elk support? #144
Comments
|
Hey, sorry for the issue! Recently, we changed it so the fermi energy has to be given the DensityOfStates class to initialize. I forgot to update the elk code. I pushed the update to GitHub so clone the repository from there to have the updates. Here are the commands for that: pip uninstall pyprocar
git clone git@github.com:romerogroup/pyprocar.git
cd pyprocar
pip install .I will try to get this in the Pypi version as soon as possible. There are some further additions to the elk interface I would like to add before updating PyPi. code = "elk"
Here are the bands as well: code = "elk" pyprocar.bandsplot( Logan Lang |
|
Thank you!
I will try it
,
Ron
…---
Ronald Cohen
Extreme Materials Initiative
Earth and Planets Laboratory
Carnegie Institution for Science
5241 Broad Branch Rd., N.W.
Washington, D.C. 20015
***@***.*** ***@***.***>
On Apr 18, 2024, at 4:24 PM, lllangWV ***@***.***> wrote:
Hey,
sorry for the issue! Recently, we changed it so the fermi energy has to be given the DensityOfStates class to initialize. I forgot to update the elk code.
I pushed the update to GitHub so clone the repository from there to have the updates. Here are the commands for that:
pip uninstall pyprocar
git clone ***@***.***:romerogroup/pyprocar.git
cd pyprocar
pip install .
I will try to get this in the Pypi version as soon as possible. There are some further additions to the elk interface I would like to add before updating PyPi.
code = "elk"
mag_type = ["non-spin-polarized","spin-polarized-colinear","non-colinear"][1]
data_dir = os.path.join(PROJECT_DIR,'data','examples',"SrVO3",code,mag_type, 'dos')
HARTREE_TO_EV = 27.211386245988
pyprocar.dosplot(
code=code,
mode='plain',
fermi=0.3218543102*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web) <https://github.com/romerogroup/pyprocar/assets/120115419/feae394d-4e79-4ca6-be87-999dd144168a>
Here are the bands as well:
code = "elk"
mag_type = ["non-spin-polarized","spin-polarized-colinear","non-colinear"][1]
data_dir = os.path.join(PROJECT_DIR,'data','examples',"SrVO3",code,mag_type, 'ebs')
pyprocar.bandsplot(
code=code,
mode='plain',
spins=[0,1],
elimit=[-10,10],
fermi=0.3218543102*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web) <https://github.com/romerogroup/pyprocar/assets/120115419/9765d0f1-aa9f-43b9-888a-3e3a1b0a5360>
Logan Lang
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Reply to this email directly, view it on GitHub <#144 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABA2R5JBJHMGTWKV4VMIEQ3Y6ATZFAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRVGI2DENJTHE>.
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Thank you so much! The plain mode for the TDOS works, but when I triy something else it fails like this:
code = "elk"
mag_type = ["non-spin-polarized","spin-polarized-colinear","non-colinear"][1]
data_dir = os.path.join('.')
HARTREE_TO_EV = 27.211386245988
atoms=[0]
spins=[0]
pyprocar.dosplot(
atoms=atoms,
spins=spins,
code=code,
mode='stack_orbitals',
fermi=0.2561435*HARTREE_TO_EV,
dirname=data_dir)
File ~/.local/lib/python3.9/site-packages/pyprocar/plotter/dos_plot.py:658, in DOSPlot.plot_stack_orbitals(self, atoms, spins, principal_q_numbers, overlay_mode, orientation)
654 atom_names = ""
655 if atoms:
656 print(
657 "The plot only considers atoms",
--> 658 np.array(self.structure.atoms)[atoms],
659 )
660 atom_names = ""
661 for ispc in np.unique(np.array(self.structure.atoms)[atoms]):
AttributeError: 'NoneType' object has no attribute 'atoms'
Not sure if I am doing something wrong!
Thank you again,
Sincerely,
Ron
… On Apr 18, 2024, at 4:27 PM, Ronald Cohen ***@***.***> wrote:
Thank you!
I will try it
,
Ron
---
Ronald Cohen
Extreme Materials Initiative
Earth and Planets Laboratory
Carnegie Institution for Science
5241 Broad Branch Rd., N.W.
Washington, D.C. 20015
***@***.*** ***@***.***>
> On Apr 18, 2024, at 4:24 PM, lllangWV ***@***.***> wrote:
>
>
> Hey,
>
> sorry for the issue! Recently, we changed it so the fermi energy has to be given the DensityOfStates class to initialize. I forgot to update the elk code.
>
> I pushed the update to GitHub so clone the repository from there to have the updates. Here are the commands for that:
>
> pip uninstall pyprocar
> git clone ***@***.***:romerogroup/pyprocar.git
> cd pyprocar
> pip install .
