dos for elk not working

[recohen]

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

[petavazohi]

Hi Ron,

Would you mind sharing your calculations with us?

Pedram

[recohen]

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 notifications@github.com 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

[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]

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

[uthpalaherath]

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 notifications@github.com 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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Tel. (304) 216-2535 Email: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: https://uthpalaherath.github.io/

[recohen]

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]

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! 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]

The bands actually look totally different!

[uthpalaherath]

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 notifications@github.com wrote:

The bands actually look totally different!

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Tel. (304) 216-2535 Email: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: https://uthpalaherath.github.io/

[recohen]

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

[uthpalaherath]

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 notifications@github.com wrote:

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

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

Tel. (304) 216-2535 Email: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: https://uthpalaherath.github.io/

[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 ukh0001@mix.wvu.edu 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 notifications@github.com 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: https://uthpalaherath.github.io/

[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 ukh0001@mix.wvu.edu 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 ukh0001@mix.wvu.edu 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 notifications@github.com 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: https://uthpalaherath.github.io/

[recohen]

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 notifications@github.com 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 ukh0001@mix.wvu.edu 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 ukh0001@mix.wvu.edu 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 notifications@github.com 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

[uthpalaherath]

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 notifications@github.com 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 notifications@github.com 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 ukh0001@mix.wvu.edu 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 ukh0001@mix.wvu.edu 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 <notifications@github.com

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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: https://uthpalaherath.github.io/

[recohen]

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?

[uthpalaherath]

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 ukh0001@mix.wvu.edu 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 notifications@github.com 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: https://uthpalaherath.github.io/

[recohen]

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 notifications@github.com 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 ukh0001@mix.wvu.edu 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 notifications@github.com 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

[uthpalaherath]

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 notifications@github.com 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 notifications@github.com 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 ukh0001@mix.wvu.edu 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 notifications@github.com 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: https://uthpalaherath.github.io/

[recohen]

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 notifications@github.com 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 notifications@github.com 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 notifications@github.com 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 ukh0001@mix.wvu.edu 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 notifications@github.com 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

[recohen]

and conda

On Mar 5, 2021, at 5:23 PM, Uthpala Herath notifications@github.com 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 notifications@github.com 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 notifications@github.com 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 ukh0001@mix.wvu.edu 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 notifications@github.com 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

[recohen]

I just reinstalled from conda and got the same error.

On Mar 5, 2021, at 5:23 PM, Uthpala Herath notifications@github.com 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 notifications@github.com 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 notifications@github.com 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 ukh0001@mix.wvu.edu 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 notifications@github.com 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

[uthpalaherath]

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 notifications@github.com 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 notifications@github.com 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 notifications@github.com 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 <notifications@github.com

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 ukh0001@mix.wvu.edu 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 < notifications@github.com> 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: https://uthpalaherath.github.io/

[recohen]

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>, )

Now it looks ok! Thank you!

the correct band a structure is:

Sincerely,

Ron

On Mar 5, 2021, at 5:31 PM, Uthpala Herath notifications@github.com 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 notifications@github.com 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 notifications@github.com 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 notifications@github.com 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 <notifications@github.com

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 ukh0001@mix.wvu.edu 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 < notifications@github.com> 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

[petavazohi]

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 notifications@github.com 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>, )

Now it looks ok! Thank you!

the correct band a structure is:

Sincerely,

Ron

On Mar 5, 2021, at 5:31 PM, Uthpala Herath notifications@github.com 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 notifications@github.com 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 <notifications@github.com

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 < notifications@github.com> 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 < notifications@github.com

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 < ukh0001@mix.wvu.edu> 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 < notifications@github.com> 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu 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 <

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.

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

Tel. (304) 216-2535 Email: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 <

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.

---

Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu 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 .

[uthpalaherath]

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 notifications@github.com 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>, )

Now it looks ok! Thank you!

the correct band a structure is:

Sincerely,

Ron

On Mar 5, 2021, at 5:31 PM, Uthpala Herath notifications@github.com 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 notifications@github.com 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 <notifications@github.com

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 < notifications@github.com> 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 < notifications@github.com

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 < ukh0001@mix.wvu.edu> 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 < notifications@github.com> 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 <

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

Tel. (304) 216-2535 Email: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: 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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---

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

Tel. (304) 216-2535 Email: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: 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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---

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— 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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 .

