Re: [Wien] converting struct file into CIF formant

2021-08-28 Thread Laurence Marks 
Kdist is useful, and it's BVS is also good. (I find it a bit clunky)

However, I suggest not using the BVS minimization as it does not work right
-- probably needs a repulsion added.

_
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, Aug 28, 2021, 08:53 Fecher, Gerhard  wrote:

> For your info,
> the Kdist programm coming with the free Kalvados program suite (
> https://urldefense.com/v3/__https://www.fzu.cz/*knizek/kalvados/__;fg!!Dq0X2DkFhyF93HkjWTBQKhk!Fog5-lEL8UuZqywe55q9IFL89dAW2s8WuAKUF0wOXrPR4CZ58yXQTGecVmrN4ESsOzQHtA$
> )
> reads and writes Wien2k struct files and can save them in different
> formats e.g.: cif
> the cif has 8 digitsafter dot for the positions such that hexagonal cases
> are ok.
>
> It allows a lot of manipulation of the structure, creation of
> superstructures, etc
>
>
> Ciao
> Gerhard
>
> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
> "I think the problem, to be quite honest with you,
> is that you have never actually known what the question is."
>
> 
> Dr. Gerhard H. Fecher
> Institut of Physics
> Johannes Gutenberg - University
> 55099 Mainz
> 
> Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von
> Laurence Marks [laurence.ma...@gmail.com]
> Gesendet: Donnerstag, 26. August 2021 10:48
> An: A Mailing list for WIEN2k users
> Betreff: Re: [Wien] converting struct file into CIF formant
>
> Dear Gavin,
>
> Unfortunately it is very possible to create problems by reducing the
> number of digits; Wien2k may not find the full symmetry.
>
> I will mention a different code, Cryscon (
> https://urldefense.com/v3/__http://www.shapesoftware.com/00_Website_Homepage/__;!!Dq0X2DkFhyF93HkjWTBQKhk!Fog5-lEL8UuZqywe55q9IFL89dAW2s8WuAKUF0wOXrPR4CZ58yXQTGecVmrN4EQm0dQKyg$
> ). It is shareware, so you are requested to pay a modest fee. In addition
> to converting struct to CIF with 8 digits, it will also transform axes and
> change symmetries which is really useful.
>
> _
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought", Albert Szent-Györgyi
> http://www.numis.northwestern.edu
>
> On Thu, Aug 26, 2021, 00:11 Gavin Abo  gabo13...@gmail.com>> wrote:
>
> Prof. Marks,
>
> Appreciate the warning and rhetorical questions.
>
> I downloaded your "ct1c00630_si_002.zip" file at [1] and extracted 1x1.cif
> from it.
>
> I opened it in the Windows 64-bit Edition of VESTA version 3.5.7 and
> exported it from VESTA as a .cif.
>
> Indeed, that VESTA version takes the 8 places after the decimal point and
> truncates the atomic positions to 6 places.
>
> I also uploaded the 1x1.cif in the Structure Data Converter & Editor of
> Bilbao Crystallographic Server [2] and it could not read the Symmetry
> Operations from the cif and truncated to 5 places.
>
>  For example, your
> .cif: Ti001  z=0.20224167
>
>  VESTA
> exported .cif: Ti001  z=0.202242
>
> From Bilbao's "Export to Standard CIF format" button: Ti001  z=0.20224
>
> Should significant digits [2] be of concern, I will have to copy the value
> from StructGen for example and use a text editor [4] to adjust the exported
> .cif from those software programs.  Or perhaps a software program like
> publCIF [5] or EnCIFer [6] would work instead of a text editor to edit the
> .cif.  Or I could use WIEN2k's .struct to .cif converter command "x
> struct2cif" (or "x cif2struct" to go the opposite way) described in the
> WIEN2k usersguide [7] as you have already mentioned.
>
> [1]
> https://urldefense.com/v3/__https://doi.org/10.1021/acs.jctc.1c00630__;!!Dq0X2DkFhyF93HkjWTBQKhk!Fog5-lEL8UuZqywe55q9IFL89dAW2s8WuAKUF0wOXrPR4CZ58yXQTGecVmrN4EQPOKOKdg$
> <
> https://urldefense.com/v3/__https://doi.org/10.1021/acs.jctc.1c00630__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpXftlM7Ng$
> >
> [2]
> https://urldefense.com/v3/__https://www.cryst.ehu.es/cgi-bin/cryst/programs/mcif2vesta/index.php__;!!Dq0X2DkFhyF93HkjWTBQKhk!Fog5-lEL8UuZqywe55q9IFL89dAW2s8WuAKUF0wOXrPR4CZ58yXQTGecVmrN4ERyIf7MGw$
> <
> https://urldefense.com/v3/__https://www.cryst.ehu.es/cgi-bin/cryst/programs/mcif2vesta/index.php__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpUXrS6OPw$
> >
> [3]
> https://urldefense.com/v3/__https://en.wikipedia.org/wiki/Significant_figures__;!!Dq0X2DkFhyF93HkjWTBQKhk!Fog5-lEL8UuZqywe55q9IFL89dAW2s8WuAKUF0wOXrPR4CZ58yXQTGecVmrN4ERBsCVbRw$
> <
> https://urldefense.com/v3/__https://en.wikipedia.org/wiki/Significant_figures__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpU6sooZAw$
> >
> [4]
> https://urldefense