> I will try to get this in the Pypi version as soon as possible. There are some further additions to the elk interface I would like to add before updating PyPi.
>
> code = "elk"
> mag_type = ["non-spin-polarized","spin-polarized-colinear","non-colinear"][1]
> data_dir = os.path.join(PROJECT_DIR,'data','examples',"SrVO3",code,mag_type, 'dos')
> HARTREE_TO_EV = 27.211386245988
> pyprocar.dosplot(
> code=code,
> mode='plain',
> fermi=0.3218543102*HARTREE_TO_EV,
> dirname=data_dir)
>
> image.png (view on web) <https://github.com/romerogroup/pyprocar/assets/120115419/feae394d-4e79-4ca6-be87-999dd144168a>
> Here are the bands as well:
>
> code = "elk"
> mag_type = ["non-spin-polarized","spin-polarized-colinear","non-colinear"][1]
> data_dir = os.path.join(PROJECT_DIR,'data','examples',"SrVO3",code,mag_type, 'ebs')
>
> pyprocar.bandsplot(
> code=code,
> mode='plain',
> spins=[0,1],
> elimit=[-10,10],
> fermi=0.3218543102*HARTREE_TO_EV,
> dirname=data_dir)
> image.png (view on web) <https://github.com/romerogroup/pyprocar/assets/120115419/9765d0f1-aa9f-43b9-888a-3e3a1b0a5360>
> Logan Lang
>
> —
> Reply to this email directly, view it on GitHub <#144 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABA2R5JBJHMGTWKV4VMIEQ3Y6ATZFAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRVGI2DENJTHE>.
> You are receiving this because you authored the thread.
>
|
|
I can't get stack or other things to work either. Attached are all the files and dropbox link. Thank you!
Sincerely,
Ron

https://www.dropbox.com/scl/fi/mlh6bcxx9h9z1iuzy6myj/pbe.tar.gz?rlkey=u15sldm2ojovc7km8q1l2794w&dl=0
… On Apr 21, 2024, at 2:47 PM, Ronald Cohen ***@***.***> wrote:
Thank you so much! The plain mode for the TDOS works, but when I triy something else it fails like this:
code = "elk"
mag_type = ["non-spin-polarized","spin-polarized-colinear","non-colinear"][1]
data_dir = os.path.join('.')
HARTREE_TO_EV = 27.211386245988
atoms=[0]
spins=[0]
pyprocar.dosplot(
atoms=atoms,
spins=spins,
code=code,
mode='stack_orbitals',
fermi=0.2561435*HARTREE_TO_EV,
dirname=data_dir)
File ~/.local/lib/python3.9/site-packages/pyprocar/plotter/dos_plot.py:658, in DOSPlot.plot_stack_orbitals(self, atoms, spins, principal_q_numbers, overlay_mode, orientation)
654 atom_names = ""
655 if atoms:
656 print(
657 "The plot only considers atoms",
--> 658 np.array(self.structure.atoms)[atoms],
659 )
660 atom_names = ""
661 for ispc in np.unique(np.array(self.structure.atoms)[atoms]):
AttributeError: 'NoneType' object has no attribute 'atoms'
Not sure if I am doing something wrong!
Thank you again,
Sincerely,
Ron
> On Apr 18, 2024, at 4:27 PM, Ronald Cohen ***@***.***> wrote:
>
> Thank you!
> I will try it
> ,
> Ron
>
> ---
> Ronald Cohen
> Extreme Materials Initiative
> Earth and Planets Laboratory
> Carnegie Institution for Science
> 5241 Broad Branch Rd., N.W.
> Washington, D.C. 20015
> ***@***.*** ***@***.***>
>
>
>> On Apr 18, 2024, at 4:24 PM, lllangWV ***@***.***> wrote:
>>
>>
>> Hey,
>>
>> sorry for the issue! Recently, we changed it so the fermi energy has to be given the DensityOfStates class to initialize. I forgot to update the elk code.
>>
>> I pushed the update to GitHub so clone the repository from there to have the updates. Here are the commands for that:
>>
>> pip uninstall pyprocar
>> git clone ***@***.***:romerogroup/pyprocar.git
>> cd pyprocar
>> pip install .
>> I will try to get this in the Pypi version as soon as possible. There are some further additions to the elk interface I would like to add before updating PyPi.
