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dos for elk not working

Open recohen opened this issue 3 years ago • 63 comments

I am trying to plot the dos for elk. I have the proper files: cohen@tomcat:/home/beegfs/rcohen/ELK/PTO/Yangzheng/EDOS/R3c/110GPa/LMIREP$ ls -ltr DOS -rw-r--r-- 1 rcohen tomcat 342 Mar 2 23:12 FERMIDOS.OUT -rw-r--r-- 1 rcohen tomcat 14802 Mar 2 23:30 TDOS.OUT -rw-r--r-- 1 rcohen tomcat 236832 Mar 2 23:31 PDOS_S01_A0001.OUT -rw-r--r-- 1 rcohen tomcat 236832 Mar 2 23:32 PDOS_S01_A0002.OUT -rw-r--r-- 1 rcohen tomcat 236832 Mar 2 23:33 PDOS_S02_A0001.OUT -rw-r--r-- 1 rcohen tomcat 236832 Mar 2 23:33 PDOS_S02_A0002.OUT -rw-r--r-- 1 rcohen tomcat 236832 Mar 2 23:34 PDOS_S03_A0001.OUT -rw-r--r-- 1 rcohen tomcat 236832 Mar 2 23:35 PDOS_S03_A0002.OUT -rw-r--r-- 1 rcohen tomcat 236832 Mar 2 23:36 PDOS_S03_A0003.OUT -rw-r--r-- 1 rcohen tomcat 236832 Mar 2 23:37 PDOS_S03_A0004.OUT -rw-r--r-- 1 rcohen tomcat 236832 Mar 2 23:38 PDOS_S03_A0005.OUT -rw-r--r-- 1 rcohen tomcat 236832 Mar 2 23:38 PDOS_S03_A0006.OUT -rw-r--r-- 1 rcohen tomcat 14802 Mar 2 23:38 IDOS.OUT

I can plot bands but for dos I get:

pyprocar.dosplot(elimit=[-3,3],code='elk')


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | |
|
| _, || |_| _
/ __,|| |/ A Python library for electronic structure pre/post-processing.

... cript initiated code : elk vasprun file : vasprun.xml mode : plain spin : None atoms list : None orbs. list : None energy range : [-3, 3] eolormap : jet vmax : None vmin : None grid enabled : True savefig : None title : None Traceback (most recent call last): File "", line 1, in File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptDosplot.py", line 91, in dosplot fig, ax1 = dos_plot.plot_total( UnboundLocalError: local variable 'dos_plot' referenced before assignment

I have tried different options first too, but this most basic form also does run. What am I doing wrong?

I am also interested whether it is possible to plot fatbands, rather than coded bands. For bands I have a different problem that some seem to belong to no atom! But that is a different issue.

Thank you!

Ron

recohen avatar Mar 03 '21 01:03 recohen

Hi Ron,

Would you mind sharing your calculations with us?

Pedram

petavazohi avatar Mar 03 '21 16:03 petavazohi

No problem! I am doing another elk run and then will upload the files.

Sincerely,

Ron

On Mar 3, 2021, at 11:34 AM, Pedram Tavadze [email protected] wrote:

Hi Ron,

Would you mind sharing your calculations with us?

Pedram

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Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

recohen avatar Mar 03 '21 16:03 recohen

Here are the files I think you need. If more, please let me know. The file was >10MB so here is a dropbox link: https://www.dropbox.com/s/9fw33j6hu9ooq7c/cohendata.tar.gz?dl=0

recohen avatar Mar 03 '21 17:03 recohen

Even worse, it seems the bandplot is incorrect. I attach here the bands from elk-bands (pdf) and also from pyprocar (png file) with Ti colors. I don't understand how the bands can be totally different. elk-bands.pdf bandplotTi

recohen avatar Mar 03 '21 18:03 recohen

Dear Ronald,

Can you try plotting again with "kdirect=False" in the pyprocar.bandsplot please? Also set the energy limits with elimit=[emin,emax] for an easier comparison.

Thanks,

Best, Uthpala

On Wed, Mar 3, 2021 at 1:35 PM Ronald Cohen [email protected] wrote:

Even worse, it seems the bandplot is incorrect. I attach here the bands from elk-bands (pdf) and also from pyprocar (png file) with Ti colors. I don't understand how the bands can be totally different. elk-bands.pdf https://github.com/romerogroup/pyprocar/files/6078313/elk-bands.pdf [image: bandplotTi] https://user-images.githubusercontent.com/4303093/109854599-3a60f900-7c25-11eb-9864-7160fc713b4e.png

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-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

uthpalaherath avatar Mar 03 '21 18:03 uthpalaherath

I tried this and I got: pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)

... Elk non spin calculation detected.

Traceback (most recent call last): File "", line 1, in File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py", line 223, in bandsplot procarFile = ElkParser(kdirect=kdirect) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/elkparser/elkparser.py", line 63, in init self._read_bands() File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/elkparser/elkparser.py", line 212, in _read_bands rf = open(self.file_names[0], "r") FileNotFoundError: [Errno 2] No such file or directory: 'BANDS.OUT'

I then tried ln -s BAND.OUT BANDS.OUT and get: Traceback (most recent call last): File "", line 1, in File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py", line 223, in bandsplot procarFile = ElkParser(kdirect=kdirect) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/elkparser/elkparser.py", line 63, in init self._read_bands() File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/elkparser/elkparser.py", line 248, in _read_bands self.kpoints = np.dot(self.kpoints, self.reclat) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/elkparser/elkparser.py", line 339, in reclat lattice_array = np.array(lattice_block[1].split(), dtype=float) IndexError: list index out of range

recohen avatar Mar 03 '21 18:03 recohen

OK--it seems it depends what the task is in elk.in! I had changed it t o get the dos. Now I changed it back to 22 and get a plot. You can see it here without kdirect=False, and there are extra bands! bandplotTi2 I also tried adding kdirect=False and get this error: pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False) Python library for electronic structure pre/post-processing.

Version 5.5.2 created on July 27th, 2020

Please cite: Herath, U., Tavadze, P., He, X., Bousquet, E., Singh, S., Muñoz, F. & Romero, A., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.

Script initiated code : elk input file : None mode : parametric spin comp. : 0 atoms list : [2, 3] orbs. list : [-1] fermi energy : None energy range : [-15, 15] colormap : jet markersize : 0.02 permissive : False vmax : None vmin : None grid enabled : True human : False savefig : None title : None outcar : None k-grid : cartesian (Remember to provide an output file for this case to work.)

Elk non spin calculation detected.

Traceback (most recent call last): File "", line 1, in File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py", line 223, in bandsplot procarFile = ElkParser(kdirect=kdirect) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/elkparser/elkparser.py", line 63, in init self._read_bands() File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/elkparser/elkparser.py", line 248, in _read_bands self.kpoints = np.dot(self.kpoints, self.reclat) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/elkparser/elkparser.py", line 339, in reclat lattice_array = np.array(lattice_block[1].split(), dtype=float) IndexError: list index out of range

recohen avatar Mar 03 '21 19:03 recohen

The bands actually look totally different!

recohen avatar Mar 03 '21 19:03 recohen

Just to confirm we are comparing elk-bands.pdf and the plot you got with kdirect=False, yes?

On Wed, Mar 3, 2021 at 2:06 PM Ronald Cohen [email protected] wrote:

The bands actually look totally different!

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-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

uthpalaherath avatar Mar 03 '21 19:03 uthpalaherath

No--with kdirect=False it crashes with IndexError: list index out of range It runs without kdirect=False

recohen avatar Mar 03 '21 19:03 recohen

Okay thanks for the information. I'll check the calculation and update you.