---

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Tel. (304) 216-2535 Email: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: https://uthpalaherath.github.io/

[recohen]

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 rcohen@carnegiescience.edu 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>, )

Now it looks ok! Thank you!

the correct band a structure is: Sincerely, Ron > On Mar 5, 2021, at 5:31 PM, Uthpala Herath > 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 > > 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 > > > 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 > > > > 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 > > > > > > > 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 > > > > > 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 < > > notifications@github.com > > > > > > > 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: ukh0001@mix.wvu.edu > > > > > > > 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: ukh0001@mix.wvu.edu > > > > > > 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 > > > > rcohen@carnegiescience.edu > > > > > 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: ukh0001@mix.wvu.edu > > > > 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 > > rcohen@carnegiescience.edu > > > office: 202-478-8937 > > skype: ronaldcohen > > twitter: @recohen3 > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub > > >, > > or unsubscribe > > > > > . > > > > > -- > Uthpala Herath > PhD Candidate > Department of Physics and Astronomy > West Virginia University > Morgantown, WV 26505 > > Tel. (304) 216-2535 > Email: ukh0001@mix.wvu.edu > > Website: https://uthpalaherath.github.io/ > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub , or unsubscribe . > --- Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 rcohen@carnegiescience.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

[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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/usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtbegin.o /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 /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 /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 /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 -m elf_x86_64 /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crt1.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtbegin.o -lopenctm -lgcc -lgcc_s -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -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 -lgcc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtend.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../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 -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 -ldl -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -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 -lgcc -lgcc_s -Bstatic -lirc_s -Bdynamic -ldl -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -lirng -Bdynamic -Bstatic -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]

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]

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 rcohen@carnegiescience.edu 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

> On Mar 8, 2021, at 12:07 PM, Ronald Cohen > 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) > (

, ) > > Now it looks ok! Thank you! > > > the correct band a structure is: > > > > Sincerely, > > Ron > >> On Mar 5, 2021, at 5:31 PM, Uthpala Herath > 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 > >> 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 > >> > 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 > >> > > 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 >> > > >> > > > 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 > >> > > > 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 < >> > notifications@github.com > >> > > > > > 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: ukh0001@mix.wvu.edu > >> > > > > > 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: ukh0001@mix.wvu.edu > >> > > > > 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 >> > > > rcohen@carnegiescience.edu > >> > > > 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: ukh0001@mix.wvu.edu > >> > > 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 >> > rcohen@carnegiescience.edu > >> > office: 202-478-8937 >> > skype: ronaldcohen >> > twitter: @recohen3 >> > >> > — >> > You are receiving this because you commented. >> > Reply to this email directly, view it on GitHub >> > >, >> > or unsubscribe >> > > >> > . >> > >> >> >> -- >> Uthpala Herath >> PhD Candidate >> Department of Physics and Astronomy >> West Virginia University >> Morgantown, WV 26505 >> >> Tel. (304) 216-2535 >> Email: ukh0001@mix.wvu.edu > >> Website: https://uthpalaherath.github.io/ >> — >> You are receiving this because you authored the thread. >> Reply to this email directly, view it on GitHub , or unsubscribe . >> > > --- > Ronald Cohen > Extreme Materials Initiative > Carnegie Institution for Science > 5251 Broad Branch Rd., N.W. > Washington, D.C. 20015 > rcohen@carnegiescience.edu > 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 rcohen@carnegiescience.edu 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 rcohen@carnegiescience.edu mailto:rcohen@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen twitter: @recohen3

[recohen]

I finally got pyprocar to install and run. The solution was strange. I needed to install with pip in a new conda environment, and then set PYTHONPATH=$HOME:$PATHONPATH and then it imported the first time. After the first time I don't need the PYTHONPATH anymore. It seems an issue with trimesh which needs to build some codes.

Dosplot still doesn't work. I see you are still working on that. Again for dosplot I get:

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

Anyway now the band plot is OK, except that the color scale is still bad--how do I change the colormap? 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? PDOS_S03_A0001.OUT.columns_Osp.pdf PDOS_S02_A0001.OUT.columns_Tid.pdf

[recohen]

Anyway now the band plot is OK, except that the color scale is still bad--how do I change the colormap? 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? Here are the figures as png:

[uthpalaherath]

Hello Ron,

I'm glad you got it to work. Can you also project the d-orbitals in addition to the Ti atoms? The ordering can be found here: https://romerogroup.github.io/pyprocar/bands.html#orbital-projection

You can change the colormap with the cmap argument.

As my colleague Pedram mentioned, the Elk DOS plotting function is currently undergoing debugging and will be available soon.

Best, Uthpala

On Tue, Mar 9, 2021 at 9:12 AM Ronald Cohen notifications@github.com wrote:

Anyway now the band plot is OK, except that the color scale is still bad--how do I change the colormap? 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? Here are the figures as png: [image: PDOS_S02_A0001 OUT columns_Tid] https://user-images.githubusercontent.com/4303093/110483191-7a0d6200-80b7-11eb-8e44-607cb542f51d.png [image: PDOS_S03_A0001 OUT columns_Osp] https://user-images.githubusercontent.com/4303093/110483193-7aa5f880-80b7-11eb-9d64-67685d7b487b.png [image: PastedGraphic-2] https://user-images.githubusercontent.com/4303093/110483195-7aa5f880-80b7-11eb-89f6-68d04b84e6d5.png

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-793949718, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMLOIL6PLE3SFWPF24DTCYNCPANCNFSM4YQDCDQQ .