Re: [Wien] converting struct file into CIF formant

2021-08-28 Thread Fecher, Gerhard 
For your info,
the Kdist programm coming with the free Kalvados program suite 
(https://www.fzu.cz/~knizek/kalvados/)
reads and writes Wien2k struct files and can save them in different formats 
e.g.: cif
the cif has 8 digitsafter dot for the positions such that hexagonal cases are 
ok.

It allows a lot of manipulation of the structure, creation of superstructures, 
etc


Ciao
Gerhard

DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."


Dr. Gerhard H. Fecher
Institut of Physics
Johannes Gutenberg - University
55099 Mainz

Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Laurence 
Marks [laurence.ma...@gmail.com]
Gesendet: Donnerstag, 26. August 2021 10:48
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] converting struct file into CIF formant

Dear Gavin,

Unfortunately it is very possible to create problems by reducing the number of 
digits; Wien2k may not find the full symmetry.

I will mention a different code, Cryscon 
(http://www.shapesoftware.com/00_Website_Homepage/). It is shareware, so you 
are requested to pay a modest fee. In addition to converting struct to CIF with 
8 digits, it will also transform axes and change symmetries which is really 
useful.

_
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 Thu, Aug 26, 2021, 00:11 Gavin Abo 
mailto:gabo13...@gmail.com>> wrote:

Prof. Marks,

Appreciate the warning and rhetorical questions.

I downloaded your "ct1c00630_si_002.zip" file at [1] and extracted 1x1.cif from 
it.

I opened it in the Windows 64-bit Edition of VESTA version 3.5.7 and exported 
it from VESTA as a .cif.

Indeed, that VESTA version takes the 8 places after the decimal point and 
truncates the atomic positions to 6 places.

I also uploaded the 1x1.cif in the Structure Data Converter & Editor of Bilbao 
Crystallographic Server [2] and it could not read the Symmetry Operations from 
the cif and truncated to 5 places.

 For example, your 
.cif: Ti001  z=0.20224167

 VESTA exported 
.cif: Ti001  z=0.202242

>From Bilbao's "Export to Standard CIF format" button: Ti001  z=0.20224

Should significant digits [2] be of concern, I will have to copy the value from 
StructGen for example and use a text editor [4] to adjust the exported .cif 
from those software programs.  Or perhaps a software program like publCIF [5] 
or EnCIFer [6] would work instead of a text editor to edit the .cif.  Or I 
could use WIEN2k's .struct to .cif converter command "x struct2cif" (or "x 
cif2struct" to go the opposite way) described in the WIEN2k usersguide [7] as 
you have already mentioned.

[1] 
https://doi.org/10.1021/acs.jctc.1c00630
[2] 
https://www.cryst.ehu.es/cgi-bin/cryst/programs/mcif2vesta/index.php
[3] 
https://en.wikipedia.org/wiki/Significant_figures
[4] 
https://en.wikipedia.org/wiki/List_of_text_editors
[5] 
https://journals.iucr.org/services/cif/publcif/
[6] 
https://www.ccdc.cam.ac.uk/Community/csd-community/encifer/
[7] 
http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf

Thanks,

Gavin

On 8/25/2021 6:35 AM, Laurence Marks wrote:
Sorry Gavin, but I would be very cautious about these versions. Do they 
preserve symmetry, and do they have 8 digits? Do they truly obey the CIF 
definitions? (struct2cif somewhat does).

_