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

Qiwen YAO Yao.Qiwen at nims.go.jp
Mon Dec 5 13:20:23 CET 2011


OK thank you!
I now know what you and prof. Blaha said I about the coordinates conversion... don't know how I didn't pick this up a few months earlier ... oh well.

I was looking at the Bilbao server site (http://www.cryst.ehu.es/)  - trying to figure out which/where to go for the coordinates conversion - but couldn't figure it out. Would you mind to send me the steps in using this web tool for converting this particular structure ? Thank you so much for your time.

Maybe just send to my email so to save others' time - as this, I am sure most users already know how to do this?

thank you again.
Wen


------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 05:29:13 PM(+0530)
>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
>
>**********************************************************
>
>_______________________________________________
>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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