                   'X-rays, Mo Ka'
_diffrn_radiation_wavelength             0.71073
_diffrn_reflns_number                    564
_exptl_absorpt_coefficient_mu            36.56
_exptl_absorpt_correction_type           yes
_computing_structure_solution
'starting values derived from related structure'

_refine_ls_number_parameters             ?
_refine_ls_number_reflns                 480
_refine_ls_R_factor_all                  0.029
_refine_ls_wR_factor_all                 0.031
_computing_structure_refinement          SDP

# End of data set 1405830
###########################################

------Original Message------
From:"Ghosh SUDDHASATTWA"<ssghosh at igcar.gov.in>
To:"'A Mailing list for WIEN2k users'"<wien at zeus.theochem.tuwien.ac.at>
Cc:
Subject:Re: [Wien] Initialization issue with core leak out of sphere And RMT
Sums Greater than NN-DIST
Date:12/05/2011 04:18:52 PM(+0530)
>Do the following 
>1. Import the cif into struct file by using cif2struct 
>
>2. use w2web to enter the atomic positions (do not enter Z) 
>
>Check R0 in the struct file after initialization. 
>
>Moreover, see the UG for entering data for rhombohedral systems. 
>
>Convert the R-3m:r to R-3m:h using Bilbao server (alternative settings
>program) and use the atomic positions accordingly
>
>Cheers
>
>
>-----Original Message-----
>From: wien-bounces at zeus.theochem.tuwien.ac.at
>[mailto:wien-bounces at zeus.theochem.tuwien.ac.at] On Behalf Of Qiwen YAO
>Sent: Monday, December 05, 2011 3:55 PM
>To: A Mailing list for WIEN2k users
>Subject: [Wien] Initialization issue with core leak out of sphere And RMT
>Sums Greater than NN-DIST
>
>Dear all,
>I have been facing a few compounds that I am unable to do the
initialization
>(using w2web) for the calculation.
>
>The problem is:
>I was facing both "core leak out of sphere, and  RMT Sums Greater than
>NN-DIST" at the same time.
>
>A recent example: I am trying to do an calculation initialization on the
>LuFe2O4  (R-3m group) crystal (cell parameters are from the Pearson's
>Crystal Data sheet 382676, a=b=0.3435nm, c=2.525nm, Alpha=Beta=90 degree,
>Theta=120 degree. Atomic positions:
>O1: 0  0  0.1295 
>Fe:  0  0  0.2141 
>O2: 0  0  0.2914 
>Lu:  0  0  0 
>).
>
>Using the WIEN default RMT values and the default ENERGY to separate core
>and valence states (-6) , I was facing core electrons leak out of MT-sphere
>message for all four atoms. So I go back to the <x start> step and change
>the separation energy to the lowest possible value (-10 in this case) - if
>going any lower than -10, I will be seeing the error message after running
><x start>, like these:
>
>forrtl: severe (24): end-of-file during read, unit -4, file stdin
>error: command   /home/wen/WIEN2K11/wien2k11install/lstart lstart.def
>failed
>
>So, the natural step I took next is to increase the RMT values for the
atoms
>correspondingly (according to each atom's core leak value). Then I am
facing
>an another problem:  If I am to increase the RMT values too large, then in
>the <x nn> step I will be seeing errors like 
>
>ERROR !!!!!!!!!!!!!!!
> RMT(  1)=0.53000 AND RMT(  1)=0.53000
> SUMS TO 1.06000 GT NNN-DIST= 0.84061
>
>But if the RMT value is not increased enough then the core leaking message
>will still be there.
>
>So how would I solve such problems? I have been facing these for a few
>compounds - for example, the other compound I tried was BiAlO3 which would
>lead me to the same bottle-neck problem.
>
>Is there an automatic approaching way that I can take to get rid of both
>error message at the same time? For cases like these, if there is no
>practical solution to the initialization would that means the unit cell
>parameters were out of touch (reality)?
>
>Thank you for reading. I have been searching the archive for a solution but
>no luck.
>
>Kind regards,
>Wen
>
>**********************************************************
>
>Dr QiWen YAO
>JSPS Fellow
>Multifunctional Materials Group
>Optical and Electronic Materials Unit
>Environment and Energy Materials Research Division
>
>National Institute for Materials Science
>
>1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
>Phone: +81-29-851-3354, ext. no. 6482, Fax: +81-29-859-2501
>
>**********************************************************
>
>_______________________________________________
>Wien mailing list
>Wien at zeus.theochem.tuwien.ac.at
>http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>
>_______________________________________________
>Wien mailing list
>Wien at zeus.theochem.tuwien.ac.at
>http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien

**********************************************************

Dr QiWen YAO
JSPS Fellow
Multifunctional Materials Group
Optical and Electronic Materials Unit
Environment and Energy Materials Research Division

National Institute for Materials Science

1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
Phone: +81-29-851-3354, ext. no. 6482, Fax: +81-29-859-2501

**********************************************************

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