[Wien] Generating struct from space group and coordinates
Gavin Abo
gsabo at crimson.ua.edu
Mon Nov 13 00:27:37 CET 2017
The Cr (0, 0, 0.3302) and Ge (0, 0, 0.059) in R-3: h of both posts are
the same. So, it should be easy to see that.
In the struct file created by StructGen, you can also see that the Te
positions (which are in the R-3: r setting in the struct file) are the same:
ATOM -1: X=0.08879999 Y=0.44779000 Z=0.71880000 <- The nonequivalent
position Te (0.00367, 0.36633, 0.08513) in R-3: h
MULT= 6 ISPLIT= 8
ATOM -1:X= 0.91120001 Y=0.55221000 Z=0.28120000<- The equivalent
position Te (0.6631, -0.0331, 0.24825) in R-3: h
ATOM -1:X= 0.44779000 Y=0.71880000 Z=0.08879999
ATOM -1:X= 0.55221000 Y=0.28120000 Z=0.91120001
ATOM -1:X= 0.71880000 Y=0.08879999 Z=0.44779000
ATOM -1:X= 0.28120000 Y=0.91120001 Z=0.55221000
Te NPT= 781 R0=0.00001000 RMT= 2.4000 Z: 52.000
SETSTRU input:
# Comments start with #
# Space Group ITA number
148
# Lattice parameters
6.8275 6.8275 20.5619 90 90 120
# Number of independent atoms in the asymmetric unit
3
# [atom type] [number] [WP] [x] [y] [z]
Te 1 - 0.6631 -0.0331 0.24825
Ge 2 - 0 0 0.059
Cr 3 - 0 0 0.3302
SETSTRU output
Final Setting: R-3:r (148)148 #R-3:r
7.9066 7.9066 7.9066 51.16 51.16 51.16
3
Te 1 - 0.911350 -0.447950 0.281350
Ge 2 - 0.059000 0.059000 0.059000
Cr 3 - 0.330200 0.330200 0.330200
The y = -0.447950 of Te is the same as 0.55205 [=1+(-0.447950)].
On 11/12/2017 4:07 PM, Md. Fhokrul Islam wrote:
>
> Hi Delamora,
>
>
> Thank you for your reply. Both form of the data are equivalent and
> also listed
>
> in Springer database. The form of the data you mentioned is from the
> original
>
> experimental work, which is then transformed into a standardized form in
>
> Springer database.
>
>
>
> Regards,
>
> Fhokrul
>
>
>
> ------------------------------------------------------------------------
> *From:* Wien <wien-bounces at zeus.theochem.tuwien.ac.at> on behalf of
> delamora <delamora at unam.mx>
> *Sent:* Sunday, November 12, 2017 10:37 PM
> *To:* wien at zeus.theochem.tuwien.ac.at
> *Subject:* Re: [Wien] Generating struct from space group and coordinates
> I find different data, I do not know if they are equivalent:
> Title Crystallographic, magnetic and electronic structures of a
> new layered
> ferromagnetic compound Cr2 Ge2 Te6
> Author(s) Carteaux, V.;Brunet, D.;Ouvrard, G.;Andre, G.
> Reference Journal of Physics: Condensed Matter
>
> Atom # OX SITE x y z SOF H
> ITF(B)
> Te 1 -2 18 f 0.663(1) -.033(1) 0.2482(5) 1. 0
> 0.5
> Cr 1 +2 6 c 0 0 0.3302(1) 1. 0
> 0.5
> Ge 1 +4 6 c 0 0 0.0590(6) 1. 0
> 0.5
>
> and they have two symilar structures
>
> ------------------------------------------------------------------------
> *De:* Wien <wien-bounces at zeus.theochem.tuwien.ac.at> en nombre de
> Gavin Abo <gsabo at crimson.ua.edu>
> *Enviado:* domingo, 12 de noviembre de 2017 12:41:13 p. m.
> *Para:* wien at zeus.theochem.tuwien.ac.at
> *Asunto:* Re: [Wien] Generating struct from space group and coordinates
>
> I did this rather quickly. So you will have to double check if it
> looks correct or not.
>
>
> It looks like both your lattice parameters and atomic positions are in
> the R-3 hexagonal setting. So enter in SETSTRU [
> http://www.cryst.ehu.es/cryst/setstru.html ]:
>
> Transform a structure to an alternative setting
> <http://www.cryst.ehu.es/cryst/setstru.html>
> www.cryst.ehu.es
> The program transforms the initial structure to an specified ITA setting.
>
>
>
>
> # Comments start with #
> # Space Group ITA number
> 148
> # Lattice parameters
> 6.8275 6.8275 20.5619 90 90 120
> # Number of independent atoms in the asymmetric unit
> 3
> # [atom type] [number] [WP] [x] [y] [z]
> Te 1 - 0.00367 0.36633 0.08513
> Ge 2 - 0 0 0.059
> Cr 3 - 0 0 0.3302
>
>
> Click Transform Structure
>
>
> Select R-3: h for initial and R-3:r for Final. Then, SETSTRU should
> output the rhombohedral settings:
>
>
> Final Setting: R-3:r (148)148 #R-3:r
> 7.9066 7.9066 7.9066 51.16 51.16 51.16
> 3
> Te 1 - 0.088800 0.447790 -0.281200
> Ge 2 - 0.059000 0.059000 0.059000
> Cr 3 - 0.330200 0.330200 0.330200
>
> In StructGen, select 148_R-3 for the spacegroup.
>
>
> Enter the "hexagonal" for the lattice parameters:
>
>
> a = 6.8275 ang, b = 6.8275 ang, c = 20.5619 ang, alpha = 90 deg, beta
> = 90 deg, gamma = 120 deg
>
>
> For the atomic positions, enter the inequivalent "rhombohedral" positions:
>
>
> Te 0.088800 0.447790 -0.281200
> Ge 0.059000 0.059000 0.059000
> Cr 0.330200 0.330200 0.330200
>
>
> After you save the structure and come back and view in StructGen
> again, take note of the StructGen message under Inequivalent Atoms:
>
> "positions must be specified in rhombohedral coordinates"
>
>
> See if the structure looks okay now (for example in XCrySDen or VESTA).
>
> Reference:
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12704.html
>
> On 11/12/2017 8:55 AM, Md. Fhokrul Islam wrote:
>>
>> Dear Wien2k users,
>>
>>
>> I am trying to build the struct file of Cr2Ge2Te6 crystal from space
>> group and atomic position using w2web.
>> I have obtained the information about this crystal from springer database
>> http://materials.springer.com/isp/crystallographic/docs/sd_1622000
>>
>> Space group: 148 (R-3 h)
>> Lattice constants a, b, c: 0.68275 (nm), 0.68275 (nm), 2.05619 (nm)
>> Angle alpha, beta, gamma: 90, 90, 120
>>
>> atom Wychoff x y z
>> Te 18f 0.00367 0.36633 0.08513
>> Ge 6c 0 0 0.059
>> Cr 6c 0 0 0.3302
>>
>> But if I use the coordinates of each of these three atoms and space
>> group in w2web, I don't get the correct crystal structure.
>> Although I have managed to get the structure from other online
>> sources but I am wondering if anyone can tell me how can
>> I use these info to generate the structure usingw2web.
>>
>>
>> Thanks,
>> Fhokrul
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