Re: [Wien] Cif File
24.04.2021 15:21, 413119...@nitt.edu wrote: I am using wien2k in my ubuntu system and Iam not able to open this cif file into structgen.when i click use this file iam getting an error in error files such that "this cif file cannot be acccessed.Also i want to know how can i make this as an input file for AFM calculation for Yb ions. If I change the name to simpler - sd.cif, cif2struct starts working with the file, but also gives errors: cif2struct sd.cif Cell dimension(s) missing! F F F So try to change the name and then look again at the diagnostic of structgen. Best wishes Lyudmila Dobysheva -- http://ftiudm.ru/content/view/25/103/lang,english/ Institute of Physics and Technology, Udmurt Federal Research Center, Ural Br. of Rus.Ac.Sci. 426000 Izhevsk Kirov str. 132 Russia --- Tel. +7 (34I2)43-24-59 (office), +7 (9I2)OI9-795O (home) Skype: lyuka18 (office), lyuka17 (home) E-mail: lyuk...@mail.ru (office), lyuk...@gmail.com (home) ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Fwd: test-suite.log Error 1
If it is just the hyb_mgga_x_js18 functional that you see failing in libxc-5.1.2/testsuite/xc-run_testsuite.log, it probably can be ignored as long as you are not using the hyb_mgga_x_js18 functional. The testsuite is also failing for me with libxc-5.1.2 and libxc-5.1.3. I have submitted a report of the error to the libxc developers, which should be viewable at the link: https://gitlab.com/libxc/libxc/-/issues/318 On 4/23/2021 2:14 AM, Ramazan KATIRCI wrote: Hello, I could not install the libxcx-5.1.2 software correctly for wien2k. I am getting the error showed below. I could not solve this problem. I am using mkl library. Thank you in advance for your help. I used the command below. ./configure CC=c99 FC=ifort -prefix=/. make make check (I am getting the error here) make[3]: Entering directory `/truba/home/rkatirci/kutuphaneler/libxc-5.1.2/testsuite' make[4]: Entering directory `/truba/home/rkatirci/kutuphaneler/libxc-5.1.2/testsuite' FAIL: xc-run_testsuite Testsuite summary for libxc 5.1.2 # TOTAL: 1 # PASS: 0 # SKIP: 0 # XFAIL: 0 # FAIL: 1 # XPASS: 0 # ERROR: 0 See testsuite/test-suite.log Please report to li...@tddft.org make[4]: *** [test-suite.log] Error 1 make[4]: Leaving directory `/truba/home/rkatirci/kutuphaneler/libxc-5.1.2/testsuite' make[3]: *** [check-TESTS] Error 2 make[3]: Leaving directory `/truba/home/rkatirci/kutuphaneler/libxc-5.1.2/testsuite' make[2]: *** [check-am] Error 2 make[2]: Leaving directory `/truba/home/rkatirci/kutuphaneler/libxc-5.1.2/testsuite' make[1]: *** [check-recursive] Error 1 make[1]: Leaving directory `/truba/home/rkatirci/kutuphaneler/libxc-5.1.2/testsuite' make: *** [check-recursive] Error 1 (base) -bash-4.2$ libxc@tddft.orgli...@tddft.org ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Cif File
For example, in the cif file below you see the lattice parameters (in the hexagonal setting) and spacegroup: _cell_length_a 3.35 _cell_length_b 3.35 _cell_length_c 16.53 _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 120 ... _symmetry_space_group_name_H-M 'R-3m' _symmetry_Int_Tables_number 166 So in StructGen of w2web, select "Lattice parameters in A" and put a=3.35, b=3.35, and c=16.53 for the lattice constants. For Lattice, select "166_R-3m". You will also need to put the lattice angles and atom coordinates into StructGen. Keep in mind for the atom coordinates that since the above is for a R lattice spacegroup, those need to be in the rhombohedral setting as mentioned in the posts at the following three links: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05554.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11017.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18489.html If you are a beginner, it is usually best to use runsp_lapw (and not runafm_lapw) as described at: http://susi.theochem.tuwien.ac.at/reg_user/faq/afm.html As seen in StructGen (or the case.struct file), the atom coordinates are for the 'inequivalent' atomic positions. So if end up with Yb having only 1 inequivalent atomic position in StructGen. You wouldn't be able to specify an AFM configuration later with instgen_lapw during init_lapw as you can only specify a single up or down (ferromagnet configuration). If that is the case, you will need to create a supercell (change the spacegroup) by using special labels to make some or all of the 'equivalent' atomic positions into inequivalent ones so that you can specify