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

Thu Jul 16 19:55:37 CEST 2020

Now I am getting
import-im6.q16: unable to grab mouse `': Resource temporarily unavailable @
error/xwindow.c/XSelectWindow/9186.
when I do
import mcu

On Thu, Jul 16, 2020 at 11:15 PM Hung Pham <phamx494 at umn.edu> wrote:

> 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
> _______________________________________________
> 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
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