  • Uthpala

On Wed, Mar 3, 2021 at 2:17 PM Ronald Cohen [email protected] wrote:

No--with kdirect=False it crashes with IndexError: list index out of range It runs without kdirect=False

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-789990019, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMKFX6UB2IVIPOAMAADTB2DOPANCNFSM4YQDCDQQ .

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

uthpalaherath avatar Mar 03 '21 19:03 uthpalaherath

Dear Ronald,

Do you have the output data of the band structure calculation you ran with tasks: 22? If so please send them to me and I can try and figure out what's going on.

I tried to run the calculation with your elk.in but the xc types you used weren't available in my system.

Thank you,

Best regards, Uthpala

On Wed, Mar 3, 2021 at 2:24 PM Uthpala Herath [email protected] wrote:

Okay thanks for the information. I'll check the calculation and update you.

  • Uthpala

On Wed, Mar 3, 2021 at 2:17 PM Ronald Cohen [email protected] wrote:

No--with kdirect=False it crashes with IndexError: list index out of range It runs without kdirect=False

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-789990019, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMKFX6UB2IVIPOAMAADTB2DOPANCNFSM4YQDCDQQ .

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

uthpalaherath avatar Mar 05 '21 13:03 uthpalaherath

In the meantime, I fixed the issue with kdirect=False. With this the k-path would be in cartesian coordinates.

On Fri, Mar 5, 2021 at 8:22 AM Uthpala Herath [email protected] wrote:

Dear Ronald,

Do you have the output data of the band structure calculation you ran with tasks: 22? If so please send them to me and I can try and figure out what's going on.

I tried to run the calculation with your elk.in but the xc types you used weren't available in my system.

Thank you,

Best regards, Uthpala

On Wed, Mar 3, 2021 at 2:24 PM Uthpala Herath [email protected] wrote:

Okay thanks for the information. I'll check the calculation and update you.

  • Uthpala

On Wed, Mar 3, 2021 at 2:17 PM Ronald Cohen [email protected] wrote:

No--with kdirect=False it crashes with IndexError: list index out of range It runs without kdirect=False

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-789990019, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMKFX6UB2IVIPOAMAADTB2DOPANCNFSM4YQDCDQQ .

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

uthpalaherath avatar Mar 05 '21 17:03 uthpalaherath

Sorry—I just so this.I sent all the files to you in a dropbox link a couple days ago,

Sincerely,

Ron

On Mar 5, 2021, at 12:30 PM, Uthpala Herath [email protected] wrote:

In the meantime, I fixed the issue with kdirect=False. With this the k-path would be in cartesian coordinates.

On Fri, Mar 5, 2021 at 8:22 AM Uthpala Herath [email protected] wrote:

Dear Ronald,

Do you have the output data of the band structure calculation you ran with tasks: 22? If so please send them to me and I can try and figure out what's going on.

I tried to run the calculation with your elk.in but the xc types you used weren't available in my system.

Thank you,

Best regards, Uthpala

On Wed, Mar 3, 2021 at 2:24 PM Uthpala Herath [email protected] wrote:

Okay thanks for the information. I'll check the calculation and update you.

  • Uthpala

On Wed, Mar 3, 2021 at 2:17 PM Ronald Cohen [email protected] wrote:

No--with kdirect=False it crashes with IndexError: list index out of range It runs without kdirect=False

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-789990019, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMKFX6UB2IVIPOAMAADTB2DOPANCNFSM4YQDCDQQ .

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791567932, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5NTV33ZJD6VGUFUDLDTCEIMVANCNFSM4YQDCDQQ.


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

recohen avatar Mar 05 '21 18:03 recohen

Dear Ron,

I plot the band structure based on the calculated data you provided. A comparison between PyProcar's bands and the ones you provided are attached. They seem to be pretty much similar, however, since your calculation directory didn't have EFERMI.OUT and LATTICE.out (to get the reciprocal lattice vectors for converting from reduced to cartesian coordinates) I copied them from a calculation I did with a different set of xctypes. This probably explains the shift in Fermi energy. I can't seem to find many differences including the extra bands you mentioned, otherwise. Please correct me if I'm wrong.

Thank you,

Best regards, Uthpala

On Fri, Mar 5, 2021 at 1:42 PM Ronald Cohen [email protected] wrote:

Sorry—I just so this.I sent all the files to you in a dropbox link a couple days ago,

Sincerely,

Ron

On Mar 5, 2021, at 12:30 PM, Uthpala Herath [email protected] wrote:

In the meantime, I fixed the issue with kdirect=False. With this the k-path would be in cartesian coordinates.

On Fri, Mar 5, 2021 at 8:22 AM Uthpala Herath [email protected] wrote:

Dear Ronald,

Do you have the output data of the band structure calculation you ran with tasks: 22? If so please send them to me and I can try and figure out what's going on.

I tried to run the calculation with your elk.in but the xc types you used weren't available in my system.

Thank you,

Best regards, Uthpala

On Wed, Mar 3, 2021 at 2:24 PM Uthpala Herath [email protected] wrote:

Okay thanks for the information. I'll check the calculation and update you.

  • Uthpala

On Wed, Mar 3, 2021 at 2:17 PM Ronald Cohen <[email protected]

wrote:

No--with kdirect=False it crashes with IndexError: list index out of range It runs without kdirect=False

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-789990019>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AG3ZXMKFX6UB2IVIPOAMAADTB2DOPANCNFSM4YQDCDQQ

.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791567932>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABA2R5NTV33ZJD6VGUFUDLDTCEIMVANCNFSM4YQDCDQQ .


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

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-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

uthpalaherath avatar Mar 05 '21 19:03 uthpalaherath

I do not see your plots. I sent you before the comparison. The extra bands are the bottom two conduction bands. The rest of the bands are totally different too. But you have changed the code now?

recohen avatar Mar 05 '21 20:03 recohen

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:37 PM Uthpala Herath [email protected] wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:03 PM Ronald Cohen [email protected] wrote:

I do not see your plots. I sent you before the comparison. The extra bands are the bottom two conduction bands. The rest of the bands are totally different too. But you have changed the code now?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791650618, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMJLBXVELPCHMSK4HT3TCE2KJANCNFSM4YQDCDQQ .

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

uthpalaherath avatar Mar 05 '21 20:03 uthpalaherath

I didn’t get any attachments—now either. I tried your new version on gitup and get this:

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.5.2 created on July 27th, 2020

Please cite: Herath, U., Tavadze, P., He, X., Bousquet, E., Singh, S., Muñoz, F. & Romero, A., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.

Script initiated code : elk input file : None mode : parametric spin comp. : 0 atoms list : [2, 3] orbs. list : [-1] fermi energy : None energy range : [-15, 15] colormap : jet markersize : 0.02 permissive : False vmax : None vmin : None grid enabled : True human : False savefig : None title : None outcar : None k-grid : cartesian (Remember to provide an output file for this case to work.)

Elk non spin calculation detected.

Fermi energy : 0.4962075012 eV (from Elk output) Traceback (most recent call last): File "", line 1, in File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py", line 326, in bandsplot data = ProcarSelect(procarFile, deepCopy=True, mode=mode) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py", line 57, in init self.setData(ProcarData, deepCopy) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py", line 74, in setData self.spd = ProcarData.spd.copy() AttributeError: 'NoneType' object has no attribute 'copy'

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)

Ron

On Mar 5, 2021, at 3:39 PM, Uthpala Herath [email protected] wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:37 PM Uthpala Herath [email protected] wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:03 PM Ronald Cohen [email protected] wrote:

I do not see your plots. I sent you before the comparison. The extra bands are the bottom two conduction bands. The rest of the bands are totally different too. But you have changed the code now?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791650618, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMJLBXVELPCHMSK4HT3TCE2KJANCNFSM4YQDCDQQ .

