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Published 20 hours ago • verified publisher icon romerogroup

elk support?

Open recohen opened this issue 10 months ago • 42 comments

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)

recohen avatar Apr 12 '24 17:04 recohen

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 [email protected]: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

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

Logan Lang

lllangWV avatar Apr 18 '24 20:04 lllangWV

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 https://github.com/romerogroup/pyprocar/issues/144#issuecomment-2065242539, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5JBJHMGTWKV4VMIEQ3Y6ATZFAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRVGI2DENJTHE. You are receiving this because you authored the thread.

recohen avatar Apr 18 '24 20:04 recohen

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 https://github.com/romerogroup/pyprocar/issues/144#issuecomment-2065242539, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5JBJHMGTWKV4VMIEQ3Y6ATZFAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRVGI2DENJTHE. You are receiving this because you authored the thread.

recohen avatar Apr 21 '24 18:04 recohen

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 https://github.com/romerogroup/pyprocar/issues/144#issuecomment-2065242539, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5JBJHMGTWKV4VMIEQ3Y6ATZFAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRVGI2DENJTHE. You are receiving this because you authored the thread.

recohen avatar Apr 21 '24 19:04 recohen

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

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

pyprocar.dosplot(
                code=code,
                mode='stack_orbitals',
                # elimit=[-5,5],
                fermi=0.2561435077*HARTREE_TO_EV,
                dirname=data_dir)

image

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

pyprocar.dosplot(
                code=code,
                mode='overlay_orbitals',
                # elimit=[-5,5],
                fermi=0.2561435077*HARTREE_TO_EV,
                dirname=data_dir)

image

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

Logan Lang

lllangWV avatar Apr 23 '24 16:04 lllangWV

I forgot to mention, I pushed these updates to Git Hub repo, so get the updated version from there.

Logan Lang

lllangWV avatar Apr 23 '24 16:04 lllangWV

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 https://github.com/romerogroup/pyprocar/issues/144#issuecomment-2072846516, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5PBXTI347LTOIWH34DY62CKHAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZSHA2DMNJRGY . You are receiving this because you authored the thread.Message ID: @.***>

recohen avatar Apr 25 '24 18:04 recohen

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 https://github.com/romerogroup/pyprocar/issues/144#issuecomment-2072846516, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5PBXTI347LTOIWH34DY62CKHAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZSHA2DMNJRGY . You are receiving this because you authored the thread.Message ID: @.***>

recohen avatar Apr 25 '24 18:04 recohen

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!

lllangWV avatar Apr 25 '24 19:04 lllangWV

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

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recohen avatar Apr 25 '24 19:04 recohen

For the overlay_orbtial not displaying the f orbitals. It should include f orbitals

image

lllangWV avatar Apr 25 '24 19:04 lllangWV

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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recohen avatar Apr 25 '24 19:04 recohen

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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recohen avatar May 29 '24 18:05 recohen

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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recohen avatar May 29 '24 18:05 recohen

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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recohen avatar May 31 '24 16:05 recohen

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

lllangWV avatar May 31 '24 18:05 lllangWV

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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recohen avatar Jun 03 '24 15:06 recohen

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.

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.

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:

  1. The first set is the total (absolute magnetization)
  2. The second is the x-projection of the spin
  3. The third is the y-projection
  4. The third is the z-projection

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] orbitals=[4,5,6,7,8] spins=[0] pyprocar.dosplot( code='vasp', mode='parametric', fermi=5.5962, atoms=atoms, orbitals=orbitals, spins=spins, dirname=data_dir)

Changing spins=[1] would represents the contribution of the d-orbitals of the first atom to the x-projection magnetization. Changing spins=[2] would represents the contribution of the d-orbitals of the first atom to the y-projection magnetization. Changing spins=[3] would represents the contribution of the d-orbitals of the first atom to the z-projection magnetization.

# 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  0.941

Logan Lang

lllangWV avatar Jun 03 '24 15:06 lllangWV

Dear Logan Lang,

Thank you so much for this. It has been a while but I was stuck doing other things. So now if something is ferromagnetic how would one see the DOS for up and down total or along z with spin-orbit? I seem to be seeing only the majority spins. Maybe I am not understanding something major. Thank you so much,

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 Mon, Jun 3, 2024 at 11:57 AM lllangWV @.***> wrote:

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.

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.

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 https://www.vasp.at/wiki/index.php/PROCAR at the bottom of the page.

The blocks represent the following are as follow:

  1. The first set is the total (absolute magnetization)
  2. The second is the x-projection of the spin
  3. The third is the y-projection
  4. The third is the z-projection

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] orbitals=[4,5,6,7,8] spins=[0] pyprocar.dosplot( code='vasp', mode='parametric', fermi=5.5962, atoms=atoms, orbitals=orbitals, spins=spins, dirname=data_dir)

Changing spins=[1] would represents the contribution of the d-orbitals of the first atom to the x-projection magnetization. Changing spins=[2] would represents the contribution of the d-orbitals of the first atom to the y-projection magnetization. Changing spins=[3] would represents the contribution of the d-orbitals of the first atom to the z-projection magnetization.

