[Wien] converting struct file into CIF formant
413119008 at nitt.edu
413119008 at nitt.edu
Sun Aug 29 17:42:00 CEST 2021
Thank You sir.
Quoting Laurence Marks <laurence.marks at gmail.com>:
> 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 <fecher at uni-mainz.de> 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-bounces at zeus.theochem.tuwien.ac.at] im Auftrag von
>> Laurence Marks [laurence.marks at 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<http://www.numis.northwestern.edu>
>>
>> On Thu, Aug 26, 2021, 00:11 Gavin Abo <gabo13279 at gmail.com<mailto:
>> gabo13279 at 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.com/v3/__https://en.wikipedia.org/wiki/List_of_text_editors__;!!Dq0X2DkFhyF93HkjWTBQKhk!Fog5-lEL8UuZqywe55q9IFL89dAW2s8WuAKUF0wOXrPR4CZ58yXQTGecVmrN4ERtHc6Usg$
>> <
>> https://urldefense.com/v3/__https://en.wikipedia.org/wiki/List_of_text_editors__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpV2G4zGEg$
>> >
>> [5]
>> https://urldefense.com/v3/__https://journals.iucr.org/services/cif/publcif/__;!!Dq0X2DkFhyF93HkjWTBQKhk!Fog5-lEL8UuZqywe55q9IFL89dAW2s8WuAKUF0wOXrPR4CZ58yXQTGecVmrN4EQCzEAqZw$
>> <
>> https://urldefense.com/v3/__https://journals.iucr.org/services/cif/publcif/__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpWDsd3Arw$
>> >
>> [6]
>> https://urldefense.com/v3/__https://www.ccdc.cam.ac.uk/Community/csd-community/encifer/__;!!Dq0X2DkFhyF93HkjWTBQKhk!Fog5-lEL8UuZqywe55q9IFL89dAW2s8WuAKUF0wOXrPR4CZ58yXQTGecVmrN4EQ4fN067w$
>> <
>> https://urldefense.com/v3/__https://www.ccdc.cam.ac.uk/Community/csd-community/encifer/__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpU33r7mOA$
>> >
>> [7]
>> https://urldefense.com/v3/__http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf__;!!Dq0X2DkFhyF93HkjWTBQKhk!Fog5-lEL8UuZqywe55q9IFL89dAW2s8WuAKUF0wOXrPR4CZ58yXQTGecVmrN4EQ1YeBIAw$
>> <
>> https://urldefense.com/v3/__http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf__;!!Dq0X2DkFhyF93HkjWTBQKhk!ClBSYJ_VC4eq5JWBvdGTKrSdzNRF9yTNv8oCw0D5JJOEZIi9nN0otEmrykeORpXPqHimLw$
>> >
>>
>> 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).
>>
>> _____
>> 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<http://www.numis.northwestern.edu>
>>
>> On Wed, Aug 25, 2021, 07:32 Gavin Abo <gabo13279 at gmail.com<mailto:
>> gabo13279 at gmail.com>> wrote:
>> See VESTA's website [1] on how it exports cif [2] and opens a .struct file.
>>
>> CrystalMaker also has a "Import Data From: WIEN2k Structure" and "Export
>> Data To: CIF" according to its website [3].
>>
>> [1]
>> https://urldefense.com/v3/__https://jp-minerals.org/vesta/en/__;!!Dq0X2DkFhyF93HkjWTBQKhk!C_JxdE8odmmFbEg_k6yfO4xFqawhI9g4ti7tweHCZt4sH2crsKyqO2XT0p8NJKL-f_jFpQ$
>> [2]
>> https://urldefense.com/v3/__https://youtu.be/lxMbH71JvHA__;!!Dq0X2DkFhyF93HkjWTBQKhk!C_JxdE8odmmFbEg_k6yfO4xFqawhI9g4ti7tweHCZt4sH2crsKyqO2XT0p8NJKKY62ZEnw$
>> [3]
>> https://urldefense.com/v3/__http://crystalmaker.com/crystalmaker/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!C_JxdE8odmmFbEg_k6yfO4xFqawhI9g4ti7tweHCZt4sH2crsKyqO2XT0p8NJKJ4aeXwDg$
>>
>> On 8/25/2021 5:56 AM, 413119008 at nitt.edu<mailto:413119008 at nitt.edu> wrote:
>> > Respected sir,
>> >
>> >
>> > Is there any way to convert a .struct file into .cif file
>> > format?
>> _______________________________________________
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