Re: [Wien] Cif File

2021-04-24 Thread Lyudmila Dobysheva

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
--
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Institute of Physics and Technology,
Udmurt Federal Research Center, Ural Br. of Rus.Ac.Sci.
426000 Izhevsk Kirov str. 132
Russia
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Re: [Wien] Fwd: test-suite.log Error 1

2021-04-24 Thread Gavin Abo
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

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Re: [Wien] Cif File

2021-04-24 Thread Gavin Abo
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

2021-04-24 Thread Laurence Marks
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
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[Wien] Cif File

2021-04-24 Thread 413119008


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
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