<div dir="ltr"><div dir="ltr">Hello, Rekha<div><br></div><div> 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.</div><div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">rekha sharma <<a href="mailto:rekha1997jpr@gmail.com">rekha1997jpr@gmail.com</a>> 于2020年7月17日周五 上午3:20写道:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr">Sir,<div><div>I am running it on Ubuntu18.04</div><div></div></div><div><br></div><div>steps I followed are:</div><div><br></div><div>git clone -b dev <a href="https://github.com/hungpham2017/mcu.git" target="_blank">https://github.com/hungpham2017/mcu.git</a> <br></div><div>cd mcu</div><div>sudo python3.7 setup.py install</div><div><br></div><div>updated path in ~/.bashrc as</div><div><br></div><div>export PYTHONPATH=/home/rekha/mcu:$PYTHONPATH<br></div><div><br></div><div>source ~/.bashrc</div><div><br></div><div>cd ~/case</div><div><br></div><div><br></div><div>my mcu.py is</div><div><div><br></div><div>#!/usr/bin/env python<br>import mcu<br>work = mcu.CELL(cif='conventional.cif')<br>prim_cell = work.to_prim_cell()<br>work.write_cif(prim_cell, filename='primitive')<br></div><div><br></div><div>the ~/case directory is having a conventional.cif file.</div></div><div><br></div><div><br></div><div>Now I run</div><div><div>python3.7 mcu.py</div><div></div></div></div><div><br></div><div><br></div>I am getting the same error what i get at the start:<div><br></div><div>Traceback (most recent call last):<br> File "mcu.py", line 2, in <module><br> import mcu<br> File "/home/rekha/case/mcu.py", line 3, in <module><br> work = mcu.CELL(cif='conventional.cif')<br>AttributeError: module 'mcu' has no attribute 'CELL'</div><div><br></div><div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jul 16, 2020 at 11:35 PM Hung Pham <<a href="mailto:phamx494@umn.edu" target="_blank">phamx494@umn.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>It looks me like there is some problem with the Python interpreter in your environment, not the code itself.<br></div><div>You can try to add this following line at the beginning of your python script and rerun it:</div><div><span style="text-align:left;color:rgb(136,0,0);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Menlo,Monaco,"Courier New",monospace;font-size:12px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:pre-wrap;float:none;background-color:rgb(245,245,245)">#!/usr/bin/env python</span><b></b><i></i><u></u><sub></sub><sup></sup><strike></strike><br></div><div>I found a similar problem <a href="https://answers.ros.org/question/164091/rosrun-of-a-working-python-script-fails/" target="_blank">here</a>: </div><div>by the way, are you running it on a Window? </div><div><br></div></div></div></div></div><br><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Thu, Jul 16, 2020 at 12:56 PM rekha sharma <<a href="mailto:rekha1997jpr@gmail.com" target="_blank">rekha1997jpr@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left:1px solid rgb(204,204,204)"><div dir="ltr">Now I am getting <div>import-im6.q16: unable to grab mouse `': Resource temporarily unavailable @ error/xwindow.c/XSelectWindow/9186.<br><div>when I do</div><div>import mcu<br></div></div></div><br><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Thu, Jul 16, 2020 at 11:15 PM Hung Pham <<a href="mailto:phamx494@umn.edu" target="_blank">phamx494@umn.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left:1px solid rgb(204,204,204)"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>Hell Rekha,</div><div><br></div><div>I guess you downloaded the master branch, I haven't had time to document the codes yet with many new functions.</div><div>Hence, the latest code remains in the dev branch, please:</div><div><br></div><div><span style="text-align:left;color:rgb(35,40,45);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Menlo,Consolas,monaco,monospace;font-size:inherit;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:pre-wrap;float:none;background-color:rgb(244,244,244)">git clone -b dev <a href="https://github.com/hungpham2017/mcu.git" target="_blank">https://github.com/hungpham2017/mcu.git</a>
<font color="#004000" face="Arial,Helvetica,sans-serif" style="background-color:rgb(255,255,255)">let me know if you have any other questions.