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

Tel. (304) 216-2535 Email: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: https://uthpalaherath.github.io/

[uthpalaherath]

Also, when I performed the DFT calculation myself from scratch using the structure you provided this is what I got: [image: image.png] Here you can see that the lower conduction band is indeed of Ti-d in nature.

When I used the output data from your calculation and using LATTICE.out and EFERMI.out from my own calculation (since they weren't in your directory so this is not very accurate) I get this: [image: image.png] which is similar to your latest plots.

Now, I don't know enough about PbTiO3 but double check your DFT calculation inputs to make sure everything is in order.

Best, Uthpala

On Tue, Mar 9, 2021 at 9:22 AM Uthpala Herath ukh0001@mix.wvu.edu wrote:

Hello Ron,

I'm glad you got it to work. Can you also project the d-orbitals in addition to the Ti atoms? The ordering can be found here: https://romerogroup.github.io/pyprocar/bands.html#orbital-projection

You can change the colormap with the cmap argument.

As my colleague Pedram mentioned, the Elk DOS plotting function is currently undergoing debugging and will be available soon.

Best, Uthpala

On Tue, Mar 9, 2021 at 9:12 AM Ronald Cohen notifications@github.com wrote:

Anyway now the band plot is OK, except that the color scale is still bad--how do I change the colormap? 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? Here are the figures as png: [image: PDOS_S02_A0001 OUT columns_Tid] https://user-images.githubusercontent.com/4303093/110483191-7a0d6200-80b7-11eb-8e44-607cb542f51d.png [image: PDOS_S03_A0001 OUT columns_Osp] https://user-images.githubusercontent.com/4303093/110483193-7aa5f880-80b7-11eb-9d64-67685d7b487b.png [image: PastedGraphic-2] https://user-images.githubusercontent.com/4303093/110483195-7aa5f880-80b7-11eb-89f6-68d04b84e6d5.png

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-793949718, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMLOIL6PLE3SFWPF24DTCYNCPANCNFSM4YQDCDQQ .

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

Tel. (304) 216-2535 Email: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu 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: ukh0001@mix.wvu.edu ukherathmudiyanselag@mix.wvu.edu Website: https://uthpalaherath.github.io/

[recohen]

your images do not show still. See the github website--no images there. Same in email. You use my elk.in and get a different result?

[recohen]

Your email looks like this: Also, when I performed the DFT calculation myself from scratch using the structure you provided this is what I got: [image: image.png] Here you can see that the lower conduction band is indeed of Ti-d in nature.

When I used the output data from your calculation and using LATTICE.out and EFERMI.out from my own calculation (since they weren't in your directory so this is not very accurate) I get this: [image: image.png] which is similar to your latest plots.

Now, I don't know enough about PbTiO3 but double check your DFT calculation inputs to make sure everything is in order.

Best, Uthpala

[recohen]

Here are LATTICE.OUT and EFERMI.OUT. You also need my Pb.in Ti.in and O.in because the distributed ones will not work well, certainly not at these high pressures. Archive.zip

[uthpalaherath]

Sorry the images don't seem to attach when I respond through email. Here's the plot again:

This is the input I used:

`! Plotting bands for PbTiO3

tasks 0 22

! 10

highq .true.

!xctype !100 118 130

spinpol .false.

lmirep .true.

demaxbnd 4.5

nrmtscf 4

lradstp 2

epspot 1.d-7

epsengy 1.d-5

mixtype 3

nempty 20

ngridk 12 12 12

wplot 400 400 1 -0.11025 0.11025

plot1d 7 300 0.5 0.0 0.0 : L 0.0 0.0 0.0 : \Gamma 0.5 0.5 0.0 : F 0.5 0.0 0.0 : L 0.5 0.5 0.5 : Z 0.0 0.0 0.0 : \Gamma 0.0 0.0 0.5 : M

sppath '/home/uthpala/elk/elk-7.0.12/species/'

!scrpath ! '/scratch/'

avec 0.9563710635 0.2065845938 0.2065845938 0.2065845938 0.9563710635 0.2065845938 0.2065845938 0.2065845938 0.9563710635

scale 9.1364949914

atoms 3 : nspecies 'Pb.in' : spfname 2 0.994300000000000 0.994300000000000 0.994300000000000 0.00000000 0.00000000 0.00000000 0.494300000000000 0.494300000000000 0.494300000000000 0.00000000 0.00000000 0.00000000 'Ti.in' : spfname 2 0.227250000000000 0.227250000000000 0.227250000000000 0.00000000 0.00000000 0.00000000 0.727250000000000 0.727250000000000 0.727250000000000 0.00000000 0.00000000 0.00000000 'O.in' : spfname 6 0.535770000000000 0.932780000000000 0.046220000000000 0.00000000 0.00000000 0.00000000 0.432780000000000 0.035770000000000 0.546220000000000 0.00000000 0.00000000 0.00000000 0.546220000000000 0.432780000000000 0.035770000000000 0.00000000 0.00000000 0.00000000 0.035770000000000 0.546220000000000 0.432780000000000 0.00000000 0.00000000 0.00000000 0.932780000000000 0.046220000000000 0.535770000000000 0.00000000 0.00000000 0.00000000 0.046220000000000 0.535770000000000 0.932780000000000 0.00000000 0.00000000 0.00000000 `

I'll check with your pseudos too.

