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

rekha sharma rekha1997jpr at gmail.com
Fri Jul 17 16:06:18 CEST 2020 

Dear Sir,
In the mcu directory, I am getting what you got.

ipython
Python 3.6.3 |Anaconda, Inc.| (default, Oct 13 2017, 12:02:49)
Type 'copyright', 'credits' or 'license' for more information
IPython 6.1.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import mcu

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

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

But in the other working directory, I am getting error

In [1]: import mcu
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-1-d555ababf828> in <module>()
----> 1 import mcu

~/case/mcu.py in <module>()
      1 #!/usr/bin/env python
      2 import mcu
----> 3 work = mcu.CELL(cif='conventional.cif')
      4 prim_cell = work.to_prim_cell()
      5 work.write_cif(prim_cell, filename='primitive')

AttributeError: module 'mcu' has no attribute 'CELL'

On Fri, Jul 17, 2020 at 9:49 AM Yue-Wen Fang <yuewen.fang at gmail.com> wrote:

> 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
>
>
>
> _______________________________________________
> 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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