Hung</font></span><br></div></div></div></div></div><br><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Thu, Jul 16, 2020 at 12:40 PM rekha sharma <<a href="mailto:rekha1997jpr@gmail.com" target="_blank">rekha1997jpr@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left:1px solid rgb(204,204,204)"><div dir="ltr"><div dir="ltr">Dear Sir,<div>I have cloned it and then added the path to ~/.bashrc.</div><div><br></div><div>But my import mcu is not working.</div><div><br></div><div>My python path is:</div><div>export PYTHONPATH=/home/rekha/mcu:$PYTHONPATH<br></div><div><br></div><div>I have created a file "mcu.py" in which I kept </div></div><span style="font-size:13.33px">import mcu</span><br style="font-size:13.33px"><span style="font-size:13.33px">work = mcu.CELL(cif='conventional.</span><span style="font-size:13.33px">cif')</span><br style="font-size:13.33px"><span style="font-size:13.33px">prim_cell = work.to_prim_cell()</span><br style="font-size:13.33px"><span style="font-size:13.33px">work.write_cif(prim_cell, filename='primitive')</span><div><span style="font-size:13.33px"><br></span></div><div><span style="font-size:13.33px">and then invoked</span></div><div><span style="font-size:13.33px"><br></span></div><div><span style="font-size:13.33px">python mcu.py</span></div><div><span style="font-size:13.33px"><br></span></div><div><span style="font-size:13.33px">this gives me error</span></div><div><span style="font-size:13.33px"><br></span></div><div>Traceback (most recent call last):<br> File "mcu.py", line 1, in <module><br> import mcu<br> File "/home/rekha/case/mcu.py", line 2, in <module><br> work = mcu.CELL(cif='conventional.cif')<br>AttributeError: module 'mcu' has no attribute 'CELL'</div><div><br></div><div><br></div><div>I am having my conventional.cif in "/home/rekha/case/" directory.</div><div><br></div><div><br></div><div>What should I do now?</div><div><br></div><div><br><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Thu, Jul 16, 2020 at 10:44 PM Hung Pham <<a href="mailto:phamx494@umn.edu" target="_blank">phamx494@umn.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left:1px solid rgb(204,204,204)"><div dir="ltr"><div dir="ltr"><div dir="ltr">Sorry, there was a typo in the example script, it should be this:</div><blockquote style="padding:0px;margin-top:0px;margin-right:0px;margin-bottom:0px" dir="ltr"><div><span style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:normal;float:none;background-color:rgb(255,255,255)">import mcu</span><br style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal"><span style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:normal;float:none;background-color:rgb(255,255,255)">work = mcu.CELL(cif='conventional.</span><span style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:normal;float:none;background-color:rgb(255,255,255)">cif')</span><br style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal"><span style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:normal;float:none;background-color:rgb(255,255,255)">prim_cell = work.to_prim_cell()</span><br style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal"><span style="text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;font-family:Arial,Helvetica,sans-serif;font-size:13.33px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;display:inline;white-space:normal;float:none;background-color:rgb(255,255,255)">work.write_cif(prim_cell, filename='primitive')</span></div><div><b></b><i></i><u></u><sub></sub><sup></sup><strike></strike><br></div></blockquote><div>Hung Pham</div></div></div><br><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Thu, Jul 16, 2020 at 12:12 PM Hung Pham <<a href="mailto:phamx494@umn.edu" target="_blank">phamx494@umn.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left:1px solid rgb(204,204,204)"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>Hello Rekha,</div><div><br></div><div><a href="https://spglib.github.io/spglib/index.html" target="_blank">Spglib library</a> is doing what you are looking for. Spglib has a python interface and can be easily installed via Pip or conda..</div><div>But you need to make a cell tuple (from CIF) which contains the lattice information, this requires some minimal Python programming.</div><div>My <a href="https://github.com/hungpham2017/mcu/tree/dev" target="_blank">MCU</a> 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:</div><blockquote style="padding:0px;margin-top:0px;margin-right:0px;margin-bottom:0px"><div>import mcu<br>work = mcu.CELL(cif='conventional.cif')<br>primitive = work.to_prim_cell()<br>work.write_cif(prim_cell, filename='primitive')<strike></strike></div></blockquote><div>If you are interested in this, I can assist further.</div><div>Hung Pham</div><div><br></div></div></div></div></div><br><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Thu, Jul 16, 2020 at 11:57 AM rekha sharma <<a href="mailto:rekha1997jpr@gmail.com" target="_blank">rekha1997jpr@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left:1px solid rgb(204,204,204)"><div dir="auto"><div>Thank you very much sir,</div><div dir="auto"><br></div><div dir="auto">My materials are very new and not available in any database.<br><br><div class="gmail_quote" dir="auto"><div class="gmail_attr" dir="ltr">On Thu, Jul 16, 2020, 22:24 Yuvam Bhateja <<a href="mailto:yuvamb16@gmail.com" target="_blank">yuvamb16@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left:1px solid rgb(204,204,204)"><div dir="auto">Hello Rekha<div dir="auto"><br></div><div dir="auto">You can check out "Material Project".</div><div dir="auto">It's a database where researchers share their findings and results of several different types of materials and of different applications.</div><div dir="auto"><br></div><div dir="auto">Every compound is available in primitive, conventional, computed and symmetric unit cell, etc.</div><div dir="auto">Hope you find this useful.</div><div dir="auto"><br></div><div dir="auto">Regards</div><div dir="auto">Yuvam Bhateja</div></div><br><div class="gmail_quote"><div class="gmail_attr" dir="ltr">On Thu, 16 Jul 2020, 7:40 pm rekha sharma, <<a href="mailto:rekha1997jpr@gmail.com" rel="noreferrer" target="_blank">rekha1997jpr@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left:1px solid rgb(204,204,204)"><div dir="ltr">Dear Expert Users,<div><br><div>It is possible that this question has been answered many times before but I could not find it on the forum.</div><div><br></div><div>I have few complex structures and it is not possible to handle on my system in the conventional form.</div><div><br></div><div>Can you please advise any tool that can help me to convert a conventional cell cif file to a primitive cell file?</div><div><br></div><div>I have tried with VEST (niggli cell reduction) but it does not work for me. </div><div><br></div><div>Thank you very much.</div><div><div>Rekha<br></div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div></div></div></div></div></div></div></div></div>