>>
>> code = "elk"
>> mag_type = ["non-spin-polarized","spin-polarized-colinear","non-colinear"][1]
>> data_dir = os.path.join(PROJECT_DIR,'data','examples',"SrVO3",code,mag_type, 'dos')
>> HARTREE_TO_EV = 27.211386245988
>> pyprocar.dosplot(
>> code=code,
>> mode='plain',
>> fermi=0.3218543102*HARTREE_TO_EV,
>> dirname=data_dir)
>>
>> image.png (view on web) <https://github.com/romerogroup/pyprocar/assets/120115419/feae394d-4e79-4ca6-be87-999dd144168a>
>> Here are the bands as well:
>>
>> code = "elk"
>> mag_type = ["non-spin-polarized","spin-polarized-colinear","non-colinear"][1]
>> data_dir = os.path.join(PROJECT_DIR,'data','examples',"SrVO3",code,mag_type, 'ebs')
>>
>> pyprocar.bandsplot(
>> code=code,
>> mode='plain',
>> spins=[0,1],
>> elimit=[-10,10],
>> fermi=0.3218543102*HARTREE_TO_EV,
>> dirname=data_dir)
>> image.png (view on web) <https://github.com/romerogroup/pyprocar/assets/120115419/9765d0f1-aa9f-43b9-888a-3e3a1b0a5360>
>> Logan Lang
>>
>> —
>> Reply to this email directly, view it on GitHub <#144 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABA2R5JBJHMGTWKV4VMIEQ3Y6ATZFAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRVGI2DENJTHE>.
>> You are receiving this because you authored the thread.
>>
>
|
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Hey! sorry for the late reply, I only have a couple of times a week to work on pyprocar. I looked into the issue, without going into details, it had to do with how the main parser got the DOS and Structure object. This density of states looks a little strange with the giant peak near -5eV. I am just curious what does the band structure look like? Here are the plots for the density of states for different modes: pyprocar.dosplot(
code=code,
mode='parametric',
orbitals=[4,5,6,7,8],
# elimit=[-2,2],
clim =[0,1],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
pyprocar.dosplot(
code=code,
mode='parametric_line',
orbitals=[4,5,6,7,8],
# elimit=[-5,5],
clim =[0,1],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
pyprocar.dosplot(
code=code,
mode='stack_orbitals',
# elimit=[-5,5],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
pyprocar.dosplot(
code=code,
mode='stack_species',
orbitals=[4,5,6,7,8],
# elimit=[-5,5],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
pyprocar.dosplot(
code=code,
mode='overlay_orbitals',
# elimit=[-5,5],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
pyprocar.dosplot(
code=code,
mode='overlay_species',
orbitals=[4,5,6,7,8],
# elimit=[-5,5],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
Logan Lang |
|
I forgot to mention, I pushed these updates to Git Hub repo, so get the updated version from there. Logan Lang |
|
Thanks! This is to be expected. So I wonder why the Fermi level is needed
as input when elk actually makes all the dos files have 0 as the Fermi
level.
Ron
…---
Ronald Cohen
Extreme Materials Initiative
Earth and Planets Laboratory
Carnegie Institution for Science
5241 Broad Branch Rd., N.W.
Washington, D.C. 20015
***@***.***
On Tue, Apr 23, 2024 at 12:15 PM lllangWV ***@***.***> wrote:
Hey!
sorry for the late reply, I only have a couple of times a week to work on
pyprocar. I looked into the issue, without going into details, it had to do
with how the main parser got the DOS and Structure object.
This density of states looks a little strange with the giant peak near
-5eV. I am just curious what does the band structure look like?
Here are the plots for the density of states for different modes:
pyprocar.dosplot(
code=code,
mode='parametric',
orbitals=[4,5,6,7,8],
# elimit=[-2,2],
clim =[0,1],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web)
<https://github.com/romerogroup/pyprocar/assets/120115419/b9f26a05-a38e-446b-9e00-506128e1ae3c>
pyprocar.dosplot(
code=code,
mode='parametric_line',
orbitals=[4,5,6,7,8],
# elimit=[-5,5],
clim =[0,1],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web)
<https://github.com/romerogroup/pyprocar/assets/120115419/f43e7bc6-a283-4ec6-9d51-d65c2b3a0329>
pyprocar.dosplot(
code=code,
mode='stack_orbitals',
# elimit=[-5,5],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web)
<https://github.com/romerogroup/pyprocar/assets/120115419/69572b79-6ea0-470f-86b6-65f3d5c0eb7a>
pyprocar.dosplot(
code=code,
mode='stack_species',
orbitals=[4,5,6,7,8],
# elimit=[-5,5],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web)
<https://github.com/romerogroup/pyprocar/assets/120115419/b6b04e8d-e3f0-4a3a-bcb8-4751ab51ad6f>
pyprocar.dosplot(
code=code,
mode='overlay_orbitals',
# elimit=[-5,5],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web)
<https://github.com/romerogroup/pyprocar/assets/120115419/d74e3587-b517-43f2-95ca-306090593439>
pyprocar.dosplot(
code=code,
mode='overlay_species',
orbitals=[4,5,6,7,8],
# elimit=[-5,5],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web)
<https://github.com/romerogroup/pyprocar/assets/120115419/c0ddca9f-eb78-4885-80f2-57d3e63d732c>
Logan Lang
—
Reply to this email directly, view it on GitHub
<#144 (comment)>,
or unsubscribe
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You are receiving this because you authored the thread.Message ID:
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overlay_orbitals is only labeling d states. Is there a way to also
plotf states? Thanks!
