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

Yue-Wen Fang yuewen.fang at gmail.com
Fri Jul 17 06:18:21 CEST 2020 

Good, you have already used the dev branch. Then you can check more details
through ipython (exceute "ipython" in your terminal)
In the python IDE,

In [1]: import mcu

In [2]: mcu
Out[2]: <module 'mcu' from '/Users/fang/mcu/mcu/__init__.py'>

In [3]: mcu.CELL
Out[3]: mcu.cell.main.CELL

You can examine that the loaded MCU is indeed the one you used or not.

rekha sharma <rekha1997jpr at gmail.com> 于2020年7月17日周五 下午1:01写道：

> 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
> _______________________________________________
> 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
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