[Wien] Structure optimization of Beta -Sn

Xavier Rocquefelte xavier.rocquefelte at univ-rennes1.fr
Thu Jun 4 09:13:11 CEST 2020


Dear Fabien

This is strange... Perhaps a conversion problem. Yes I have used the 
following cif file and cif2struct works for me!

Regards

Xavier



Le 04/06/2020 à 09:10, Tran, Fabien a écrit :
>
> Dear Xavier,
>
> I read your email from yesterday, but I thought that his struct 
> filewas correct, because I got the same struct file from this cif file:
>
> http://rruff.geo.arizona.edu/AMS/download.php?id=13353.cif&down=cif
>
> But you are right; if I visualize it, I can see that it is not 
> beta-Sn.  Besides, I can not convert cif to struct other cif files 
> like the one that you sent. With cif2struct, I get "unknown space 
> group name: I41/amds" and no struct file is generated.
>
> Did cif2struct​ work for you?
>
>
>
> ------------------------------------------------------------------------
> *From:* Wien <wien-bounces at zeus.theochem.tuwien.ac.at> on behalf of 
> Xavier Rocquefelte <xavier.rocquefelte at univ-rennes1.fr>
> *Sent:* Wednesday, June 3, 2020 11:54 PM
> *To:* wien at zeus.theochem.tuwien.ac.at
> *Subject:* Re: [Wien] Structure optimization of Beta -Sn
>
> Dear Fabien,
>
> I explained to Shamik that the structure he was using was not correct.
>
> I also sent cif and struct file.
>
> See below a proper case.struct file.
>
> Shamik could you please send email only to the wienlist to avoid 
> multiple answers from the list and many people trying to help you 
> without having all the details?
>
>
> blebleble
> B   LATTICE,NONEQUIV.ATOMS:  1 141 I41/amd
> MODE OF CALC=RELA unit=bohr
>  11.019938 11.019938  6.011975 90.000000 90.000000 90.000000
> ATOM   1: X=0.50000000 Y=0.25000000 Z=0.12500000
>           MULT= 2          ISPLIT=-2
>        1: X=0.00000000 Y=0.25000000 Z=0.37500000
> Sn1        NPT=  781  R0=.000010000 RMT= 2.50000     Z:  50.
> LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
>                      0.0000000 1.0000000 0.0000000
>                      0.0000000 0.0000000 1.0000000
>   16      NUMBER OF SYMMETRY OPERATIONS
>  1 0 0 0.00000000
>  0 1 0 0.00000000
>  0 0 1 0.00000000
>        1
> -1 0 0 0.50000000
>  0-1 0 0.00000000
>  0 0 1 0.50000000
>        2
>  0-1 0 0.25000000
>  1 0 0 0.75000000
>  0 0 1 0.25000000
>        3
>  0 1 0 0.25000000
> -1 0 0 0.25000000
>  0 0 1 0.75000000
>        4
> -1 0 0 0.50000000
>  0 1 0 0.00000000
>  0 0-1 0.50000000
>        5
>  1 0 0 0.00000000
>  0-1 0 0.00000000
>  0 0-1 0.00000000
>        6
>  0 1 0 0.25000000
>  1 0 0 0.75000000
>  0 0-1 0.25000000
>        7
>  0-1 0 0.25000000
> -1 0 0 0.25000000
>  0 0-1 0.75000000
>        8
> -1 0 0 0.00000000
>  0-1 0 0.00000000
>  0 0-1 0.00000000
>        9
>  1 0 0 0.50000000
>  0 1 0 0.00000000
>  0 0-1 0.50000000
>       10
>  0 1 0 0.75000000
> -1 0 0 0.25000000
>  0 0-1 0.75000000
>       11
>  0-1 0 0.75000000
>  1 0 0 0.75000000
>  0 0-1 0.25000000
>       12
>  1 0 0 0.50000000
>  0-1 0 0.00000000
>  0 0 1 0.50000000
>       13
> -1 0 0 0.00000000
>  0 1 0 0.00000000
>  0 0 1 0.00000000
>       14
>  0-1 0 0.75000000
> -1 0 0 0.25000000
>  0 0 1 0.75000000
>       15
>  0 1 0 0.75000000
>  1 0 0 0.75000000
>  0 0 1 0.25000000
>       16
>
>
>
>
>
> Le 03/06/2020 à 21:38, Tran, Fabien a écrit :
>>
>> Using a RKmax above 7 should not lead to completely wrong results. 
>> One important point is how the lattice constants a and c were varied. 
>> In a meaningful way?
>>
>>
>> ------------------------------------------------------------------------
>> *From:* Wien <wien-bounces at zeus.theochem.tuwien.ac.at> on behalf of 
>> shamik chakrabarti <shamik15041981 at gmail.com>
>> *Sent:* Wednesday, June 3, 2020 8:40 PM
>> *To:* A Mailing list for WIEN2k users
>> *Subject:* Re: [Wien] Structure optimization of Beta -Sn
>> Dear Dr. Tran,
>>
>>                   I have used both plain GGA & nlvdw independently & 
>> in both cases the results are same. I have used Rmr*Kmax=9 for nlvdw 
>> & 7 for GGA. Do you think moving to larger Rmt*Kmax may solve the 
>> problem? I am currently going through the literature you have sent..
>>
>> with regards,
>>
>> On Wed, 3 Jun 2020 at 23:53, Tran, Fabien <fabien.tran at tuwien.ac.at 
>> <mailto:fabien.tran at tuwien.ac.at>> wrote:
>>
>>     At first sight you struct file seems ok, but this is difficult to
>>     help you without more details. For instance: Which functional
>>     have you used? Are you keeping the c/a ratio fixed? Have you
>>     looked into the literature:
>>
>>     https://aip.scitation.org/doi/abs/10.1063/1.4948434
>>
>>
>>     ------------------------------------------------------------------------
>>     *From:* Wien <wien-bounces at zeus.theochem.tuwien.ac.at
>>     <mailto:wien-bounces at zeus.theochem.tuwien.ac.at>> on behalf of
>>     shamik chakrabarti <shamik15041981 at gmail.com
>>     <mailto:shamik15041981 at gmail.com>>
>>     *Sent:* Wednesday, June 3, 2020 8:06 PM
>>     *To:* A Mailing list for WIEN2k users
>>     *Subject:* [Wien] Structure optimization of Beta -Sn
>>     Dear wien2k users,
>>
>>                                      I am trying to optimize the
>>     structure of Beta - Sn. However, even after 20% increment of the
>>     volume there is no sign of energy minima. I am attaching the
>>     struct file herewith this mail for your consideration.
>>
>>     Looking forward to hearing from you.
>>
>>     with regards,
>>
>>     -- 
>>     Dr. Shamik Chakrabarti
>>     Research Fellow
>>     Department of Physics
>>     Indian Institute of Technology Patna
>>     Bihta-801103
>>     Patna
>>     Bihar, India
>>     _______________________________________________
>>     Wien mailing list
>>     Wien at zeus.theochem.tuwien.ac.at
>>     <mailto:Wien at 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
>>
>>
>>
>> -- 
>> Dr. Shamik Chakrabarti
>> Research Fellow
>> Department of Physics
>> Indian Institute of Technology Patna
>> Bihta-801103
>> Patna
>> Bihar, India
>>
>> _______________________________________________
>> Wien mailing list
>> Wien at 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
> -- 
> ------------------------
> Institut des Sciences Chimiques de Rennes (ISCR)
> Univ Rennes - CNRS - UMR6226, France
> https://iscr.univ-rennes1.fr/cti/people/permanent-staff/rocquefelte-xavier
> ------------------------
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-- 
------------------------
Institut des Sciences Chimiques de Rennes (ISCR)
Univ Rennes - CNRS - UMR6226, France
https://iscr.univ-rennes1.fr/cti/people/permanent-staff/rocquefelte-xavier
------------------------
ICAMM2019 : VASP Workshop and International Materials Modelling Conf
June 26-July 3 2019, Rennes France
icamm2019.sciencesconf.org  : Registration opening soon, see you there!

