recohen
commented
1 year 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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petavazohi
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