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791674421, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5JBLXREG6762DE7J5TTCE6RFANCNFSM4YQDCDQQ.


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

recohen avatar Mar 05 '21 21:03 recohen

You seem to be using an out-dated version of PyProcar (5.5.2). Please update to the current version (5.6.3) and give it another try.

Here's the link to the images: https://drive.google.com/file/d/1fFE8tgWC5aorwBmmAT12sexRhNztzFU5/view?usp=sharing https://drive.google.com/file/d/1LhUS0bJCaKWAta78XgecL__5xJoPg-tw/view?usp=sharing

  • Uthpala

On Fri, Mar 5, 2021 at 4:39 PM Ronald Cohen [email protected] wrote:

I didn’t get any attachments—now either. I tried your new version on gitup and get this:

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.5.2 created on July 27th, 2020

Please cite: Herath, U., Tavadze, P., He, X., Bousquet, E., Singh, S., Muñoz, F. & Romero, A., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.

Script initiated code : elk input file : None mode : parametric spin comp. : 0 atoms list : [2, 3] orbs. list : [-1] fermi energy : None energy range : [-15, 15] colormap : jet markersize : 0.02 permissive : False vmax : None vmin : None grid enabled : True human : False savefig : None title : None outcar : None k-grid : cartesian (Remember to provide an output file for this case to work.)

Elk non spin calculation detected.

Fermi energy : 0.4962075012 eV (from Elk output) Traceback (most recent call last): File "", line 1, in File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py", line 326, in bandsplot data = ProcarSelect(procarFile, deepCopy=True, mode=mode) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py", line 57, in init self.setData(ProcarData, deepCopy) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py", line 74, in setData self.spd = ProcarData.spd.copy() AttributeError: 'NoneType' object has no attribute 'copy'

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)

Ron

On Mar 5, 2021, at 3:39 PM, Uthpala Herath [email protected] wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:37 PM Uthpala Herath [email protected] wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:03 PM Ronald Cohen [email protected] wrote:

I do not see your plots. I sent you before the comparison. The extra bands are the bottom two conduction bands. The rest of the bands are totally different too. But you have changed the code now?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791650618>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AG3ZXMJLBXVELPCHMSK4HT3TCE2KJANCNFSM4YQDCDQQ

.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791674421>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABA2R5JBLXREG6762DE7J5TTCE6RFANCNFSM4YQDCDQQ .


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791726504, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMLPSVQCEKYJND47HSLTCFFQPANCNFSM4YQDCDQQ .

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

uthpalaherath avatar Mar 05 '21 22:03 uthpalaherath

I got this from git hub. Just now: git pull https://github.com/romerogroup/pyprocar.git https://github.com/romerogroup/pyprocar.git Can you please put the current version on github?

Ron

On Mar 5, 2021, at 5:23 PM, Uthpala Herath [email protected] wrote:

You seem to be using an out-dated version of PyProcar (5.5.2). Please update to the current version (5.6.3) and give it another try.

Here's the link to the images: https://drive.google.com/file/d/1fFE8tgWC5aorwBmmAT12sexRhNztzFU5/view?usp=sharing https://drive.google.com/file/d/1LhUS0bJCaKWAta78XgecL__5xJoPg-tw/view?usp=sharing

  • Uthpala

On Fri, Mar 5, 2021 at 4:39 PM Ronald Cohen [email protected] wrote:

I didn’t get any attachments—now either. I tried your new version on gitup and get this:

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.5.2 created on July 27th, 2020

Please cite: Herath, U., Tavadze, P., He, X., Bousquet, E., Singh, S., Muñoz, F. & Romero, A., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.

Script initiated code : elk input file : None mode : parametric spin comp. : 0 atoms list : [2, 3] orbs. list : [-1] fermi energy : None energy range : [-15, 15] colormap : jet markersize : 0.02 permissive : False vmax : None vmin : None grid enabled : True human : False savefig : None title : None outcar : None k-grid : cartesian (Remember to provide an output file for this case to work.)

Elk non spin calculation detected.

Fermi energy : 0.4962075012 eV (from Elk output) Traceback (most recent call last): File "", line 1, in File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py", line 326, in bandsplot data = ProcarSelect(procarFile, deepCopy=True, mode=mode) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py", line 57, in init self.setData(ProcarData, deepCopy) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py", line 74, in setData self.spd = ProcarData.spd.copy() AttributeError: 'NoneType' object has no attribute 'copy'

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)

Ron

On Mar 5, 2021, at 3:39 PM, Uthpala Herath [email protected] wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:37 PM Uthpala Herath [email protected] wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:03 PM Ronald Cohen [email protected] wrote:

I do not see your plots. I sent you before the comparison. The extra bands are the bottom two conduction bands. The rest of the bands are totally different too. But you have changed the code now?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791650618>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AG3ZXMJLBXVELPCHMSK4HT3TCE2KJANCNFSM4YQDCDQQ

.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791674421>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABA2R5JBLXREG6762DE7J5TTCE6RFANCNFSM4YQDCDQQ .


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791726504, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMLPSVQCEKYJND47HSLTCFFQPANCNFSM4YQDCDQQ .

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791750210, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5K4GYIXD52L6TR25CLTCFKWZANCNFSM4YQDCDQQ.


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

recohen avatar Mar 05 '21 22:03 recohen

and conda

On Mar 5, 2021, at 5:23 PM, Uthpala Herath [email protected] wrote:

You seem to be using an out-dated version of PyProcar (5.5.2). Please update to the current version (5.6.3) and give it another try.

Here's the link to the images: https://drive.google.com/file/d/1fFE8tgWC5aorwBmmAT12sexRhNztzFU5/view?usp=sharing https://drive.google.com/file/d/1LhUS0bJCaKWAta78XgecL__5xJoPg-tw/view?usp=sharing

  • Uthpala

On Fri, Mar 5, 2021 at 4:39 PM Ronald Cohen [email protected] wrote:

I didn’t get any attachments—now either. I tried your new version on gitup and get this:

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.5.2 created on July 27th, 2020

Please cite: Herath, U., Tavadze, P., He, X., Bousquet, E., Singh, S., Muñoz, F. & Romero, A., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.

Script initiated code : elk input file : None mode : parametric spin comp. : 0 atoms list : [2, 3] orbs. list : [-1] fermi energy : None energy range : [-15, 15] colormap : jet markersize : 0.02 permissive : False vmax : None vmin : None grid enabled : True human : False savefig : None title : None outcar : None k-grid : cartesian (Remember to provide an output file for this case to work.)

Elk non spin calculation detected.

Fermi energy : 0.4962075012 eV (from Elk output) Traceback (most recent call last): File "", line 1, in File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py", line 326, in bandsplot data = ProcarSelect(procarFile, deepCopy=True, mode=mode) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py", line 57, in init self.setData(ProcarData, deepCopy) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py", line 74, in setData self.spd = ProcarData.spd.copy() AttributeError: 'NoneType' object has no attribute 'copy'

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)

Ron

On Mar 5, 2021, at 3:39 PM, Uthpala Herath [email protected] wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:37 PM Uthpala Herath [email protected] wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:03 PM Ronald Cohen [email protected] wrote:

I do not see your plots. I sent you before the comparison. The extra bands are the bottom two conduction bands. The rest of the bands are totally different too. But you have changed the code now?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791650618>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AG3ZXMJLBXVELPCHMSK4HT3TCE2KJANCNFSM4YQDCDQQ

.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791674421>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABA2R5JBLXREG6762DE7J5TTCE6RFANCNFSM4YQDCDQQ .