your AFM configuration during instgen_lapw. Some guidance on making supercells can be found at: http://susi.theochem.tuwien.ac.at/reg_user/faq/supercells.html Other guidance on making supercells can be found in past posts in the mailing list archive. I think there used to be a good presentation on calculating different magnetic configurations, but I haven't been able to find it again. I think the website that was hosting it did not put it up again when that website seemed to have gone down from a transition to a new server. It might have been the "Magnetic and charge order phase transition in YBaFe2O5" presentation mentioned in the post at: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20603.html Since it looked like that was Prof. Blaha's presentation, you might be able to request a copy of it from him. username@computername:~/Desktop/cif$ cat sd_1006604\ \(2\).cif ##CIF_1.1 data_sm_global #Used dictionaries loop_ _audit_conform_dict_name _audit_conform_dict_version _audit_conform_dict_location cif_core.dic 2.4.2 . cif_pd.dic 1.0.1 . cif_sm.dic 0.1 'redaktion.landolt-boernstein(at)springer.com' #About this content and reference _sm_credits_copyright ;PAULING FILE Multinaries Edition - 2012. SpringerMaterials Release 2014. http://www.paulingfile.com Unique LPF ID Number SD1006604 Project Coordinator: Shuichi Iwata Section-Editors: Karin Cenzual (Crystal Structures), Hiroaki Okamoto (Phase Diagrams), Fritz Hulliger (Physical Properties) (c) Springer & Material Phases Data System (MPDS), Switzerland & National Institute for Materials Science (NIMS), Japan 2014. (Data generated pre-2002: (c) Springer & MPDS & NIMS; post-2001: (c) Springer & MPDS) All Rights Reserved. Version 2014.06. ; _audit_creation_method ;This data have been compiled from the crystallographic datasheet for "NaYbO2 Crystal Structure" taken from SpringerMaterials (sm_isp_sd_1006604). ; _publ_section_references ;Brüesch P., Schüler C.: Raman and Infrared Spectra of Crystals with α-NaFeO2 Structure. Journal of Physics and Chemistry of Solids 32 (1971) 1025-1038. ; #Phase classification _sm_phase_labels 'NaYbO2' _chemical_name_mineral '' _sm_chemical_compound_class 'oxide' _sm_phase_prototype 'NaFeO2 ' _sm_pearson_symbol 'hR12' _symmetry_Int_Tables_number 166 _sm_sample_details ;sample prepared from Yb2O3, Na2O2 ; _sm_measurement_details ; ; _sm_interpretation_details ;complete structure determined ; data_sm_isp_SD1006604-standardized_unitcell #Cell Parameters _cell_length_a 3.35 _cell_length_b 3.35 _cell_length_c 16.53 _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 120 _sm_length_ratio_ab 1.000 _sm_length_ratio_bc 0.203 _sm_length_ratio_ca 4.934 _cell_volume 160.7 _symmetry_space_group_name_H-M 'R-3m' _symmetry_Int_Tables_number 166 _cell_formula_units_Z 3 _sm_cell_transformation ;origin shift 0 0 1/2 ; #Atom
Re: [Wien] Cif File
Your cif file has 3 datasets, the last one looks like it is corrupted. I am not sure that cif2struct works right with multiple datasets. I suggest, similar to Lyudmila, that you read and edit the file by hand. _ Professor Laurence Marks "Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Györgyi www.numis.northwestern.edu On Sat, Apr 24, 2021, 06:22 <413119...@nitt.edu> wrote: > > sir > > > I am using wien2k in my ubuntu system and Iam not able to open this > cif file into structgen.when i click use this file iam getting an > error in error files such that "this cif file cannot be acccessed.Also > i want to know how can i make this as an input file for AFM > calculation for Yb ions. > > > with regards > > Narayanan Namboodirir P > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > > https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!Gawkunx4IJ7Buk-wHkjNUZprL_M-ieoB9VjCatOAgzkJAfjKRQKEUIqBoza5_Kiv-u2zug$ > SEARCH the MAILING-LIST at: > https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!Gawkunx4IJ7Buk-wHkjNUZprL_M-ieoB9VjCatOAgzkJAfjKRQKEUIqBoza5_Kg1L9na0A$ > ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Cif File
sir I am using wien2k in my ubuntu system and Iam not able to open this cif file into structgen.when i click use this file iam getting an error in error files such that "this cif file cannot be acccessed.Also i want to know how can i make this as an input file for AFM calculation for Yb ions. with regards Narayanan Namboodirir P sd_1006604 (2).cif Description: x-unknown/cif ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html