Ron
…---
Ronald Cohen
Extreme Materials Initiative
Earth and Planets Laboratory
Carnegie Institution for Science
5241 Broad Branch Rd., N.W.
Washington, D.C. 20015
***@***.***
On Tue, Apr 23, 2024 at 12:15 PM lllangWV ***@***.***> wrote:
Hey!
sorry for the late reply, I only have a couple of times a week to work on
pyprocar. I looked into the issue, without going into details, it had to do
with how the main parser got the DOS and Structure object.
This density of states looks a little strange with the giant peak near
-5eV. I am just curious what does the band structure look like?
Here are the plots for the density of states for different modes:
pyprocar.dosplot(
code=code,
mode='parametric',
orbitals=[4,5,6,7,8],
# elimit=[-2,2],
clim =[0,1],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web)
<https://github.com/romerogroup/pyprocar/assets/120115419/b9f26a05-a38e-446b-9e00-506128e1ae3c>
pyprocar.dosplot(
code=code,
mode='parametric_line',
orbitals=[4,5,6,7,8],
# elimit=[-5,5],
clim =[0,1],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web)
<https://github.com/romerogroup/pyprocar/assets/120115419/f43e7bc6-a283-4ec6-9d51-d65c2b3a0329>
pyprocar.dosplot(
code=code,
mode='stack_orbitals',
# elimit=[-5,5],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web)
<https://github.com/romerogroup/pyprocar/assets/120115419/69572b79-6ea0-470f-86b6-65f3d5c0eb7a>
pyprocar.dosplot(
code=code,
mode='stack_species',
orbitals=[4,5,6,7,8],
# elimit=[-5,5],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web)
<https://github.com/romerogroup/pyprocar/assets/120115419/b6b04e8d-e3f0-4a3a-bcb8-4751ab51ad6f>
pyprocar.dosplot(
code=code,
mode='overlay_orbitals',
# elimit=[-5,5],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web)
<https://github.com/romerogroup/pyprocar/assets/120115419/d74e3587-b517-43f2-95ca-306090593439>
pyprocar.dosplot(
code=code,
mode='overlay_species',
orbitals=[4,5,6,7,8],
# elimit=[-5,5],
fermi=0.2561435077*HARTREE_TO_EV,
dirname=data_dir)
image.png (view on web)
<https://github.com/romerogroup/pyprocar/assets/120115419/c0ddca9f-eb78-4885-80f2-57d3e63d732c>
Logan Lang
—
Reply to this email directly, view it on GitHub
<#144 (comment)>,
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Hey! We require users to specify the Fermi energy to maintain a consistent functional interface across various DFT codes. Our goal is for For instance, with VASP, the Fermi energy in the bands or density of states directory is not the self-consistent Fermi energy, which is located in a different directory. This complicates maintaining a uniform interface. While ELK naturally sets the Fermi energy to 0, solving this issue, we initially decided to standardize the interface by requiring all users, regardless of the DFT code, to specify the Fermi energy. Thinking about this more, I am exploring alternative solutions that could exempt users from specifying the Fermi energy when it is available in the same directory used by I'll see what I can do, and let you know! |
|
I think I am getting this sorted. Thank you! It is working now!
Sincerely,
Ron
…---
Ronald Cohen
Extreme Materials Initiative
Earth and Planets Laboratory
Carnegie Institution for Science
5241 Broad Branch Rd., N.W.
Washington, D.C. 20015
***@***.***
On Thu, Apr 25, 2024 at 2:58 PM Ronald Cohen ***@***.***>
wrote:
overlay_orbitals is only labeling d states. Is there a way to also plotf states? Thanks!
Ron
---
Ronald Cohen
Extreme Materials Initiative
Earth and Planets Laboratory
Carnegie Institution for Science
5241 Broad Branch Rd., N.W.
Washington, D.C. 20015
***@***.***
On Tue, Apr 23, 2024 at 12:15 PM lllangWV ***@***.***>
wrote:
> Hey!