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791726504, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMLPSVQCEKYJND47HSLTCFFQPANCNFSM4YQDCDQQ .

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791750210, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5K4GYIXD52L6TR25CLTCFKWZANCNFSM4YQDCDQQ.


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

recohen avatar Mar 05 '21 22:03 recohen

I just reinstalled from conda and got the same error.

On Mar 5, 2021, at 5:23 PM, Uthpala Herath [email protected] wrote:

You seem to be using an out-dated version of PyProcar (5.5.2). Please update to the current version (5.6.3) and give it another try.

Here's the link to the images: https://drive.google.com/file/d/1fFE8tgWC5aorwBmmAT12sexRhNztzFU5/view?usp=sharing https://drive.google.com/file/d/1LhUS0bJCaKWAta78XgecL__5xJoPg-tw/view?usp=sharing

  • Uthpala

On Fri, Mar 5, 2021 at 4:39 PM Ronald Cohen [email protected] wrote:

I didn’t get any attachments—now either. I tried your new version on gitup and get this:

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.5.2 created on July 27th, 2020

Please cite: Herath, U., Tavadze, P., He, X., Bousquet, E., Singh, S., Muñoz, F. & Romero, A., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.

Script initiated code : elk input file : None mode : parametric spin comp. : 0 atoms list : [2, 3] orbs. list : [-1] fermi energy : None energy range : [-15, 15] colormap : jet markersize : 0.02 permissive : False vmax : None vmin : None grid enabled : True human : False savefig : None title : None outcar : None k-grid : cartesian (Remember to provide an output file for this case to work.)

Elk non spin calculation detected.

Fermi energy : 0.4962075012 eV (from Elk output) Traceback (most recent call last): File "", line 1, in File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py", line 326, in bandsplot data = ProcarSelect(procarFile, deepCopy=True, mode=mode) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py", line 57, in init self.setData(ProcarData, deepCopy) File "/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py", line 74, in setData self.spd = ProcarData.spd.copy() AttributeError: 'NoneType' object has no attribute 'copy'

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)

Ron

On Mar 5, 2021, at 3:39 PM, Uthpala Herath [email protected] wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:37 PM Uthpala Herath [email protected] wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:03 PM Ronald Cohen [email protected] wrote:

I do not see your plots. I sent you before the comparison. The extra bands are the bottom two conduction bands. The rest of the bands are totally different too. But you have changed the code now?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791650618>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AG3ZXMJLBXVELPCHMSK4HT3TCE2KJANCNFSM4YQDCDQQ

.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791674421>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABA2R5JBLXREG6762DE7J5TTCE6RFANCNFSM4YQDCDQQ .


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791726504, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMLPSVQCEKYJND47HSLTCFFQPANCNFSM4YQDCDQQ .

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791750210, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5K4GYIXD52L6TR25CLTCFKWZANCNFSM4YQDCDQQ.


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

recohen avatar Mar 05 '21 22:03 recohen

Yes, that is the current version. If you go to setup.json you can see that the version is 5.6.3.

The conda version is out-dated. Please install with either setup.py on github or pip with pip install pyprocar --upgrade.

Thanks

On Fri, Mar 5, 2021 at 5:26 PM Ronald Cohen [email protected] wrote:

I got this from git hub. Just now: git pull https://github.com/romerogroup/pyprocar.git < https://github.com/romerogroup/pyprocar.git> Can you please put the current version on github?

Ron

On Mar 5, 2021, at 5:23 PM, Uthpala Herath [email protected] wrote:

You seem to be using an out-dated version of PyProcar (5.5.2). Please update to the current version (5.6.3) and give it another try.

Here's the link to the images:

https://drive.google.com/file/d/1fFE8tgWC5aorwBmmAT12sexRhNztzFU5/view?usp=sharing

https://drive.google.com/file/d/1LhUS0bJCaKWAta78XgecL__5xJoPg-tw/view?usp=sharing

  • Uthpala

On Fri, Mar 5, 2021 at 4:39 PM Ronald Cohen [email protected] wrote:

I didn’t get any attachments—now either. I tried your new version on gitup and get this:

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.5.2 created on July 27th, 2020

Please cite: Herath, U., Tavadze, P., He, X., Bousquet, E., Singh, S., Muñoz, F. & Romero, A., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.

Script initiated code : elk input file : None mode : parametric spin comp. : 0 atoms list : [2, 3] orbs. list : [-1] fermi energy : None energy range : [-15, 15] colormap : jet markersize : 0.02 permissive : False vmax : None vmin : None grid enabled : True human : False savefig : None title : None outcar : None k-grid : cartesian (Remember to provide an output file for this case to work.)

Elk non spin calculation detected.

Fermi energy : 0.4962075012 eV (from Elk output) Traceback (most recent call last): File "", line 1, in File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py",

line 326, in bandsplot data = ProcarSelect(procarFile, deepCopy=True, mode=mode) File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py",

line 57, in init self.setData(ProcarData, deepCopy) File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py",

line 74, in setData self.spd = ProcarData.spd.copy() AttributeError: 'NoneType' object has no attribute 'copy'

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)

Ron

On Mar 5, 2021, at 3:39 PM, Uthpala Herath <[email protected]

wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:37 PM Uthpala Herath [email protected] wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:03 PM Ronald Cohen < [email protected]> wrote:

I do not see your plots. I sent you before the comparison. The extra bands are the bottom two conduction bands. The rest of the bands are totally different too. But you have changed the code now?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <

https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791650618>,

or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AG3ZXMJLBXVELPCHMSK4HT3TCE2KJANCNFSM4YQDCDQQ

.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <

https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791674421>,

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.


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791726504>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AG3ZXMLPSVQCEKYJND47HSLTCFFQPANCNFSM4YQDCDQQ

.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791750210>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABA2R5K4GYIXD52L6TR25CLTCFKWZANCNFSM4YQDCDQQ .


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791752068, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMLOWEH33PRURLI5I4LTCFLBPANCNFSM4YQDCDQQ .

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

uthpalaherath avatar Mar 05 '21 22:03 uthpalaherath

Thank you so much. I finally got the latest version installed.

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.6.3 created on Mar 5th, 2021

Please cite: Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080. ..

knames : ['$L$', '$\Gamma$', '$F$', '$L$', '$Z$', '$\Gamma$', '$M$'] kticks : [0, 46, 101, 148, 203, 253, 299] Fermi energy : 0.4446091604 eV (from Elk output) spd shape : (300, 251, 1, 11, 18) [kpoints, bands, spins, atoms+1, orbitals+2] normalizing to : (0.0, 0.9204) (<Figure size 1400x950 with 2 Axes>, <AxesSubplot:ylabel='$E-E_f$ [eV]'>)

Now it looks ok! Thank you!

the correct band a structure is:

Sincerely,

Ron

On Mar 5, 2021, at 5:31 PM, Uthpala Herath [email protected] wrote:

Yes, that is the current version. If you go to setup.json you can see that the version is 5.6.3.

The conda version is out-dated. Please install with either setup.py on github or pip with pip install pyprocar --upgrade.