• Uthpala

[recohen]

Thanks. I think the code must have reduced the MT radii ? It is surprising how different they are. However, you did LDA, and I did WC GGA, which could be quite different. WC is also built in, but you need to use the current development version of elk—the release has a problem with WC xc. Ron

On Mar 11, 2021, at 10:48 AM, Uthpala Herath @.***> wrote:

Sorry the images don't seem to attach when I respond through email. Here's the plot again:

https://user-images.githubusercontent.com/28810161/110813943-f9856780-8256-11eb-8594-358777e440b2.png This is the input I used:

`! Plotting bands for PbTiO3

tasks 0 22

! 10

highq .true.

!xctype !100 118 130

spinpol .false.

lmirep .true.

demaxbnd 4.5

nrmtscf 4

lradstp 2

epspot 1.d-7

epsengy 1.d-5

mixtype 3

nempty 20

ngridk 12 12 12

wplot 400 400 1 -0.11025 0.11025

plot1d 7 300 0.5 0.0 0.0 : L 0.0 0.0 0.0 : \Gamma 0.5 0.5 0.0 : F 0.5 0.0 0.0 : L 0.5 0.5 0.5 : Z 0.0 0.0 0.0 : \Gamma 0.0 0.0 0.5 : M

sppath '/home/uthpala/elk/elk-7.0.12/species/'

!scrpath ! '/scratch/'

avec 0.9563710635 0.2065845938 0.2065845938 0.2065845938 0.9563710635 0.2065845938 0.2065845938 0.2065845938 0.9563710635

scale 9.1364949914

atoms 3 : nspecies 'Pb.in' : spfname 2 0.994300000000000 0.994300000000000 0.994300000000000 0.00000000 0.00000000 0.00000000 0.494300000000000 0.494300000000000 0.494300000000000 0.00000000 0.00000000 0.00000000 'Ti.in' : spfname 2 0.227250000000000 0.227250000000000 0.227250000000000 0.00000000 0.00000000 0.00000000 0.727250000000000 0.727250000000000 0.727250000000000 0.00000000 0.00000000 0.00000000 'O.in' : spfname 6 0.535770000000000 0.932780000000000 0.046220000000000 0.00000000 0.00000000 0.00000000 0.432780000000000 0.035770000000000 0.546220000000000 0.00000000 0.00000000 0.00000000 0.546220000000000 0.432780000000000 0.035770000000000 0.00000000 0.00000000 0.00000000 0.035770000000000 0.546220000000000 0.432780000000000 0.00000000 0.00000000 0.00000000 0.932780000000000 0.046220000000000 0.535770000000000 0.00000000 0.00000000 0.00000000 0.046220000000000 0.535770000000000 0.932780000000000 0.00000000 0.00000000 0.00000000 `

I'll check with your pseudos too.

Uthpala — 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-796833566, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5L32VYFPAWDSSTRZG3TDDJ3JANCNFSM4YQDCDQQ.

---

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

[recohen]

I ran with my species files Pb.in etc with LDA and get the same result as you. So it is LDA that gives the different bands structure. I have a different colormap: pyprocar.bandsplot(elimit=[-15,15],cmap='rainbow',mode='parametric',code='elk',atoms=[2,3],kdirect=False,orbitals=[4,5,6,7,8],vmin=0.0,vmax=0.5)

On Mar 11, 2021, at 11:13 AM, Ronald Cohen @.***> wrote:

Thanks. I think the code must have reduced the MT radii ? It is surprising how different they are. However, you did LDA, and I did WC GGA, which could be quite different. WC is also built in, but you need to use the current development version of elk—the release has a problem with WC xc. Ron

On Mar 11, 2021, at 10:48 AM, Uthpala Herath @. @.>> wrote:

Sorry the images don't seem to attach when I respond through email. Here's the plot again:

https://user-images.githubusercontent.com/28810161/110813943-f9856780-8256-11eb-8594-358777e440b2.png This is the input I used:

`! Plotting bands for PbTiO3

tasks 0 22

! 10

highq .true.

!xctype !100 118 130

spinpol .false.

lmirep .true.

demaxbnd 4.5

nrmtscf 4

lradstp 2

epspot 1.d-7

epsengy 1.d-5

mixtype 3

nempty 20

ngridk 12 12 12

wplot 400 400 1 -0.11025 0.11025

plot1d 7 300 0.5 0.0 0.0 : L 0.0 0.0 0.0 : \Gamma 0.5 0.5 0.0 : F 0.5 0.0 0.0 : L 0.5 0.5 0.5 : Z 0.0 0.0 0.0 : \Gamma 0.0 0.0 0.5 : M

sppath '/home/uthpala/elk/elk-7.0.12/species/'

!scrpath ! '/scratch/'

avec 0.9563710635 0.2065845938 0.2065845938 0.2065845938 0.9563710635 0.2065845938 0.2065845938 0.2065845938 0.9563710635

scale 9.1364949914

atoms 3 : nspecies 'Pb.in' : spfname 2 0.994300000000000 0.994300000000000 0.994300000000000 0.00000000 0.00000000 0.00000000 0.494300000000000 0.494300000000000 0.494300000000000 0.00000000 0.00000000 0.00000000 'Ti.in' : spfname 2 0.227250000000000 0.227250000000000 0.227250000000000 0.00000000 0.00000000 0.00000000 0.727250000000000 0.727250000000000 0.727250000000000 0.00000000 0.00000000 0.00000000 'O.in' : spfname 6 0.535770000000000 0.932780000000000 0.046220000000000 0.00000000 0.00000000 0.00000000 0.432780000000000 0.035770000000000 0.546220000000000 0.00000000 0.00000000 0.00000000 0.546220000000000 0.432780000000000 0.035770000000000 0.00000000 0.00000000 0.00000000 0.035770000000000 0.546220000000000 0.432780000000000 0.00000000 0.00000000 0.00000000 0.932780000000000 0.046220000000000 0.535770000000000 0.00000000 0.00000000 0.00000000 0.046220000000000 0.535770000000000 0.932780000000000 0.00000000 0.00000000 0.00000000 `

I'll check with your pseudos too.

Uthpala — 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-796833566, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5L32VYFPAWDSSTRZG3TDDJ3JANCNFSM4YQDCDQQ.

---

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

[uthpalaherath]

That is interesting indeed. Have you tried with other DFT codes to check if there are similar differences between LDA and GGA?

On Thu, Mar 11, 2021 at 12:24 PM Ronald Cohen @.***> wrote:

I ran with my species files Pb.in etc with LDA and get the same result as you. So it is LDA that gives the different bands structure. I have a different colormap:

pyprocar.bandsplot(elimit=[-15,15],cmap='rainbow',mode='parametric',code='elk',atoms=[2,3],kdirect=False,orbitals=[4,5,6,7,8],vmin=0.0,vmax=0.5)

On Mar 11, 2021, at 11:13 AM, Ronald Cohen @.***> wrote:

Thanks. I think the code must have reduced the MT radii ? It is surprising how different they are. However, you did LDA, and I did WC GGA, which could be quite different. WC is also built in, but you need to use the current development version of elk—the release has a problem with WC xc. Ron

On Mar 11, 2021, at 10:48 AM, Uthpala Herath @. @.>> wrote:

Sorry the images don't seem to attach when I respond through email. Here's the plot again:

< https://user-images.githubusercontent.com/28810161/110813943-f9856780-8256-11eb-8594-358777e440b2.png

This is the input I used:

`! Plotting bands for PbTiO3

tasks 0 22

! 10

highq .true.

!xctype !100 118 130

spinpol .false.

lmirep .true.

demaxbnd 4.5

nrmtscf 4

lradstp 2

epspot 1.d-7

epsengy 1.d-5

mixtype 3

nempty 20

ngridk 12 12 12

wplot 400 400 1 -0.11025 0.11025

plot1d 7 300 0.5 0.0 0.0 : L 0.0 0.0 0.0 : \Gamma 0.5 0.5 0.0 : F 0.5 0.0 0.0 : L 0.5 0.5 0.5 : Z 0.0 0.0 0.0 : \Gamma 0.0 0.0 0.5 : M

sppath '/home/uthpala/elk/elk-7.0.12/species/'

!scrpath ! '/scratch/'

avec 0.9563710635 0.2065845938 0.2065845938 0.2065845938 0.9563710635 0.2065845938 0.2065845938 0.2065845938 0.9563710635

scale 9.1364949914

atoms 3 : nspecies 'Pb.in' : spfname 2 0.994300000000000 0.994300000000000 0.994300000000000 0.00000000 0.00000000 0.00000000 0.494300000000000 0.494300000000000 0.494300000000000 0.00000000 0.00000000 0.00000000 'Ti.in' : spfname 2 0.227250000000000 0.227250000000000 0.227250000000000 0.00000000 0.00000000 0.00000000 0.727250000000000 0.727250000000000 0.727250000000000 0.00000000 0.00000000 0.00000000 'O.in' : spfname 6 0.535770000000000 0.932780000000000 0.046220000000000 0.00000000 0.00000000 0.00000000 0.432780000000000 0.035770000000000 0.546220000000000 0.00000000 0.00000000 0.00000000 0.546220000000000 0.432780000000000 0.035770000000000 0.00000000 0.00000000 0.00000000 0.035770000000000 0.546220000000000 0.432780000000000 0.00000000 0.00000000 0.00000000 0.932780000000000 0.046220000000000 0.535770000000000 0.00000000 0.00000000 0.00000000 0.046220000000000 0.535770000000000 0.932780000000000 0.00000000 0.00000000 0.00000000 `

I'll check with your pseudos too.

Uthpala — 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-796833566>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABA2R5L32VYFPAWDSSTRZG3TDDJ3JANCNFSM4YQDCDQQ .

---

Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 @. @.> 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 @. @.> 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-796905553, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMO5EKGQWWKTY7ZT6HTTDD4EHANCNFSM4YQDCDQQ .

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

Tel. (304) 216-2535 Email: @. @.> Website: https://uthpalaherath.github.io/

[recohen]

No but I trust elk. I have compared energy differences with qe and they agree. Ron

On Mar 13, 2021, at 8:56 PM, Uthpala Herath @.***> wrote:

That is interesting indeed. Have you tried with other DFT codes to check if there are similar differences between LDA and GGA?

On Thu, Mar 11, 2021 at 12:24 PM Ronald Cohen @.***> wrote:

I ran with my species files Pb.in etc with LDA and get the same result as you. So it is LDA that gives the different bands structure. I have a different colormap:

pyprocar.bandsplot(elimit=[-15,15],cmap='rainbow',mode='parametric',code='elk',atoms=[2,3],kdirect=False,orbitals=[4,5,6,7,8],vmin=0.0,vmax=0.5)

On Mar 11, 2021, at 11:13 AM, Ronald Cohen @.***> wrote:

Thanks. I think the code must have reduced the MT radii ? It is surprising how different they are. However, you did LDA, and I did WC GGA, which could be quite different. WC is also built in, but you need to use the current development version of elk—the release has a problem with WC xc. Ron

On Mar 11, 2021, at 10:48 AM, Uthpala Herath @. @.>> wrote:

Sorry the images don't seem to attach when I respond through email. Here's the plot again:

< https://user-images.githubusercontent.com/28810161/110813943-f9856780-8256-11eb-8594-358777e440b2.png

This is the input I used:

`! Plotting bands for PbTiO3

tasks 0 22

! 10

highq .true.

!xctype !100 118 130

spinpol .false.

lmirep .true.

demaxbnd 4.5

nrmtscf 4

lradstp 2

epspot 1.d-7

epsengy 1.d-5

mixtype 3

nempty 20

ngridk 12 12 12

wplot 400 400 1 -0.11025 0.11025

plot1d 7 300 0.5 0.0 0.0 : L 0.0 0.0 0.0 : \Gamma 0.5 0.5 0.0 : F 0.5 0.0 0.0 : L 0.5 0.5 0.5 : Z 0.0 0.0 0.0 : \Gamma 0.0 0.0 0.5 : M

sppath '/home/uthpala/elk/elk-7.0.12/species/'

!scrpath ! '/scratch/'

avec 0.9563710635 0.2065845938 0.2065845938 0.2065845938 0.9563710635 0.2065845938 0.2065845938 0.2065845938 0.9563710635

scale 9.1364949914

atoms 3 : nspecies 'Pb.in' : spfname 2 0.994300000000000 0.994300000000000 0.994300000000000 0.00000000 0.00000000 0.00000000 0.494300000000000 0.494300000000000 0.494300000000000 0.00000000 0.00000000 0.00000000 'Ti.in' : spfname 2 0.227250000000000 0.227250000000000 0.227250000000000 0.00000000 0.00000000 0.00000000 0.727250000000000 0.727250000000000 0.727250000000000 0.00000000 0.00000000 0.00000000 'O.in' : spfname 6 0.535770000000000 0.932780000000000 0.046220000000000 0.00000000 0.00000000 0.00000000 0.432780000000000 0.035770000000000 0.546220000000000 0.00000000 0.00000000 0.00000000 0.546220000000000 0.432780000000000 0.035770000000000 0.00000000 0.00000000 0.00000000 0.035770000000000 0.546220000000000 0.432780000000000 0.00000000 0.00000000 0.00000000 0.932780000000000 0.046220000000000 0.535770000000000 0.00000000 0.00000000 0.00000000 0.046220000000000 0.535770000000000 0.932780000000000 0.00000000 0.00000000 0.00000000 `

I'll check with your pseudos too.

Uthpala — 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-796833566>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABA2R5L32VYFPAWDSSTRZG3TDDJ3JANCNFSM4YQDCDQQ .

---

Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 @. @.> 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 @. @.> 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-796905553, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG3ZXMO5EKGQWWKTY7ZT6HTTDD4EHANCNFSM4YQDCDQQ .

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

Tel. (304) 216-2535 Email: @. @.> 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-798816140, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5MBULDBUF4PGZYENJTTDQJTLANCNFSM4YQDCDQQ.

---

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

[recohen]

BTW there was a problem with that run--there were ghost bands! The current bands with wc is attached. I was wondering if you were able to fix the dos for elk?

[recohen]

SOrry here re the bands for 150 GPa. BandsTid_R3c_150GPa.pdf They now look similar to the LDA bands.

[recohen]

I was wondering if the dos plotting for elk was fixed? If so, do Ineed to do anything special to use it? Thanks, Ron

---

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

On Mar 9, 2021, at 9:22 AM, Uthpala Herath @.***> wrote:

Hello Ron,

I'm glad you got it to work. Can you also project the d-orbitals in addition to the Ti atoms? The ordering can be found here: https://romerogroup.github.io/pyprocar/bands.html#orbital-projection

You can change the colormap with the cmap argument.

As my colleague Pedram mentioned, the Elk DOS plotting function is currently undergoing debugging and will be available soon.

Best, Uthpala

On Tue, Mar 9, 2021 at 9:12 AM Ronald Cohen @.***> wrote:

Anyway now the band plot is OK, except that the color scale is still bad--how do I change the colormap? 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? Here are the figures as png: [image: PDOS_S02_A0001 OUT columns_Tid] https://user-images.githubusercontent.com/4303093/110483191-7a0d6200-80b7-11eb-8e44-607cb542f51d.png [image: PDOS_S03_A0001 OUT columns_Osp] https://user-images.githubusercontent.com/4303093/110483193-7aa5f880-80b7-11eb-9d64-67685d7b487b.png [image: PastedGraphic-2] https://user-images.githubusercontent.com/4303093/110483195-7aa5f880-80b7-11eb-89f6-68d04b84e6d5.png

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

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[recohen]

Some years later I tried plotting an elk dos and it is still not working? Or is there an example? I try:

import pyprocar

pyprocar.dosplot(filename='elk.in',code='elk')

---

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

Version 5.6.6 created on March 6th, 2022

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.

... Script initiated code : vasp File name : elk.in mode : plain spins : None atoms list : None orbs. list : None energy range : None 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/rec38/lib/python3.8/site-packages/pyprocar/scriptDosplot.py", line 364, in dosplot vaspxml = VaspXML( File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 33, in init self.data = self.read() File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 52, in read return parse_vasprun(self.filename) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 512, in parse_vasprun tree = ET.parse(vasprun) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/xml/etree/ElementTree.py", line 1202, in parse tree.parse(source, parser) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/xml/etree/ElementTree.py", line 595, in parse self._root = parser._parse_whole(source) xml.etree.ElementTree.ParseError: syntax error: line 1, column 0

[petavazohi]

We’re updating our elk parser. If there aren’t any complications it will be done by tomorrow. We will contact you as soon as it is ready to use.

-Pedram

From: Ronald Cohen @.> Sent: Sunday, March 26, 2023 8:13 PM To: romerogroup/pyprocar @.> Cc: Pedram Tavadze @.>; Comment @.> Subject: Re: [romerogroup/pyprocar] dos for elk not working (#46)

Some years later I tried plotting an elk dos and it is still not working? Or is there an example? I try:

import pyprocar

pyprocar.dosplot(filename='elk.in',code='elk')

---

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

Version 5.6.6 created on March 6th, 2022

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.

... Script initiated code : vasp File name : elk.in mode : plain spins : None atoms list : None orbs. list : None energy range : None 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/rec38/lib/python3.8/site-packages/pyprocar/scriptDosplot.py", line 364, in dosplot vaspxml = VaspXML( File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 33, in init self.data = self.read() File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 52, in read return parse_vasprun(self.filename) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 512, in parse_vasprun tree = ET.parse(vasprun) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/xml/etree/ElementTree.py", line 1202, in parse tree.parse(source, parser) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/xml/etree/ElementTree.py", line 595, in parse self._root = parser._parse_whole(source) xml.etree.ElementTree.ParseError: syntax error: line 1, column 0

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[recohen]

Great! Thank you! Ron

---

Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 @.***

On Mar 30, 2023 at 8:54 AM -0400, Pedram Tavadze @.***>, wrote:

We’re updating our elk parser. If there aren’t any complications it will be done by tomorrow. We will contact you as soon as it is ready to use.

-Pedram

From: Ronald Cohen @.> Sent: Sunday, March 26, 2023 8:13 PM To: romerogroup/pyprocar @.> Cc: Pedram Tavadze @.>; Comment @.> Subject: Re: [romerogroup/pyprocar] dos for elk not working (#46)

Some years later I tried plotting an elk dos and it is still not working? Or is there an example? I try:

import pyprocar

pyprocar.dosplot(filename='elk.in',code='elk')

---

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

Version 5.6.6 created on March 6th, 2022

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.