>
> sorry for the late reply, I only have a couple of times a week to work on
> pyprocar. I looked into the issue, without going into details, it had to do
> with how the main parser got the DOS and Structure object.
>
> This density of states looks a little strange with the giant peak near
> -5eV. I am just curious what does the band structure look like?
>
> Here are the plots for the density of states for different modes:
>
> pyprocar.dosplot(
> code=code,
> mode='parametric',
> orbitals=[4,5,6,7,8],
> # elimit=[-2,2],
> clim =[0,1],
> fermi=0.2561435077*HARTREE_TO_EV,
> dirname=data_dir)
>
> image.png (view on web)
> <https://github.com/romerogroup/pyprocar/assets/120115419/b9f26a05-a38e-446b-9e00-506128e1ae3c>
>
> pyprocar.dosplot(
> code=code,
> mode='parametric_line',
> orbitals=[4,5,6,7,8],
> # elimit=[-5,5],
> clim =[0,1],
> fermi=0.2561435077*HARTREE_TO_EV,
> dirname=data_dir)
>
> image.png (view on web)
> <https://github.com/romerogroup/pyprocar/assets/120115419/f43e7bc6-a283-4ec6-9d51-d65c2b3a0329>
>
> pyprocar.dosplot(
> code=code,
> mode='stack_orbitals',
> # elimit=[-5,5],
> fermi=0.2561435077*HARTREE_TO_EV,
> dirname=data_dir)
>
> image.png (view on web)
> <https://github.com/romerogroup/pyprocar/assets/120115419/69572b79-6ea0-470f-86b6-65f3d5c0eb7a>
>
> pyprocar.dosplot(
> code=code,
> mode='stack_species',
> orbitals=[4,5,6,7,8],
> # elimit=[-5,5],
> fermi=0.2561435077*HARTREE_TO_EV,
> dirname=data_dir)
>
> image.png (view on web)
> <https://github.com/romerogroup/pyprocar/assets/120115419/b6b04e8d-e3f0-4a3a-bcb8-4751ab51ad6f>
>
> pyprocar.dosplot(
> code=code,
> mode='overlay_orbitals',
> # elimit=[-5,5],
> fermi=0.2561435077*HARTREE_TO_EV,
> dirname=data_dir)
>
> image.png (view on web)
> <https://github.com/romerogroup/pyprocar/assets/120115419/d74e3587-b517-43f2-95ca-306090593439>
>
> pyprocar.dosplot(
> code=code,
> mode='overlay_species',
> orbitals=[4,5,6,7,8],
> # elimit=[-5,5],
> fermi=0.2561435077*HARTREE_TO_EV,
> dirname=data_dir)
>
> image.png (view on web)
> <https://github.com/romerogroup/pyprocar/assets/120115419/c0ddca9f-eb78-4885-80f2-57d3e63d732c>
>
> Logan Lang
>
> —
> Reply to this email directly, view it on GitHub
> <#144 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/ABA2R5PBXTI347LTOIWH34DY62CKHAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZSHA2DMNJRGY>
> .
> You are receiving this because you authored the thread.Message ID:
> ***@***.***>
>
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For the
|
|
Thanks! That sounds like a good idea,
Ron
…---
Ronald Cohen
Extreme Materials Initiative
Earth and Planets Laboratory
Carnegie Institution for Science
5241 Broad Branch Rd., N.W.
Washington, D.C. 20015
***@***.***
On Thu, Apr 25, 2024 at 3:29 PM lllangWV ***@***.***> wrote:
Hey!
We require users to specify the Fermi energy to maintain a consistent
functional interface across various DFT codes. Our goal is for dosplot
and bandsplot functions to have uniform arguments for all DFT codes,
differing only in the code argument. However, there are challenges in
standardizing the Fermi energy across different DFT codes.
For instance, with VASP, the Fermi energy in the bands or density of
states directory is not the self-consistent Fermi energy, which is located
in a different directory. This complicates maintaining a uniform interface.
While ELK naturally sets the Fermi energy to 0, solving this issue, we
initially decided to standardize the interface by requiring all users,
regardless of the DFT code, to specify the Fermi energy.
Thinking about this more, I am exploring alternative solutions that could
exempt users from specifying the Fermi energy when it is available in the
same directory used by bandsplot or dosplot. This would be the case for
Quantum Espress and ELK.
I'll see what I can do, and let you know!