Thanks

On Fri, Mar 5, 2021 at 5:26 PM Ronald Cohen [email protected] wrote:

I got this from git hub. Just now: git pull https://github.com/romerogroup/pyprocar.git < https://github.com/romerogroup/pyprocar.git> Can you please put the current version on github?

Ron

On Mar 5, 2021, at 5:23 PM, Uthpala Herath [email protected] wrote:

You seem to be using an out-dated version of PyProcar (5.5.2). Please update to the current version (5.6.3) and give it another try.

Here's the link to the images:

https://drive.google.com/file/d/1fFE8tgWC5aorwBmmAT12sexRhNztzFU5/view?usp=sharing

https://drive.google.com/file/d/1LhUS0bJCaKWAta78XgecL__5xJoPg-tw/view?usp=sharing

  • Uthpala

On Fri, Mar 5, 2021 at 4:39 PM Ronald Cohen [email protected] wrote:

I didn’t get any attachments—now either. I tried your new version on gitup and get this:

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.5.2 created on July 27th, 2020

Please cite: Herath, U., Tavadze, P., He, X., Bousquet, E., Singh, S., Muñoz, F. & Romero, A., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.

Script initiated code : elk input file : None mode : parametric spin comp. : 0 atoms list : [2, 3] orbs. list : [-1] fermi energy : None energy range : [-15, 15] colormap : jet markersize : 0.02 permissive : False vmax : None vmin : None grid enabled : True human : False savefig : None title : None outcar : None k-grid : cartesian (Remember to provide an output file for this case to work.)

Elk non spin calculation detected.

Fermi energy : 0.4962075012 eV (from Elk output) Traceback (most recent call last): File "", line 1, in File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py",

line 326, in bandsplot data = ProcarSelect(procarFile, deepCopy=True, mode=mode) File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py",

line 57, in init self.setData(ProcarData, deepCopy) File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py",

line 74, in setData self.spd = ProcarData.spd.copy() AttributeError: 'NoneType' object has no attribute 'copy'

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)

Ron

On Mar 5, 2021, at 3:39 PM, Uthpala Herath <[email protected]

wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:37 PM Uthpala Herath [email protected] wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:03 PM Ronald Cohen < [email protected]> wrote:

I do not see your plots. I sent you before the comparison. The extra bands are the bottom two conduction bands. The rest of the bands are totally different too. But you have changed the code now?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <

https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791650618>,

or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AG3ZXMJLBXVELPCHMSK4HT3TCE2KJANCNFSM4YQDCDQQ

.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <

https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791674421>,

or unsubscribe <

https://github.com/notifications/unsubscribe-auth/ABA2R5JBLXREG6762DE7J5TTCE6RFANCNFSM4YQDCDQQ

.


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791726504>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AG3ZXMLPSVQCEKYJND47HSLTCFFQPANCNFSM4YQDCDQQ

.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791750210>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABA2R5K4GYIXD52L6TR25CLTCFKWZANCNFSM4YQDCDQQ .


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791752068, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMLOWEH33PRURLI5I4LTCFLBPANCNFSM4YQDCDQQ .

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791758596, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5NUJ7I3VLVVQQ6FKSDTCFLUVANCNFSM4YQDCDQQ.


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

recohen avatar Mar 08 '21 17:03 recohen

Ron,

Just wanted to let you know, we're working on the debugging of DOS for elk. It should be done soon.

Pedram

On Mon, Mar 8, 2021 at 12:07 PM Ronald Cohen [email protected] wrote:

Thank you so much. I finally got the latest version installed.

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.6.3 created on Mar 5th, 2021

Please cite: Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080. ..

knames : ['$L$', '$\Gamma$', '$F$', '$L$', '$Z$', '$\Gamma$', '$M$'] kticks : [0, 46, 101, 148, 203, 253, 299] Fermi energy : 0.4446091604 eV (from Elk output) spd shape : (300, 251, 1, 11, 18) [kpoints, bands, spins, atoms+1, orbitals+2] normalizing to : (0.0, 0.9204) (<Figure size 1400x950 with 2 Axes>, <AxesSubplot:ylabel='$E-E_f$ [eV]'>)

Now it looks ok! Thank you!

the correct band a structure is:

Sincerely,

Ron

On Mar 5, 2021, at 5:31 PM, Uthpala Herath [email protected] wrote:

Yes, that is the current version. If you go to setup.json you can see that the version is 5.6.3.

The conda version is out-dated. Please install with either setup.py on github or pip with pip install pyprocar --upgrade.

Thanks

On Fri, Mar 5, 2021 at 5:26 PM Ronald Cohen [email protected] wrote:

I got this from git hub. Just now: git pull https://github.com/romerogroup/pyprocar.git < https://github.com/romerogroup/pyprocar.git> Can you please put the current version on github?

Ron

On Mar 5, 2021, at 5:23 PM, Uthpala Herath <[email protected]

wrote:

You seem to be using an out-dated version of PyProcar (5.5.2). Please update to the current version (5.6.3) and give it another try.

Here's the link to the images:

https://drive.google.com/file/d/1fFE8tgWC5aorwBmmAT12sexRhNztzFU5/view?usp=sharing

https://drive.google.com/file/d/1LhUS0bJCaKWAta78XgecL__5xJoPg-tw/view?usp=sharing

  • Uthpala

On Fri, Mar 5, 2021 at 4:39 PM Ronald Cohen < [email protected]> wrote:

I didn’t get any attachments—now either. I tried your new version on gitup and get this:

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.5.2 created on July 27th, 2020

Please cite: Herath, U., Tavadze, P., He, X., Bousquet, E., Singh, S., Muñoz, F. & Romero, A., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.

Script initiated code : elk input file : None mode : parametric spin comp. : 0 atoms list : [2, 3] orbs. list : [-1] fermi energy : None energy range : [-15, 15] colormap : jet markersize : 0.02 permissive : False vmax : None vmin : None grid enabled : True human : False savefig : None title : None outcar : None k-grid : cartesian (Remember to provide an output file for this case to work.)

Elk non spin calculation detected.

Fermi energy : 0.4962075012 eV (from Elk output) Traceback (most recent call last): File "", line 1, in File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py",

line 326, in bandsplot data = ProcarSelect(procarFile, deepCopy=True, mode=mode) File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py",

line 57, in init self.setData(ProcarData, deepCopy) File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py",

line 74, in setData self.spd = ProcarData.spd.copy() AttributeError: 'NoneType' object has no attribute 'copy'

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)

Ron

On Mar 5, 2021, at 3:39 PM, Uthpala Herath < [email protected]

wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:37 PM Uthpala Herath < [email protected]> wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:03 PM Ronald Cohen < [email protected]> wrote:

I do not see your plots. I sent you before the comparison. The extra bands are the bottom two conduction bands. The rest of the bands are totally different too. But you have changed the code now?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <

https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791650618>,

or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AG3ZXMJLBXVELPCHMSK4HT3TCE2KJANCNFSM4YQDCDQQ

.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <

https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791674421>,

or unsubscribe <

https://github.com/notifications/unsubscribe-auth/ABA2R5JBLXREG6762DE7J5TTCE6RFANCNFSM4YQDCDQQ

.


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <

https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791726504>,

or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AG3ZXMLPSVQCEKYJND47HSLTCFFQPANCNFSM4YQDCDQQ

.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <

https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791750210>,

or unsubscribe <

https://github.com/notifications/unsubscribe-auth/ABA2R5K4GYIXD52L6TR25CLTCFKWZANCNFSM4YQDCDQQ

.


