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

Fri Jul 17 06:01:19 CEST 2020

Dear Sir,
This is what I am getting with git log (posting only part of the output)

commit 2155314c447b9f8b7b3a837b532cd2baa350c8f4
Author: hungpham2017 <phamx494 at umn.edu>
Date:   Tue Jul 14 14:06:02 2020 -0500

    small bug in detecting BAND block in fort.25 of CRYSTAL

commit 334da12cc2c165d0bf5521f864ab364685979a13
Author: hungpham2017 <phamx494 at umn.edu>
Date:   Tue Jul 14 12:57:10 2020 -0500

    small bug in detecting BAND block in fort.25 of CRYSTAL

commit 90c3ded86771ae49516a1e58b90668a7c432a20b
Author: hungpham2017 <phamx494 at umn.edu>
Date:   Sun Jul 12 15:33:42 2020 -0500

    MCU for ELK; revising VASP; make str_format general

commit ab29fc4fb5ffbd52fe5a730614b2f04442e85e80
Author: hungpham2017 <phamx494 at umn.edu>
Date:   Thu Jul 2 13:06:59 2020 -0500

    Bug fixed in vasprun.py

commit 13c96588eab73c0d3f8bc08b4723dec4d94fdb88
Author: hungpham2017 <phamx494 at umn.edu>

On Fri, Jul 17, 2020 at 8:55 AM Yue-Wen Fang <yuewen.fang at gmail.com> wrote:

> Hello, Rekha
>
> It seemed the latest version of 'dev' branch of MCU wasn't properly loaded
> in your case. Can you execute the "git log" in the cloned MCU? That can
> help us to know which branch you are using.
>
> rekha sharma <rekha1997jpr at gmail.com> 于2020年7月17日周五 上午3:20写道：
>
>> Sir,
>> I am running it on Ubuntu18.04
>>
>> steps I followed are:
>>
>> git clone -b dev https://github.com/hungpham2017/mcu.git
>> cd mcu
>> sudo python3.7 setup.py  install
>>
>> updated path in ~/.bashrc as
>>
>> export PYTHONPATH=/home/rekha/mcu:$PYTHONPATH
>>
>> source ~/.bashrc
>>
>> cd ~/case
>>
>>
>> my mcu.py is
>>
>> #!/usr/bin/env python
>> import mcu
>> work = mcu.CELL(cif='conventional.cif')
>> prim_cell = work.to_prim_cell()
>> work.write_cif(prim_cell, filename='primitive')
>>
>> the ~/case directory is having a conventional.cif file.
>>
>>
>> Now I run
>> python3.7 mcu.py
>>
>>
>> I am getting  the same error what i get at the start:
>>
>> Traceback (most recent call last):
>>   File "mcu.py", line 2, in <module>
>>     import mcu
>>   File "/home/rekha/case/mcu.py", line 3, in <module>
>>     work = mcu.CELL(cif='conventional.cif')
>> AttributeError: module 'mcu' has no attribute 'CELL'
>>
>>
>> On Thu, Jul 16, 2020 at 11:35 PM Hung Pham <phamx494 at umn.edu> wrote:
>>
>>> It looks me like there is some problem with the Python interpreter in
>>> your environment, not the code itself.
>>> You can try to add this following line at the beginning of your python
>>> script and rerun it:
>>> #!/usr/bin/env python
>>> I found a similar problem here
>>> <https://answers.ros.org/question/164091/rosrun-of-a-working-python-script-fails/>
>>> :
>>> by the way, are you running it on a Window?
>>>
>>>
>>> On Thu, Jul 16, 2020 at 12:56 PM rekha sharma <rekha1997jpr at gmail.com>
>>> wrote:
>>>
>>>> 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
>>>> _______________________________________________
>>>> 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
>> _______________________________________________
>> 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
>
>
>
> --
>
> ------------------------------------------------------------------------------------------------------------
> Yue-Wen FANG, PhD
> Tokyo Institute of Technology, Japan
>
>
>
> _______________________________________________
> 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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