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Dear Logan Lang,
I am trying now to use VASP for this system as I have been having problems
with ELK. So now I am trying to use pyprocar with
vasp. It runs fine except does not plot f-orbitals. This I think is a
problem with my VASP run actually. I wonder if you have any suggestions?
Here is the INCAR:
d2C6B6
SYSTEM = "Nd2C6B6"
Electronic minimization
ENCUT = 500
EDIFF = 1E-7
*LORBIT = 11 (Trying 14 now)*
LREAL = Auto
ISYM = 2
LSORBIT = .True.
DOS
ISMEAR = -5
ICHARG - 11
Magnetism
ISPIN = 2
MAGMOM = 0 0 2 0 0 -2 36*0
SAXIS = 0 0 1
Orbital Moment
LORBMOM = T
Mixer
AMIX = 0.2
BMIX = 0.00001
AMIX_MAG = 0.8
BMIX_MAG = 0.00001
Attached is what the DOS looks like. There should be Nd f-states. I am
using theNd PAW which I think includes f-states in valence:
Atomic configuration
14 entries
n l j E occ.
1 0 0.50 -43392.6566 2.0000
2 0 0.50 -7020.4058 2.0000
2 1 1.50 -6275.1064 6.0000
3 0 0.50 -1525.9247 2.0000
3 1 1.50 -1291.0088 6.0000
3 2 2.50 -965.4525 10.0000
4 0 0.50 -306.0301 2.0000
4 1 1.50 -229.0473 6.0000
4 2 2.50 -119.6721 10.0000
5 2 2.50 -2.4140 0.5000
4 3 2.50 -4.1737 3.5000
5 0 0.50 -42.0344 2.0000
6 0 0.50 -3.7006 2.0000
5 1 1.50 -23.3535 6.0000
Description
l E TYP RCUT TYP RCUT
2 -2.4139946 23 2.300
2 13.6058260 23 2.300
3 -4.1737087 23 2.400
3 -5.5342913 23 2.400
0 -42.0343931 23 1.550
0 -3.7005734 23 2.350
1 -23.3534934 23 2.000
1 -24.7140760 23 2.000
Sincerely,
Ron
…---
Ronald Cohen
Extreme Materials Initiative
Earth and Planets Laboratory
Carnegie Institution for Science
5241 Broad Branch Rd., N.W.
Washington, D.C. 20015
***@***.***
On Thu, Apr 25, 2024 at 3:31 PM lllangWV ***@***.***> wrote:
For the overlay_orbtial not displaying the f orbitals. It should include
f orbitals
image.png (view on web)
<https://github.com/romerogroup/pyprocar/assets/120115419/e6317594-effb-4ad6-a22d-d094be3ae8d8>
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So sorry--stupid question! I used a Nd PAW with f in the core!!
Ron
…---
Ronald Cohen
Extreme Materials Initiative
Earth and Planets Laboratory
Carnegie Institution for Science
5241 Broad Branch Rd., N.W.
Washington, D.C. 20015
***@***.***
On Wed, May 29, 2024 at 2:10 PM Ronald Cohen ***@***.***>
wrote:
Dear Logan Lang,
I am trying now to use VASP for this system as I have been having problems
with ELK. So now I am trying to use pyprocar with
vasp. It runs fine except does not plot f-orbitals. This I think is a
problem with my VASP run actually. I wonder if you have any suggestions?
Here is the INCAR:
d2C6B6
SYSTEM = "Nd2C6B6"
Electronic minimization
ENCUT = 500
EDIFF = 1E-7
*LORBIT = 11 (Trying 14 now)*
LREAL = Auto
ISYM = 2
LSORBIT = .True.
DOS
ISMEAR = -5
ICHARG - 11
Magnetism
ISPIN = 2
MAGMOM = 0 0 2 0 0 -2 36*0
SAXIS = 0 0 1
Orbital Moment
LORBMOM = T
Mixer
AMIX = 0.2
BMIX = 0.00001
AMIX_MAG = 0.8
BMIX_MAG = 0.00001
Attached is what the DOS looks like. There should be Nd f-states. I am
using theNd PAW which I think includes f-states in valence:
Atomic configuration
14 entries
n l j E occ.
