[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 12:27:44 CET 2011
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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