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<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div><br clear="all"><br>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><br></div><div>Hung Q. Pham</div><div>Gagliardi Group</div><div>Office: Smith 101</div><div>Email: <a href="mailto:phamx494@umn.edu" target="_blank">phamx494@umn.edu</a></div><div>Personal page: <a href="http://hungpham2017.github.io" target="_blank">hungpham2017.github.io</a><br></div><div dir="ltr"><span style="font-size:12.8px">Department of Chemistry</span><br></div><div dir="ltr"><span style="font-size:12.8px">University of Minnesota - Twin Cities, </span><span style="font-size:12.8px">Minneapolis, MN 55455</span></div></div></div></div></div></div></div></div></div></div></div></div></div>
</blockquote></div><br clear="all"><br>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><br></div><div>Hung Q. Pham</div><div>Gagliardi Group</div><div>Office: Smith 101</div><div>Email: <a href="mailto:phamx494@umn.edu" target="_blank">phamx494@umn.edu</a></div><div>Personal page: <a href="http://hungpham2017.github.io" target="_blank">hungpham2017.github.io</a><br></div><div dir="ltr"><span style="font-size:12.8px">Department of Chemistry</span><br></div><div dir="ltr"><span style="font-size:12.8px">University of Minnesota - Twin Cities, </span><span style="font-size:12.8px">Minneapolis, MN 55455</span></div></div></div></div></div></div></div></div></div></div></div></div></div>
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<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><font face="georgia, serif" size="4"><br></font></div><div><font face="georgia, serif" size="4"><br></font></div><div><font face="georgia, serif" size="4"><br></font></div><div><font face="georgia, serif" size="4"><br></font></div><div><font face="georgia, serif" size="4">Best wishes</font></div><div><br></div><div><div><font color="#000000" face="georgia, serif" size="4">Ms. Rekha</font></div><div><span style="color:rgb(0,0,0);font-family:georgia,serif;font-size:large">Teaching Assistant,</span></div><div><font color="#000000" face="georgia, serif" size="4">Department of Physics</font></div><div><span style="color:rgb(0,0,0);font-family:georgia,serif;font-size:large">RK college, Jaipur, </span><span style="color:rgb(0,0,0);font-family:georgia,serif;font-size:large">India</span></div><div><font color="#000000" face="georgia, serif" size="4">Mob.: +11 90-95 790 71 697</font></div><div><font color="#000000" face="georgia, serif" size="4">Email: <a href="mailto:rekha1997jpr@gmail.com" target="_blank">rekha1997jpr@gmail.com</a></font></div></div></div></div></div></div></div></div>
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Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
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<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div><br clear="all"><br>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><br></div><div>Hung Q. Pham</div><div>Gagliardi Group</div><div>Office: Smith 101</div><div>Email: <a href="mailto:phamx494@umn.edu" target="_blank">phamx494@umn.edu</a></div><div>Personal page: <a href="http://hungpham2017.github.io" target="_blank">hungpham2017.github.io</a><br></div><div dir="ltr"><span style="font-size:12.8px">Department of Chemistry</span><br></div><div dir="ltr"><span style="font-size:12.8px">University of Minnesota - Twin Cities, </span><span style="font-size:12.8px">Minneapolis, MN 55455</span></div></div></div></div></div></div></div></div></div></div></div></div></div>
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Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><font face="georgia, serif" size="4"><br></font></div><div><font face="georgia, serif" size="4"><br></font></div><div><font face="georgia, serif" size="4"><br></font></div><div><font face="georgia, serif" size="4"><br></font></div><div><font face="georgia, serif" size="4">Best wishes</font></div><div><br></div><div><div><font face="georgia, serif" color="#000000" size="4">Ms. Rekha</font></div><div><span style="color:rgb(0,0,0);font-family:georgia,serif;font-size:large">Teaching Assistant,</span></div><div><font color="#000000" face="georgia, serif" size="4">Department of Physics</font></div><div><span style="color:rgb(0,0,0);font-family:georgia,serif;font-size:large">RK college, Jaipur, </span><span style="color:rgb(0,0,0);font-family:georgia,serif;font-size:large">India</span></div><div><font face="georgia, serif" color="#000000" size="4">Mob.: +11 90-95 790 71 697</font></div><div><font face="georgia, serif" color="#000000" size="4">Email: <a href="mailto:rekha1997jpr@gmail.com" target="_blank">rekha1997jpr@gmail.com</a></font></div></div></div></div></div></div></div></div>
_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">------------------------------------------------------------------------------------------------------------</div><div dir="ltr"><font face="georgia, serif">Yue-Wen FANG, PhD</font></div><div><font face="georgia, serif">Tokyo Institute of Technology, Japan</font></div><div dir="ltr"><div><div style="color:rgb(80,0,80);font-family:georgia,serif;font-size:12.8px"></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:14px;background-color:rgb(255,255,255)"><br></div></div><div><br></div><div><br></div></div></div></div></div></div></div></div></div></div></div>