1 0 0.50 -43392.6566 2.0000
2 0 0.50 -7020.4058 2.0000
2 1 1.50 -6275.1064 6.0000
3 0 0.50 -1525.9247 2.0000
3 1 1.50 -1291.0088 6.0000
3 2 2.50 -965.4525 10.0000
4 0 0.50 -306.0301 2.0000
4 1 1.50 -229.0473 6.0000
4 2 2.50 -119.6721 10.0000
5 2 2.50 -2.4140 0.5000
4 3 2.50 -4.1737 3.5000
5 0 0.50 -42.0344 2.0000
6 0 0.50 -3.7006 2.0000
5 1 1.50 -23.3535 6.0000
Description
l E TYP RCUT TYP RCUT
2 -2.4139946 23 2.300
2 13.6058260 23 2.300
3 -4.1737087 23 2.400
3 -5.5342913 23 2.400
0 -42.0343931 23 1.550
0 -3.7005734 23 2.350
1 -23.3534934 23 2.000
1 -24.7140760 23 2.000
Sincerely,
Ron
---
Ronald Cohen
Extreme Materials Initiative
Earth and Planets Laboratory
Carnegie Institution for Science
5241 Broad Branch Rd., N.W.
Washington, D.C. 20015
***@***.***
On Thu, Apr 25, 2024 at 3:31 PM lllangWV ***@***.***> wrote:
> For the overlay_orbtial not displaying the f orbitals. It should include
> f orbitals
>
> image.png (view on web)
> <https://github.com/romerogroup/pyprocar/assets/120115419/e6317594-effb-4ad6-a22d-d094be3ae8d8>
>
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Dear Logan Lang,
I am having some problems with pyprocar and VASP for a spin-orbit
spin-polarized where only one spin is plotted. I seem to see two spin
projections in the PROCAR file but cannot get them to plot.
I attach the figures and inputs and the VASP run. I would greatly
appreciate it if you could look at this. Also, I don't understand what you
were saying about VASP needing two directories. It seems to me that the
Fermi level and DOS are in the same directory.
The files are here:
https://www.dropbox.com/scl/fi/vsric227ofsq36p3p5epc/SOdos.tar.gz?rlkey=vu1bkw5ijapvkpew8fk1zjwdz&dl=0
Sincerely,
Ron
…---
Ronald Cohen
Extreme Materials Initiative
Earth and Planets Laboratory
Carnegie Institution for Science
5241 Broad Branch Rd., N.W.
Washington, D.C. 20015
***@***.***
On Tue, Apr 23, 2024 at 12:18 PM lllangWV ***@***.***> wrote:
I forgot to mention, I pushed these updates to Git Hub repo, so get the
updated version from there.
Logan Lang
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Hey Ron, I'll take a look! Hopefully, I can get to it today, but if not the next couple days I will.
What I was referring to is if you compare the OUTCAR file when you run a non-self consistent to the OUTCAR file of a self-consistent file. They are not guaranteed to be the same. I have personally, noticed this in some calculations I have performed. Ideally, the Fermi energy in a non-self-consistent calculation should be very close to that of the self-consistent calculation if the charge density is well-converged and if the same k-points and smearing methods are used. However, there can be slight differences due to the different treatment of electron density updates. This is not a problem in other codes because they have a system to retain the self-consistent fermi energy in subsequent non-self-consistent calculations. Logan |
|
I am wondering if you had a chance to look at this. Thanks,
Ron
…---
Ronald Cohen
Extreme Materials Initiative
Earth and Planets Laboratory
Carnegie Institution for Science
5241 Broad Branch Rd., N.W.
Washington, D.C. 20015
***@***.***
On Fri, May 31, 2024 at 2:50 PM lllangWV ***@***.***> wrote:
Hey Ron,
I'll take a look! Hopefully, I can get to it today, but if not the next
couple days I will.
Also, I don't understand what you
were saying about VASP needing two directories. It seems to me that the
Fermi level and DOS are in the same directory.
What I was referring to is if you compare the OUTCAR file when you run a
non-self consistent to the OUTCAR file of a self-consistent file. They are
not guaranteed to be the same. I have personally, noticed this in some
calculations I have performed. Ideally, the Fermi energy in a
non-self-consistent calculation should be very close to that of the
self-consistent calculation if the charge density is well-converged and if
the same k-points and smearing methods are used. However, there can be
slight differences due to the different treatment of electron density
updates.
This is not a problem in other codes because they have a system to retain
the self-consistent fermi energy in subsequent non-self-consistent
calculations.
Logan
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Hey Ron, I am sorry it slipped my mind. I'm taking a look at it now. Could you also send me the POSCAR file too, I can't plot without it.