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791752068>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AG3ZXMLOWEH33PRURLI5I4LTCFLBPANCNFSM4YQDCDQQ

.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791758596>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABA2R5NUJ7I3VLVVQQ6FKSDTCFLUVANCNFSM4YQDCDQQ .


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-792907346, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHBQJCI2VI7LX46TYWIIKK3TCT75JANCNFSM4YQDCDQQ .

petavazohi avatar Mar 08 '21 17:03 petavazohi

No problem. Just to sum up, it worked when you set kdirect=False and you got wrong bands when you didn't?

  • Uthpala

On Mon, Mar 8, 2021 at 12:07 PM Ronald Cohen [email protected] wrote:

Thank you so much. I finally got the latest version installed.

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.6.3 created on Mar 5th, 2021

Please cite: Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080. ..

knames : ['$L$', '$\Gamma$', '$F$', '$L$', '$Z$', '$\Gamma$', '$M$'] kticks : [0, 46, 101, 148, 203, 253, 299] Fermi energy : 0.4446091604 eV (from Elk output) spd shape : (300, 251, 1, 11, 18) [kpoints, bands, spins, atoms+1, orbitals+2] normalizing to : (0.0, 0.9204) (<Figure size 1400x950 with 2 Axes>, <AxesSubplot:ylabel='$E-E_f$ [eV]'>)

Now it looks ok! Thank you!

the correct band a structure is:

Sincerely,

Ron

On Mar 5, 2021, at 5:31 PM, Uthpala Herath [email protected] wrote:

Yes, that is the current version. If you go to setup.json you can see that the version is 5.6.3.

The conda version is out-dated. Please install with either setup.py on github or pip with pip install pyprocar --upgrade.

Thanks

On Fri, Mar 5, 2021 at 5:26 PM Ronald Cohen [email protected] wrote:

I got this from git hub. Just now: git pull https://github.com/romerogroup/pyprocar.git < https://github.com/romerogroup/pyprocar.git> Can you please put the current version on github?

Ron

On Mar 5, 2021, at 5:23 PM, Uthpala Herath <[email protected]

wrote:

You seem to be using an out-dated version of PyProcar (5.5.2). Please update to the current version (5.6.3) and give it another try.

Here's the link to the images:

https://drive.google.com/file/d/1fFE8tgWC5aorwBmmAT12sexRhNztzFU5/view?usp=sharing

https://drive.google.com/file/d/1LhUS0bJCaKWAta78XgecL__5xJoPg-tw/view?usp=sharing

  • Uthpala

On Fri, Mar 5, 2021 at 4:39 PM Ronald Cohen < [email protected]> wrote:

I didn’t get any attachments—now either. I tried your new version on gitup and get this:

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.5.2 created on July 27th, 2020

Please cite: Herath, U., Tavadze, P., He, X., Bousquet, E., Singh, S., Muñoz, F. & Romero, A., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.

Script initiated code : elk input file : None mode : parametric spin comp. : 0 atoms list : [2, 3] orbs. list : [-1] fermi energy : None energy range : [-15, 15] colormap : jet markersize : 0.02 permissive : False vmax : None vmin : None grid enabled : True human : False savefig : None title : None outcar : None k-grid : cartesian (Remember to provide an output file for this case to work.)

Elk non spin calculation detected.

Fermi energy : 0.4962075012 eV (from Elk output) Traceback (most recent call last): File "", line 1, in File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py",

line 326, in bandsplot data = ProcarSelect(procarFile, deepCopy=True, mode=mode) File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py",

line 57, in init self.setData(ProcarData, deepCopy) File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py",

line 74, in setData self.spd = ProcarData.spd.copy() AttributeError: 'NoneType' object has no attribute 'copy'

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)

Ron

On Mar 5, 2021, at 3:39 PM, Uthpala Herath < [email protected]

wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:37 PM Uthpala Herath < [email protected]> wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:03 PM Ronald Cohen < [email protected]> wrote:

I do not see your plots. I sent you before the comparison. The extra bands are the bottom two conduction bands. The rest of the bands are totally different too. But you have changed the code now?

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Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

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.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] [email protected] Website: https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791758596>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABA2R5NUJ7I3VLVVQQ6FKSDTCFLUVANCNFSM4YQDCDQQ .


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

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uthpalaherath avatar Mar 08 '21 18:03 uthpalaherath

However, I am not sure about the color shading . The attached dos shows that lowest conduction bands are Ti 3d,, but these are not shaded showing atom type 2. Is this just the color map? How to change the colormap? Thanks!

Ron

On Mar 8, 2021, at 12:07 PM, Ronald Cohen [email protected] wrote:

Thank you so much. I finally got the latest version installed.

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.6.3 created on Mar 5th, 2021

Please cite: Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080. ..

knames : ['$L$', '$\Gamma$', '$F$', '$L$', '$Z$', '$\Gamma$', '$M$'] kticks : [0, 46, 101, 148, 203, 253, 299] Fermi energy : 0.4446091604 eV (from Elk output) spd shape : (300, 251, 1, 11, 18) [kpoints, bands, spins, atoms+1, orbitals+2] normalizing to : (0.0, 0.9204) (<Figure size 1400x950 with 2 Axes>, <AxesSubplot:ylabel='$E-E_f$ [eV]'>)

Now it looks ok! Thank you!

<PastedGraphic-1.png> the correct band a structure is:

<elk-bands.pdf>

Sincerely,

Ron

On Mar 5, 2021, at 5:31 PM, Uthpala Herath <[email protected] mailto:[email protected]> wrote:

Yes, that is the current version. If you go to setup.json you can see that the version is 5.6.3.

The conda version is out-dated. Please install with either setup.py on github or pip with pip install pyprocar --upgrade.

Thanks

On Fri, Mar 5, 2021 at 5:26 PM Ronald Cohen <[email protected] mailto:[email protected]> wrote:

I got this from git hub. Just now: git pull https://github.com/romerogroup/pyprocar.git https://github.com/romerogroup/pyprocar.git < https://github.com/romerogroup/pyprocar.git https://github.com/romerogroup/pyprocar.git> Can you please put the current version on github?

Ron

On Mar 5, 2021, at 5:23 PM, Uthpala Herath <[email protected] mailto:[email protected]> wrote:

You seem to be using an out-dated version of PyProcar (5.5.2). Please update to the current version (5.6.3) and give it another try.

Here's the link to the images:

https://drive.google.com/file/d/1fFE8tgWC5aorwBmmAT12sexRhNztzFU5/view?usp=sharing https://drive.google.com/file/d/1fFE8tgWC5aorwBmmAT12sexRhNztzFU5/view?usp=sharing

https://drive.google.com/file/d/1LhUS0bJCaKWAta78XgecL__5xJoPg-tw/view?usp=sharing https://drive.google.com/file/d/1LhUS0bJCaKWAta78XgecL__5xJoPg-tw/view?usp=sharing

  • Uthpala

On Fri, Mar 5, 2021 at 4:39 PM Ronald Cohen <[email protected] mailto:[email protected]> wrote:

I didn’t get any attachments—now either. I tried your new version on gitup and get this:

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.5.2 created on July 27th, 2020

Please cite: Herath, U., Tavadze, P., He, X., Bousquet, E., Singh, S., Muñoz, F. & Romero, A., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.

Script initiated code : elk input file : None mode : parametric spin comp. : 0 atoms list : [2, 3] orbs. list : [-1] fermi energy : None energy range : [-15, 15] colormap : jet markersize : 0.02 permissive : False vmax : None vmin : None grid enabled : True human : False savefig : None title : None outcar : None k-grid : cartesian (Remember to provide an output file for this case to work.)