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#(C) 2020 by FIZ Karlsruhe - Leibniz Institute for Information Infrastructure.  All rights reserved.
data_106072-ICSD
_database_code_ICSD 106072
_audit_creation_date 2004-10-01
_audit_update_record 2017-08-01
_chemical_name_common Tin
_chemical_formula_structural Sn
_chemical_formula_sum Sn1
_chemical_name_structure_type Sn(tI4)
_exptl_crystal_density_diffrn 7.29
_diffrn_ambient_temperature 296.
_citation_title

;
X-ray investigation of thermal expansion and atomic thermal vibrations of tin,
indium, and their alloys
;
loop_
_citation_id
_citation_journal_full
_citation_year
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_citation_page_last
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primary 'Physica Status Solidi B: Basic Solid State Physics' 1981 107 245 253
PSSBBD
loop_
_citation_author_citation_id
_citation_author_name
primary 'Wolcyrz, M.'
primary 'Kubiak, R.'
primary 'Maciejewski, S.'
_cell_length_a 5.8308(2)
_cell_length_b 5.8308(2)
_cell_length_c 3.1810(2)
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 90.
_cell_volume 108.15
_cell_formula_units_Z 4
_space_group_name_H-M_alt 'I 41/a m d S'
_space_group_IT_number 141
loop_
_space_group_symop_id
_space_group_symop_operation_xyz
1 'y, -x+1/2, z+1/4'
2 '-y, x+1/2, z+1/4'
3 'y, -x, -z'
4 '-y, x, -z'
5 '-y, -x+1/2, z+1/4'
6 'y, x+1/2, z+1/4'
7 '-y, -x, -z'
8 'y, x, -z'
9 'x, -y+1/2, -z+1/4'
10 '-x, y+1/2, -z+1/4'
11 'x, -y, z'
12 '-x, y, z'
13 '-x, -y+1/2, -z+1/4'
14 'x, y+1/2, -z+1/4'
15 '-x, -y, z'
16 'x, y, z'
17 'y+1/2, -x, z+3/4'
18 '-y+1/2, x, z+3/4'
19 'y+1/2, -x+1/2, -z+1/2'
20 '-y+1/2, x+1/2, -z+1/2'
21 '-y+1/2, -x, z+3/4'
22 'y+1/2, x, z+3/4'
23 '-y+1/2, -x+1/2, -z+1/2'
24 'y+1/2, x+1/2, -z+1/2'
25 'x+1/2, -y, -z+3/4'
26 '-x+1/2, y, -z+3/4'
27 'x+1/2, -y+1/2, z+1/2'
28 '-x+1/2, y+1/2, z+1/2'
29 '-x+1/2, -y, -z+3/4'
30 'x+1/2, y, -z+3/4'
31 '-x+1/2, -y+1/2, z+1/2'
32 'x+1/2, y+1/2, z+1/2'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Sn0+ 0
loop_
_atom_site_label
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_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_B_iso_or_equiv
_atom_site_occupancy
Sn1 Sn0+ 4 a 0 0 0 . 1.
loop_
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_atom_site_aniso_U_11
_atom_site_aniso_U_22
_atom_site_aniso_U_33
_atom_site_aniso_U_12
_atom_site_aniso_U_13
_atom_site_aniso_U_23
Sn1 Sn0+ 0.0200(2) 0.0200(2) 0.0241(2) 0. 0. 0.
#End of TTdata_106072-ICSD


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