Go to the SETSTRU program http://www.cryst.ehu.es/cryst/setstru.html
And choose Space Group 166 Non-standard setting Then choose R-3m:h as initial setting R-3m:r as final setting Enter the lattice parameters and the atomic positions You are done !!!!! Cheers -----Original Message----- From: wien-boun...@zeus.theochem.tuwien.ac.at [mailto:wien-bounces at zeus.theochem.tuwien.ac.at] On Behalf Of Qiwen YAO Sent: Monday, December 05, 2011 5:50 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 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 ********************************************************** _______________________________________________ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien