Open recohen opened 3 years ago
Thank you! Ron
Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 @.***
On Apr 17, 2023 at 9:11 AM -0400, Pedram Tavadze @.***>, wrote:
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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Hi! I am wondering if this is ready now? Thanks, Ron
On Apr 17, 2023, at 9:11 AM, Pedram Tavadze @.***> wrote:
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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Hi! I am wondering if this is ready now? Thanks, RonOn Apr 17, 2023, at 9:11 AM, Pedram Tavadze @.***> wrote: 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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I tried installing the latest version on git hub but get the same problems. I am no the master branch—I assume that is the correct branch to try? I still get:
fig, ax = pyprocar.dosplot(mode='plain', plt_show=False, code='elk’)
Script initiated
code : elk
File name : vasprun.xml
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 "
In the routine scriptDosplot.py there should not seem to even exist a section for elk:
rec38) rcohen@tomcat:~/pyprocar/pyprocar$ grep code pyprocar/scripts/scriptDosplot.py
code:str="vasp",
This is used for qe and lobster codes. It specifies the directory the dosplot
code : str, optional (default 'vasp'
)
Defines the Density Functional Theory code used for the
e.g. code=vasp
, code=elk
, code=abinit
code=code,
def parse(code: str='vasp',
parser = io.lobster.LobsterParser(dirname = dirname,code = code, dos_interpolation_factor =interpolation_factor)
elif code == "vasp":
elif code == "qe":
just shows up in the doc lines as:
grep elk pyprocar/scripts/scriptDosplot.py
e.g. code=vasp
, code=elk
, code=abinit
Ron
I tried deleting all old versions of pyprocar and reinstalling the dev branch using python setup.py install and now get:
import pyprocar
pyoricar.dosplot(code='elk') Traceback (most recent call last): File "
", line 1, in NameError: name 'pyoricar' is not defined pyprocar.dosplot(code='elk') Traceback (most recent call last): File " ", line 1, in File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/PyProcar2-5.6.5-py3.8.egg/pyprocar/scripts/scriptDosplot.py", line 348, in dosplot parser = io.Parser(code = code, dir = dirname) File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/PyProcar2-5.6.5-py3.8.egg/pyprocar/io/parser.py", line 27, in init self.parse() File "/home/rcohen/.conda/envs/rec38/lib/python3.8/site-packages/PyProcar2-5.6.5-py3.8.egg/pyprocar/io/parser.py", line 51, in parse self.ebs.bands += self.ebs.efermi AttributeError: 'NoneType' object has no attribute 'bands'
Hi Ron,
We’re working on merging our elk dev branch with the master branch and updating the PyPI and conda-forge repositories today. We are also prepping the documentation and the examples. We’ll keep you posted.
Thanks,
Pedram
From: Ronald Cohen @.> Sent: Tuesday, April 25, 2023 7:24 AM To: romerogroup/pyprocar @.> Cc: Pedram Tavadze @.>; Comment @.> Subject: Re: [romerogroup/pyprocar] dos for elk not working (#46)
Hi! I am wondering if this is ready now? Thanks, RonOn Apr 17, 2023, at 9:11 AM, Pedram Tavadze @. <mailto:@.> > wrote: 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 @. <mailto:@.> > Sent: Thursday, March 30, 2023 9:33 AM To: romerogroup/pyprocar @. <mailto:@.> > Cc: Pedram Tavadze @. <mailto:@.> >; Comment @. <mailto:@.> > 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:@.> mailto:***@***.***
On Mar 30, 2023 at 8:54 AM -0400, Pedram Tavadze @. <mailto:@.> 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:@.> mailto:***@***.*** > Sent: Sunday, March 26, 2023 8:13 PM To: romerogroup/pyprocar @. <mailto:@.> mailto:***@***.*** > Cc: Pedram Tavadze @. <mailto:@.> mailto:***@***.*** >; Comment @. <mailto:@.> 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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Thank you. I tried the dev branch yesterday and it still failed—I left the error in the Issue log.
Ron
On Apr 26, 2023, at 11:11 AM, Pedram Tavadze @.***> wrote:
Hi Ron,
We’re working on merging our elk dev branch with the master branch and updating the PyPI and conda-forge repositories today. We are also prepping the documentation and the examples. We’ll keep you posted.
Thanks,
Pedram
From: Ronald Cohen @.> Sent: Tuesday, April 25, 2023 7:24 AM To: romerogroup/pyprocar @.> Cc: Pedram Tavadze @.>; Comment @.> Subject: Re: [romerogroup/pyprocar] dos for elk not working (#46)
Hi! I am wondering if this is ready now? Thanks, RonOn Apr 17, 2023, at 9:11 AM, Pedram Tavadze @. <mailto:@.> > wrote: 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 @. <mailto:@.> > Sent: Thursday, March 30, 2023 9:33 AM To: romerogroup/pyprocar @. <mailto:@.> > Cc: Pedram Tavadze @. <mailto:@.> >; Comment @. <mailto:@.> > 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:@.> mailto:***@***.***
On Mar 30, 2023 at 8:54 AM -0400, Pedram Tavadze @. <mailto:@.> 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:@.> mailto:***@***.*** > Sent: Sunday, March 26, 2023 8:13 PM To: romerogroup/pyprocar @. <mailto:@.> mailto:***@***.*** > Cc: Pedram Tavadze @. <mailto:@.> mailto:***@***.*** >; Comment @. <mailto:@.> 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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I can send the files if you would like, Ron
On Apr 26, 2023, at 11:11 AM, Pedram Tavadze @.***> wrote:
Hi Ron,
We’re working on merging our elk dev branch with the master branch and updating the PyPI and conda-forge repositories today. We are also prepping the documentation and the examples. We’ll keep you posted.
Thanks,
Pedram
From: Ronald Cohen @.> Sent: Tuesday, April 25, 2023 7:24 AM To: romerogroup/pyprocar @.> Cc: Pedram Tavadze @.>; Comment @.> Subject: Re: [romerogroup/pyprocar] dos for elk not working (#46)
Hi! I am wondering if this is ready now? Thanks, RonOn Apr 17, 2023, at 9:11 AM, Pedram Tavadze @. <mailto:@.> > wrote: 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 @. <mailto:@.> > Sent: Thursday, March 30, 2023 9:33 AM To: romerogroup/pyprocar @. <mailto:@.> > Cc: Pedram Tavadze @. <mailto:@.> >; Comment @. <mailto:@.> > 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:@.> mailto:***@***.***
On Mar 30, 2023 at 8:54 AM -0400, Pedram Tavadze @. <mailto:@.> 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:@.> mailto:***@***.*** > Sent: Sunday, March 26, 2023 8:13 PM To: romerogroup/pyprocar @. <mailto:@.> mailto:***@***.*** > Cc: Pedram Tavadze @. <mailto:@.> mailto:***@***.*** >; Comment @. <mailto:@.> 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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I would rather not post them for the public though. Ron
On Apr 26, 2023, at 11:11 AM, Pedram Tavadze @.***> wrote:
Hi Ron,
We’re working on merging our elk dev branch with the master branch and updating the PyPI and conda-forge repositories today. We are also prepping the documentation and the examples. We’ll keep you posted.
Thanks,
Pedram
From: Ronald Cohen @.> Sent: Tuesday, April 25, 2023 7:24 AM To: romerogroup/pyprocar @.> Cc: Pedram Tavadze @.>; Comment @.> Subject: Re: [romerogroup/pyprocar] dos for elk not working (#46)
Hi! I am wondering if this is ready now? Thanks, RonOn Apr 17, 2023, at 9:11 AM, Pedram Tavadze @. <mailto:@.> > wrote: 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 @. <mailto:@.> > Sent: Thursday, March 30, 2023 9:33 AM To: romerogroup/pyprocar @. <mailto:@.> > Cc: Pedram Tavadze @. <mailto:@.> >; Comment @. <mailto:@.> > 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:@.> mailto:***@***.***
On Mar 30, 2023 at 8:54 AM -0400, Pedram Tavadze @. <mailto:@.> 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:@.> mailto:***@***.*** > Sent: Sunday, March 26, 2023 8:13 PM To: romerogroup/pyprocar @. <mailto:@.> mailto:***@***.*** > Cc: Pedram Tavadze @. <mailto:@.> mailto:***@***.*** >; Comment @. <mailto:@.> 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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Is there any progress? Thank you, Ron
Ronald Cohen Extreme Materials Initiative Earth and Planets Laboratory Carnegie Institution for Science 5241 Broad Branch Rd., N.W. Washington, D.C. 20015 @.*** office: 202-478-8937 skype: ronaldcohen
On Wed, Apr 26, 2023 at 11:11 AM Pedram Tavadze @.***> wrote:
Hi Ron,
We’re working on merging our elk dev branch with the master branch and updating the PyPI and conda-forge repositories today. We are also prepping the documentation and the examples. We’ll keep you posted.
Thanks,
Pedram
From: Ronald Cohen @.> Sent: Tuesday, April 25, 2023 7:24 AM To: romerogroup/pyprocar @.> Cc: Pedram Tavadze @.>; Comment @.> Subject: Re: [romerogroup/pyprocar] dos for elk not working (#46)
Hi! I am wondering if this is ready now? Thanks, RonOn Apr 17, 2023, at 9:11 AM, Pedram Tavadze @. <mailto:@.> > wrote: 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 @. <mailto:@.> > Sent: Thursday, March 30, 2023 9:33 AM To: romerogroup/pyprocar @. <mailto:@.> > Cc: Pedram Tavadze @. <mailto:@.> >; Comment @. <mailto:@.> > 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:@.> mailto:***@***.***
On Mar 30, 2023 at 8:54 AM -0400, Pedram Tavadze @. <mailto:@.> 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:@.> mailto:***@***.***
Sent: Sunday, March 26, 2023 8:13 PM To: romerogroup/pyprocar @. <mailto:@.> mailto:***@***.***
Cc: Pedram Tavadze @. <mailto:@.> mailto:***@***.*** ; Comment @. <mailto:@.> 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
— 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: @. <mailto:@.> mailto:***@***.*** @. <mailto:@.> mailto:***@***.*** > >
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This is going on years/weeks. Please let me know if I should just give up.
Ron
Ronald Cohen Extreme Materials Initiative Carnegie Institution for Science 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 @.***
On May 1, 2023, 7:53 AM -0400, Ronald Cohen @.***>, wrote:
Is there any progress? Thank you, Ron
Ronald Cohen Extreme Materials Initiative Earth and Planets Laboratory Carnegie Institution for Science 5241 Broad Branch Rd., N.W. Washington, D.C. 20015 @.*** office: 202-478-8937 skype: ronaldcohen
On Wed, Apr 26, 2023 at 11:11 AM Pedram Tavadze @.***> wrote:
Hi Ron,
We’re working on merging our elk dev branch with the master branch and updating the PyPI and conda-forge repositories today. We are also prepping the documentation and the examples. We’ll keep you posted.
Thanks,
Pedram
From: Ronald Cohen @.> Sent: Tuesday, April 25, 2023 7:24 AM To: romerogroup/pyprocar @.> Cc: Pedram Tavadze @.>; Comment @.> Subject: Re: [romerogroup/pyprocar] dos for elk not working (#46)
Hi! I am wondering if this is ready now? Thanks, RonOn Apr 17, 2023, at 9:11 AM, Pedram Tavadze @. <mailto:@.> > wrote: 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 @. <mailto:@.> > Sent: Thursday, March 30, 2023 9:33 AM To: romerogroup/pyprocar @. <mailto:@.> > Cc: Pedram Tavadze @. <mailto:@.> >; Comment @. <mailto:@.> > 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:@.> mailto:***@***.***
On Mar 30, 2023 at 8:54 AM -0400, Pedram Tavadze @. <mailto:@.> 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:@.> mailto:***@***.*** > Sent: Sunday, March 26, 2023 8:13 PM To: romerogroup/pyprocar @. <mailto:@.> mailto:***@***.*** > Cc: Pedram Tavadze @. <mailto:@.> mailto:***@***.*** >; Comment @. <mailto:@.> 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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I STILL CANNOT PLOT DOS FOR ELK?
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