... Script initiated code : vasp File name : elk.in mode : plain spins : None atoms list : None orbs. list : None energy range : None 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/rec38/lib/python3.8/site-packages/pyprocar/scriptDosplot.py", line 364, in dosplot vaspxml = VaspXML( File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 33, in init self.data = self.read() File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 52, in read return parse_vasprun(self.filename) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 512, in parse_vasprun tree = ET.parse(vasprun) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/xml/etree/ElementTree.py", line 1202, in parse tree.parse(source, parser) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/xml/etree/ElementTree.py", line 595, in parse self._root = parser._parse_whole(source) xml.etree.ElementTree.ParseError: syntax error: line 1, column 0

— Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/46#issuecomment-1484287003 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AHBQJCNPZ7SS5CHCL7WGPWTW6DLQXANCNFSM4YQDCDQQ . You are receiving this because you commented. https://github.com/notifications/beacon/AHBQJCKV3NBCO4HUGSPFCJLW6DLQXA5CNFSM4YQDCDQ2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOLB4GYGY.gif Message ID: @. @.> >

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[recohen]

Hi! I am wondering if this was done. When I try pip install pyprocar —upgrade it doesn’t find anything new. Also I didn’t hear from you. Thank you,

Ron

---

Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 @.***

On Mar 30, 2023, 9:32 AM -0400, Ronald Cohen @.***>, wrote:

Great! Thank you! Ron

---

Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 @.***

On Mar 30, 2023 at 8:54 AM -0400, Pedram Tavadze @.***>, wrote:

We’re updating our elk parser. If there aren’t any complications it will be done by tomorrow. We will contact you as soon as it is ready to use.

-Pedram

From: Ronald Cohen @.> Sent: Sunday, March 26, 2023 8:13 PM To: romerogroup/pyprocar @.> Cc: Pedram Tavadze @.>; Comment @.> Subject: Re: [romerogroup/pyprocar] dos for elk not working (#46)

Some years later I tried plotting an elk dos and it is still not working? Or is there an example? I try:

import pyprocar

pyprocar.dosplot(filename='elk.in',code='elk')

---

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

Version 5.6.6 created on March 6th, 2022

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.

... Script initiated code : vasp File name : elk.in mode : plain spins : None atoms list : None orbs. list : None energy range : None 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/rec38/lib/python3.8/site-packages/pyprocar/scriptDosplot.py", line 364, in dosplot vaspxml = VaspXML( File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 33, in init self.data = self.read() File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 52, in read return parse_vasprun(self.filename) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 512, in parse_vasprun tree = ET.parse(vasprun) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/xml/etree/ElementTree.py", line 1202, in parse tree.parse(source, parser) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/xml/etree/ElementTree.py", line 595, in parse self._root = parser._parse_whole(source) xml.etree.ElementTree.ParseError: syntax error: line 1, column 0

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[petavazohi]

Hello,

We apologize for the inconvenience caused. We have recently updated our ELK parser for DOS and BANDS. During this process, we discovered a few bugs in other sections of the code. Our team is currently working on resolving these issues.

We have scheduled to complete the necessary updates to the ELK functionalities by next Monday, April 24th. We will continue to keep you informed on our progress.

Thank you,

Pedram

From: Ronald Cohen @.> Sent: Thursday, March 30, 2023 9:33 AM To: romerogroup/pyprocar @.> Cc: Pedram Tavadze @.>; Comment @.> Subject: Re: [romerogroup/pyprocar] dos for elk not working (#46)

Great! Thank you! Ron

---

Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 @. <mailto:@.>

On Mar 30, 2023 at 8:54 AM -0400, Pedram Tavadze @. <mailto:@.> >, wrote:

We’re updating our elk parser. If there aren’t any complications it will be done by tomorrow. We will contact you as soon as it is ready to use.

-Pedram

From: Ronald Cohen @. <mailto:@.> > Sent: Sunday, March 26, 2023 8:13 PM To: romerogroup/pyprocar @. <mailto:@.> > Cc: Pedram Tavadze @. <mailto:@.> >; Comment @. <mailto:@.> > Subject: Re: [romerogroup/pyprocar] dos for elk not working (#46)

Some years later I tried plotting an elk dos and it is still not working? Or is there an example? I try:

import pyprocar

pyprocar.dosplot(filename='elk.in',code='elk')

---

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

Version 5.6.6 created on March 6th, 2022

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.

... Script initiated code : vasp File name : elk.in mode : plain spins : None atoms list : None orbs. list : None energy range : None 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/rec38/lib/python3.8/site-packages/pyprocar/scriptDosplot.py", line 364, in dosplot vaspxml = VaspXML( File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 33, in init self.data = self.read() File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 52, in read return parse_vasprun(self.filename) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/pyprocar/vaspxml/vaspxml.py", line 512, in parse_vasprun tree = ET.parse(vasprun) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/xml/etree/ElementTree.py", line 1202, in parse tree.parse(source, parser) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/xml/etree/ElementTree.py", line 595, in parse self._root = parser._parse_whole(source) xml.etree.ElementTree.ParseError: syntax error: line 1, column 0

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