Elk non spin calculation detected.

Fermi energy : 0.4962075012 eV (from Elk output) Traceback (most recent call last): File "", line 1, in File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py",

line 326, in bandsplot data = ProcarSelect(procarFile, deepCopy=True, mode=mode) File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py",

line 57, in init self.setData(ProcarData, deepCopy) File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py",

line 74, in setData self.spd = ProcarData.spd.copy() AttributeError: 'NoneType' object has no attribute 'copy'

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)

Ron

On Mar 5, 2021, at 3:39 PM, Uthpala Herath <[email protected] mailto:[email protected]

wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:37 PM Uthpala Herath <[email protected] mailto:[email protected]> wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:03 PM Ronald Cohen < [email protected] mailto:[email protected]> wrote:

I do not see your plots. I sent you before the comparison. The extra bands are the bottom two conduction bands. The rest of the bands are totally different too. But you have changed the code now?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <

https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791650618 https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791650618>,

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.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] mailto:[email protected] <[email protected] mailto:[email protected]> Website: https://uthpalaherath.github.io/ https://uthpalaherath.github.io/

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] mailto:[email protected] <[email protected] mailto:[email protected]> Website: https://uthpalaherath.github.io/ https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <

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Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] <mailto:[email protected] mailto:[email protected]> office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791726504 https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791726504>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AG3ZXMLPSVQCEKYJND47HSLTCFFQPANCNFSM4YQDCDQQ https://github.com/notifications/unsubscribe-auth/AG3ZXMLPSVQCEKYJND47HSLTCFFQPANCNFSM4YQDCDQQ

.

-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

Tel. (304) 216-2535 Email: [email protected] mailto:[email protected] <[email protected] mailto:[email protected]> Website: https://uthpalaherath.github.io/ https://uthpalaherath.github.io/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791750210 https://github.com/romerogroup/pyprocar/issues/46#issuecomment-791750210>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABA2R5K4GYIXD52L6TR25CLTCFKWZANCNFSM4YQDCDQQ https://github.com/notifications/unsubscribe-auth/ABA2R5K4GYIXD52L6TR25CLTCFKWZANCNFSM4YQDCDQQ .


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] <mailto:[email protected] mailto:[email protected]> office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

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-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

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Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

recohen avatar Mar 08 '21 19:03 recohen

Often (usually) when I do the import it hangs, and ps shows a huge mess. Do you know what it is trying to compile and why, and why the command line is so long:

55541 pts/18 R+ 0:02 ld /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/../lib64/crt1.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtbegin.o --eh-frame-hdr --build-id -dynamic-linker /lib64/ld-linux-x86-64.so.2 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/home/beegfs/intel/oneapi/clck/2021.1.1/lib/intel64 -L/home/beegfs/intel/oneapi/ippcp/2021.1.1/lib/intel64 -L/home/beegfs/intel/oneapi/vpl/2021.1.1/lib -L/home/beegfs/intel/oneapi/ccl/2021.1.1/lib/cpu_gpu_dpcpp -L/home/beegfs/intel/oneapi/mpi/2021.1.1//libfabric/lib -L/home/beegfs/intel/oneapi/mpi/2021.1.1//lib/release -L/home/beegfs/intel/oneapi/mpi/2021.1.1//lib -L/home/beegfs/intel/oneapi/dnnl/2021.1.1/cpu_dpcpp_gpu_dpcpp/lib -L/home/beegfs/intel/oneapi/dal/2021.1.1/lib/intel64 -L/home/beegfs/intel/oneapi/ipp/2021.1.1/lib/intel64 -L/home/beegfs/intel/oneapi/mkl/latest/lib/intel64 -L/home/beegfs/intel/oneapi/compiler/2021.1.1/linux/compiler/lib/intel64_lin -L/home/beegfs/intel/oneapi/compiler/2021.1.1/linux/lib -L/home/beegfs/intel/oneapi/tbb/2021.1.1/env/../lib/intel64/gcc4.8 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../.. -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/ -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/ -L/lib/../lib64/ -L/usr/lib/../lib64/ -L/home/beegfs/intel/oneapi/clck/2021.1.1/lib/intel64/ -L/home/beegfs/intel/oneapi/ippcp/2021.1.1/lib/intel64/ -L/home/beegfs/intel/oneapi/vpl/2021.1.1/lib/ -L/home/beegfs/intel/oneapi/ccl/2021.1.1/lib/cpu_gpu_dpcpp/ -L/home/beegfs/intel/oneapi/mpi/2021.1.1//libfabric/lib/ -L/home/beegfs/intel/oneapi/mpi/2021.1.1//lib/release/ -L/home/beegfs/intel/oneapi/mpi/2021.1.1//lib/ -L/home/beegfs/intel/oneapi/dnnl/2021.1.1/cpu_dpcpp_gpu_dpcpp/lib/ -L/home/beegfs/intel/oneapi/dal/2021.1.1/lib/intel64/ -L/home/beegfs/intel/oneapi/ipp/2021.1.1/lib/intel64/ 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-lirng -Bdynamic -Bstatic -lirng -Bdynamic -L/home/beegfs/intel/oneapi/compiler/2021.1.1/linux/bin/intel64/../../compiler/lib/intel64_lin -Bstatic -lirng -Bdynamic -lc /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtend.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/../lib64/crtn.o -Bdynamic -Bstatic -limf -lsvml -lirng -Bdynamic -Bstatic -limf -Bdynamic -Bstatic -limf -Bdynamic -Bstatic -limf -Bdynamic -Bstatic -limf -Bdynamic -Bstatic -limf -Bdynamic -Bstatic -limf -Bdynamic -Bstatic -limf -Bdynamic -Bstatic -limf -Bdynamic -Bstatic -limf -Bdynamic -Bstatic -limf -Bdynamic -Bstatic -limf -Bdynamic -L/home/beegfs/intel/oneapi/compiler/2021.1.1/linux/bin/intel64/../../compiler/lib/intel64_lin -Bstatic -limf -Bdynamic -lm -Bstatic -lipgo -ldecimal -Bdynamic -lcilkrts -lstdc++ -lgcc -lgcc_s -Bstatic -lirc -lsvml -Bdynamic -Bstatic -lirng -Bdynamic -Bstat

recohen avatar Mar 08 '21 19:03 recohen

Also dosplot still doesn’t work:

pyprocar.dosplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3])


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.6.3 created on Mar 5th, 2021

Please cite: Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.

