[QE-users] Need a script that can convert primitive cell file file using conventional cell cif file

Thu Jul 16 19:44:40 CEST 2020

Hell Rekha,

I guess you downloaded the master branch, I haven't had time to document
the codes yet with many new functions.
Hence, the latest code remains in the dev branch, please:

git clone -b dev https://github.com/hungpham2017/mcu.git let me know if you
have any other questions. Hung

On Thu, Jul 16, 2020 at 12:40 PM rekha sharma <rekha1997jpr at gmail.com>
wrote:

> Dear Sir,
> I have cloned it and then added the path to ~/.bashrc.
>
> But my import mcu is not working.
>
> My python path is:
> export PYTHONPATH=/home/rekha/mcu:$PYTHONPATH
>
> I have created a file "mcu.py" in which I kept
> import mcu
> work = mcu.CELL(cif='conventional.cif')
> prim_cell = work.to_prim_cell()
> work.write_cif(prim_cell, filename='primitive')
>
> and then invoked
>
> python mcu.py
>
> this gives me error
>
> Traceback (most recent call last):
>   File "mcu.py", line 1, in <module>
>     import mcu
>   File "/home/rekha/case/mcu.py", line 2, in <module>
>     work = mcu.CELL(cif='conventional.cif')
> AttributeError: module 'mcu' has no attribute 'CELL'
>
>
> I am having my conventional.cif in "/home/rekha/case/" directory.
>
>
> What should I do now?
>
>
> On Thu, Jul 16, 2020 at 10:44 PM Hung Pham <phamx494 at umn.edu> wrote:
>
>> Sorry, there was a typo in the example script, it should be this:
>>
>> import mcu
>> work = mcu.CELL(cif='conventional.cif')
>> prim_cell = work.to_prim_cell()
>> work.write_cif(prim_cell, filename='primitive')
>>
>> Hung Pham
>>
>> On Thu, Jul 16, 2020 at 12:12 PM Hung Pham <phamx494 at umn.edu> wrote:
>>
>>> Hello Rekha,
>>>
>>> Spglib library <https://spglib.github.io/spglib/index.html> is doing
>>> what you are looking for. Spglib has a python interface and can be easily
>>> installed via Pip or conda..
>>> But you need to make a cell tuple (from CIF) which contains the lattice
>>> information, this requires some minimal Python programming.
>>> My MCU <https://github.com/hungpham2017/mcu/tree/dev> project supports
>>> CIF file as well as the QE output files and it has cell analysis functions
>>> using spglib. Within a few lines of code, you can get what you want in the
>>> desired format. For example, in a Python interpreter or script:
>>>
>>> import mcu
>>> work = mcu.CELL(cif='conventional.cif')
>>> primitive = work.to_prim_cell()
>>> work.write_cif(prim_cell, filename='primitive')
>>>
>>> If you are interested in this, I can assist further.
>>> Hung Pham
>>>
>>>
>>> On Thu, Jul 16, 2020 at 11:57 AM rekha sharma <rekha1997jpr at gmail.com>
>>> wrote:
>>>
>>>> Thank you very much sir,
>>>>
>>>> My materials are very new and not available in any database.
>>>>
>>>> On Thu, Jul 16, 2020, 22:24 Yuvam Bhateja <yuvamb16 at gmail.com> wrote:
>>>>
>>>>> Hello Rekha
>>>>>
>>>>> You can check out "Material Project".
>>>>> It's a database where researchers share their findings and results of
>>>>> several different types of materials and of different applications.
>>>>>
>>>>> Every compound is available in primitive, conventional, computed and
>>>>> symmetric unit cell, etc.
>>>>> Hope you find this useful.
>>>>>
>>>>> Regards
>>>>> Yuvam Bhateja
>>>>>
>>>>> On Thu, 16 Jul 2020, 7:40 pm rekha sharma, <rekha1997jpr at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Dear Expert Users,
>>>>>>
>>>>>> It is possible that this question has been answered many times before
>>>>>> but I could not find it on the forum.
>>>>>>
>>>>>> I have few complex structures and it is not possible to handle on my
>>>>>> system in the conventional form.
>>>>>>
>>>>>> Can you please advise any tool that can help me to convert
>>>>>> a conventional cell cif file to a primitive cell file?
>>>>>>
>>>>>> I have tried with VEST (niggli cell reduction) but it does not work
>>>>>> for me.
>>>>>>
>>>>>> Thank you very much.
>>>>>> Rekha
>>>>>> _______________________________________________
>>>>>> Quantum ESPRESSO is supported by MaX (
>>>>>> www.max-centre.eu/quantum-espresso)
>>>>>> users mailing list users at lists.quantum-espresso.org
>>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>>>
>>>>> _______________________________________________
>>>>> Quantum ESPRESSO is supported by MaX (
>>>>> www.max-centre.eu/quantum-espresso)
>>>>> users mailing list users at lists.quantum-espresso.org
>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>>
>>>> _______________________________________________
>>>> Quantum ESPRESSO is supported by MaX (
>>>> www.max-centre.eu/quantum-espresso)
>>>> users mailing list users at lists.quantum-espresso.org
>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>>
>>>
>>> --
>>>
>>> Hung Q. Pham
>>> Gagliardi Group
>>> Office: Smith 101
>>> Email: phamx494 at umn.edu
>>> Personal page: hungpham2017.github.io
>>> Department of Chemistry
>>> University of Minnesota - Twin Cities, Minneapolis, MN 55455
>>>
>>
>>
>> --
>>
>> Hung Q. Pham
>> Gagliardi Group
>> Office: Smith 101
>> Email: phamx494 at umn.edu
>> Personal page: hungpham2017.github.io
>> Department of Chemistry
>> University of Minnesota - Twin Cities, Minneapolis, MN 55455
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
>> users mailing list users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
>
> --
>
>
>
>
> Best wishes
>
> Ms. Rekha
> Teaching Assistant,
> Department of Physics
> RK college, Jaipur, India
> Mob.: +11 90-95 790 71 697
> Email: rekha1997jpr at gmail.com
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users

-- 

Hung Q. Pham
Gagliardi Group
Office: Smith 101
Email: phamx494 at umn.edu
Personal page: hungpham2017.github.io
Department of Chemistry
University of Minnesota - Twin Cities, Minneapolis, MN 55455
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