[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 05:24:47 CEST 2020
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
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