Developers:

  • Francisco Muñoz
  • Aldo Romero
  • Sobhit Singh
  • Uthpala Herath
  • Pedram Tavadze
  • Eric Bousquet
  • Xu He
  • Reese Boucher
  • Logan Lang
  • Freddy Farah

Script initiated code : elk File name : vasprun.xml mode : parametric spins : None atoms list : [2, 3] orbs. list : None energy range : [-15, 15] colormap : jet vmax : None vmin : None grid enabled : False savefig : None title : None Traceback (most recent call last): File "", line 1, in File "/home/rcohen/.conda/envs/newrec3/lib/python3.6/site-packages/pyprocar/scriptDosplot.py", line 461, in dosplot fig, ax1 = dos_plot.plot_parametric( UnboundLocalError: local variable 'dos_plot' referenced before assignment

recohen avatar Mar 08 '21 19:03 recohen

I did python -v and here is where import hangs: mport 'trimesh.exchange.misc' # <_frozen_importlib_external.SourceFileLoader object at 0x2af68773ec50>

/home/rcohen/.conda/envs/newrec3/lib/python3.6/site-packages/trimesh/exchange/pycache/assimp.cpython-36.pyc matches /home/rcohen/.conda/envs/newrec3/lib/python3.6/site-packages/trimesh/exchange/assimp.py

code object from '/home/rcohen/.conda/envs/newrec3/lib/python3.6/site-packages/trimesh/exchange/pycache/assimp.cpython-36.pyc'

import 'trimesh.exchange.assimp' # <_frozen_importlib_external.SourceFileLoader object at 0x2af6878e1f98>

/home/rcohen/.conda/envs/newrec3/lib/python3.6/site-packages/trimesh/exchange/pycache/threemf.cpython-36.pyc matches /home/rcohen/.conda/envs/newrec3/lib/python3.6/site-packages/trimesh/exchange/threemf.py

code object from '/home/rcohen/.conda/envs/newrec3/lib/python3.6/site-packages/trimesh/exchange/pycache/threemf.cpython-36.pyc'

import 'trimesh.exchange.threemf' # <_frozen_importlib_external.SourceFileLoader object at 0x2af6878e9668>

/home/rcohen/.conda/envs/newrec3/lib/python3.6/site-packages/trimesh/exchange/pycache/openctm.cpython-36.pyc matches /home/rcohen/.conda/envs/newrec3/lib/python3.6/site-packages/trimesh/exchange/openctm.py

code object from '/home/rcohen/.conda/envs/newrec3/lib/python3.6/site-packages/trimesh/exchange/pycache/openctm.cpython-36.pyc'

On Mar 8, 2021, at 2:17 PM, Ronald Cohen [email protected] wrote:

However, I am not sure about the color shading . The attached dos shows that lowest conduction bands are Ti 3d,, but these are not shaded showing atom type 2. Is this just the color map? How to change the colormap? Thanks!

Ron

<PastedGraphic-2.png> <PDOS_S02_A0001.OUT.columns_Tid.pdf> <PDOS_S03_A0001.OUT.columns_Osp.pdf>

On Mar 8, 2021, at 12:07 PM, Ronald Cohen <[email protected] mailto:[email protected]> wrote:

Thank you so much. I finally got the latest version installed.

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.6.3 created on Mar 5th, 2021

Please cite: Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz and Aldo Romero., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080. ..

knames : ['$L$', '$\Gamma$', '$F$', '$L$', '$Z$', '$\Gamma$', '$M$'] kticks : [0, 46, 101, 148, 203, 253, 299] Fermi energy : 0.4446091604 eV (from Elk output) spd shape : (300, 251, 1, 11, 18) [kpoints, bands, spins, atoms+1, orbitals+2] normalizing to : (0.0, 0.9204) (<Figure size 1400x950 with 2 Axes>, <AxesSubplot:ylabel='$E-E_f$ [eV]'>)

Now it looks ok! Thank you!

<PastedGraphic-1.png> the correct band a structure is:

<elk-bands.pdf>

Sincerely,

Ron

On Mar 5, 2021, at 5:31 PM, Uthpala Herath <[email protected] mailto:[email protected]> wrote:

Yes, that is the current version. If you go to setup.json you can see that the version is 5.6.3.

The conda version is out-dated. Please install with either setup.py on github or pip with pip install pyprocar --upgrade.

Thanks

On Fri, Mar 5, 2021 at 5:26 PM Ronald Cohen <[email protected] mailto:[email protected]> wrote:

I got this from git hub. Just now: git pull https://github.com/romerogroup/pyprocar.git https://github.com/romerogroup/pyprocar.git < https://github.com/romerogroup/pyprocar.git https://github.com/romerogroup/pyprocar.git> Can you please put the current version on github?

Ron

On Mar 5, 2021, at 5:23 PM, Uthpala Herath <[email protected] mailto:[email protected]> wrote:

You seem to be using an out-dated version of PyProcar (5.5.2). Please update to the current version (5.6.3) and give it another try.

Here's the link to the images:

https://drive.google.com/file/d/1fFE8tgWC5aorwBmmAT12sexRhNztzFU5/view?usp=sharing https://drive.google.com/file/d/1fFE8tgWC5aorwBmmAT12sexRhNztzFU5/view?usp=sharing

https://drive.google.com/file/d/1LhUS0bJCaKWAta78XgecL__5xJoPg-tw/view?usp=sharing https://drive.google.com/file/d/1LhUS0bJCaKWAta78XgecL__5xJoPg-tw/view?usp=sharing

  • Uthpala

On Fri, Mar 5, 2021 at 4:39 PM Ronald Cohen <[email protected] mailto:[email protected]> wrote:

I didn’t get any attachments—now either. I tried your new version on gitup and get this:

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)


| _ \ _ | _ \ _ __ ___ ___ __ _ _ __ | |) | | | | |) | '__/ _ \ / / _` | '| | __/| || | /| | | () | (| (| | | || _, || |_| _/ __,|| |/ A Python library for electronic structure pre/post-processing.

Version 5.5.2 created on July 27th, 2020

Please cite: Herath, U., Tavadze, P., He, X., Bousquet, E., Singh, S., Muñoz, F. & Romero, A., PyProcar: A Python library for electronic structure pre/post-processing., Computer Physics Communications 251 (2020):107080.

Script initiated code : elk input file : None mode : parametric spin comp. : 0 atoms list : [2, 3] orbs. list : [-1] fermi energy : None energy range : [-15, 15] colormap : jet markersize : 0.02 permissive : False vmax : None vmin : None grid enabled : True human : False savefig : None title : None outcar : None k-grid : cartesian (Remember to provide an output file for this case to work.)

Elk non spin calculation detected.

Fermi energy : 0.4962075012 eV (from Elk output) Traceback (most recent call last): File "", line 1, in File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/scriptBandsplot.py",

line 326, in bandsplot data = ProcarSelect(procarFile, deepCopy=True, mode=mode) File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py",

line 57, in init self.setData(ProcarData, deepCopy) File

"/home/beegfs/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/pyprocar/procarselect/procarselect.py",

line 74, in setData self.spd = ProcarData.spd.copy() AttributeError: 'NoneType' object has no attribute 'copy'

pyprocar.bandsplot(elimit=[-15,15],cmap='jet',mode='parametric',code='elk',atoms=[2,3],kdirect=False)

Ron

On Mar 5, 2021, at 3:39 PM, Uthpala Herath <[email protected] mailto:[email protected]

wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:37 PM Uthpala Herath <[email protected] mailto:[email protected]> wrote:

Sorry I sent that in .eps format which your computer may have trouble rendering. Here it is again as a .png additionally with a comparison between the lower conduction bands.

[image: compare-elk-bands-conduction.png] I am not sure where the bands are totally different. Yes there was a bug related to retrieving the reciprocal lattice vectors needed to plot the bands in cartesian coordinates instead of reduced.

Best, Uthpala

On Fri, Mar 5, 2021 at 3:03 PM Ronald Cohen < [email protected] mailto:[email protected]> wrote:

I do not see your plots. I sent you before the comparison. The extra bands are the bottom two conduction bands. The rest of the bands are totally different too. But you have changed the code now?

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Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] <mailto:[email protected] mailto:[email protected]> office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

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-- Uthpala Herath PhD Candidate Department of Physics and Astronomy West Virginia University Morgantown, WV 26505

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Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3


Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] mailto:[email protected] office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

recohen avatar Mar 08 '21 20:03 recohen