So for a spin-orbit calculation in vasp, it will automatically turn the LNONCOLINEAR flag on, so you should only see one spin. This is because there is there is no definition of spin-up or spin-down in noncolinear calculations. What you see in the PROCAR is the projected magnetizations. You can find the exact definition here PROCAR at the bottom of the page. The blocks represent the following:
When you are dealing with a non-colinear calculation in pyprocar you can specify which projection you would like to see with the following. In this plot, the color scale represents the contribution of the d-orbitals of the first atom to the total magnetization atoms=[0] Changing # of k-points: 90 # of bands: 128 # of ions: 14
k-point 1 : 0.00000000 0.00000000 0.00000000 weight = 0.00195312
band 1 # energy -27.58781017 # occ. 1.00000000
ion s py pz px dxy dyz dz2 dxz x2-y2 fy3x2 fxyz fyz2 fz3 fxz2 fzx2 fx3 tot
1 0.469 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.469
2 0.469 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.469
3 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
4 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
5 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
6 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
7 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
8 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
9 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
10 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
11 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
12 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
13 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
14 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
tot 0.941 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.941
1 -0.000 -0.000 -0.000 0.000 0.000 0.000 -0.000 0.000 -0.000 -0.000 0.000 0.000 -0.000 -0.000 0.000 0.000 -0.000
2 0.000 -0.000 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000 -0.000 0.000 0.000 0.000
3 -0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000
4 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000
5 0.000 -0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
6 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
7 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
8 -0.000 0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000
9 0.000 0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
10 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
11 -0.000 -0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000
12 -0.000 0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000
13 0.000 -0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
14 -0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000
tot 0.000 -0.000 -0.000 0.000 -0.000 0.000 0.000 0.000 0.000 -0.000 0.000 0.000 -0.000 -0.000 0.000 0.000 0.000
1 -0.000 0.000 -0.000 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 -0.000 0.000 -0.000 -0.000 0.000 0.000 -0.000
2 0.000 -0.000 -0.000 -0.000 -0.000 0.000 -0.000 -0.000 -0.000 -0.000 -0.000 -0.000 -0.000 -0.000 0.000 -0.000 0.000
3 -0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000
4 -0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000
5 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
6 0.000 -0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
7 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
8 -0.000 0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000
9 0.000 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
10 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
11 -0.000 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000
12 -0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000
13 -0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.000
14 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
tot -0.000 -0.000 0.000 0.000 0.000 0.000 -0.000 0.000 -0.000 -0.000 -0.000 0.000 -0.000 -0.000 0.000 -0.000 -0.000
1 0.469 0.000 -0.000 0.000 0.000 -0.000 0.000 -0.000 0.000 0.000 -0.000 -0.000 -0.000 0.000 -0.000 -0.000 0.469
2 0.469 0.000 -0.000 0.000 0.000 -0.000 0.000 -0.000 0.000 -0.000 -0.000 0.000 -0.000 -0.000 -0.000 0.000 0.469
3 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
4 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
5 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
6 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
7 0.000 -0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
8 0.000 -0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
9 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
10 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
11 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
12 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
13 0.000 -0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
14 0.000 -0.000 -0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
tot 0.941 0.000 -0.000 0.000 0.000 -0.000 0.000 -0.000 0.000 0.000 -0.000 -0.000 -0.000 -0.000 -0.000 0.000 0.941Logan Lang |
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I tried a simple dos with elk and get the below. But when I look at your parser page I don't even see elk.
Yet pyprocar is still listed on the elk web site
Very confused.
Thank you for any help,
Ron
pyprocar.dosplot(
code='elk',
mode='plain',
fermi=0.3568473976,
dirname="./")
ValueError Traceback (most recent call last)
Cell In[22], line 1
----> 1 pyprocar.dosplot(
2 code='elk',
3 mode='plain',
4 fermi=0.3568473976,
5 dirname=data_dir)
File /central/home/recohen/cohen_env/lib/python3.11/site-packages/pyprocar/scripts/scriptDosplot.py:278, in dosplot(code, dirname, mode, orientation, spins, atoms, orbitals, items, fermi, fermi_shift, elimit, dos_limit, savefig, labels, projection_mask, ax, show, print_plot_opts, **kwargs)
274 elif orientation[0].lower() == 'v':
275 orientation = 'vertical'
--> 278 parser = io.Parser(code = code, dir = dirname)
279 dos = parser.dos
280 structure = parser.structure
File /central/home/recohen/cohen_env/lib/python3.11/site-packages/pyprocar/io/parser.py:26, in Parser.init(self, code, dir)
23 self.code = code
24 self.dir = dir
---> 26 self.parse()
File /central/home/recohen/cohen_env/lib/python3.11/site-packages/pyprocar/io/parser.py:60, in Parser.parse(self)
57 self.ebs.bands += self.ebs.efermi
59 if self.dos:
---> 60 self.dos.energies += self.dos.efermi
61 return None
ValueError: non-broadcastable output operand with shape (500,) doesn't match the broadcast shape (4,1,16,2,500)
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