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 0.941

Logan Lang

— Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/144#issuecomment-2145576869, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5KBD5TZMBDLQ46KSW3ZFSG7PAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBVGU3TMOBWHE . You are receiving this because you authored the thread.Message ID: @.***>

recohen avatar Jun 21 '24 18:06 recohen

Ron

Is this for VASP or Quantum Espresso?.... can you share the line you used?

Thanks

::::____ Prof. Aldo Humberto Romero Director Research Computing, West Virginia University Eberly Family Distinguished Professor Fellow American Physical Society Editor Physica B, Assistant Editor EPJB, Editor Frontiers in Physics Section Editor Papers in Physics Member of the Editorial Board of “Materials” and “Symmetry Physics” https://scholar.google.com/citations?user=pwte-hQAAAAJ&hl=en

Physics and Astronomy Department West Virginia University 135 Willey Street, PO Box 6315 111 White Hall Morgantown, WV 26506 Phone: 304-293-6317 Fax: 304-293-5732 email: @.***

From: Ronald Cohen @.> Date: Friday, June 21, 2024 at 2:14 PM To: romerogroup/pyprocar @.> Cc: Subscribed @.***> Subject: Re: [romerogroup/pyprocar] elk support? (Issue #144) Dear Logan Lang,

Thank you so much for this. It has been a while but I was stuck doing other things. So now if something is ferromagnetic how would one see the DOS for up and down total or along z with spin-orbit? I seem to be seeing only the majority spins. Maybe I am not understanding something major. Thank you so much,

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 Mon, Jun 3, 2024 at 11:57 AM lllangWV @.***> wrote:

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.

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.

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 https://www.vasp.at/wiki/index.php/PROCAR at the bottom of the page.

The blocks represent the following are as follow:

  1. The first set is the total (absolute magnetization)
  2. The second is the x-projection of the spin
  3. The third is the y-projection
  4. The third is the z-projection

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] orbitals=[4,5,6,7,8] spins=[0] pyprocar.dosplot( code='vasp', mode='parametric', fermi=5.5962, atoms=atoms, orbitals=orbitals, spins=spins, dirname=data_dir)

Changing spins=[1] would represents the contribution of the d-orbitals of the first atom to the x-projection magnetization. Changing spins=[2] would represents the contribution of the d-orbitals of the first atom to the y-projection magnetization. Changing spins=[3] would represents the contribution of the d-orbitals of the first atom to the z-projection magnetization.

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 0.941

Logan Lang

— Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/144#issuecomment-2145576869, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5KBD5TZMBDLQ46KSW3ZFSG7PAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBVGU3TMOBWHE . You are receiving this because you authored the thread.Message ID: @.***>

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ahromero avatar Jun 21 '24 18:06 ahromero

Arggh. I am trying to run on another machine, and am getting: pyprocar.dosplot(code='vasp', mode='plain', elimit=[-10, 10], fermi=9.739484, orientation='horizontal', dirname='.', spins=spins, #labels=[r'$\uparrow$', r'$\downarrow$'], title=r'Total Density of States$')

AttributeError Traceback (most recent call last) Cell In[5], line 1 ----> 1 pyprocar.dosplot(code='vasp', 2 mode='plain', 3 elimit=[-10, 10], 4 fermi=10.0992, 5 orientation='horizontal', 6 dirname='.', 7 spins=spins, 8 #labels=[r'$\uparrow$', r'$\downarrow$'], 9 title=r'Total Density of States$')

File ~/cohenenv3.12/lib/python3.12/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 ~/cohenenv3.12/lib/python3.12/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 ~/cohenenv3.12/lib/python3.12/site-packages/pyprocar/io/parser.py:48, in Parser.parse(self) 45 self.parse_siesta() 47 elif self.code == "vasp": ---> 48 self.parse_vasp() 50 elif self.code == "elk": 51 self.parse_elk()

File ~/cohenenv3.12/lib/python3.12/site-packages/pyprocar/io/parser.py:267, in Parser.parse_vasp(self) 262 except Exception as e: 263 self.kpath=None --> 267 procar = vasp.Procar( 268 filename=procar, 269 structure=poscar.structure, 270 reciprocal_lattice=poscar.structure.reciprocal_lattice, 271 kpath=self.kpath, 272 n_kx=outcar.n_kx, 273 n_ky=outcar.n_ky, 274 n_kz=outcar.n_kz, 275 efermi=outcar.efermi, 276 interpolation_factor=1 277 ) 279 try: 280 vasprun = vasp.VaspXML(filename = vasprun)

File ~/cohenenv3.12/lib/python3.12/site-packages/pyprocar/io/vasp.py:618, in Procar.init(self, filename, structure, reciprocal_lattice, kpath, n_kx, n_ky, n_kz, efermi, interpolation_factor) 615 self.orbitalName_short = ["s", "p", "d", "f", "tot"] 616 self.labels = self.orbitalName_old[:-1] --> 618 self._read() 619 if self.has_phase: 620 self.carray = self.spd_phase[:, :, :, :-1, 1:-1]

File ~/cohenenv3.12/lib/python3.12/site-packages/pyprocar/io/vasp.py:760, in Procar._read(self) 758 self._read_orbitals() 759 if self.has_phase: --> 760 self._read_phases() 761 rf.close() 762 return

File ~/cohenenv3.12/lib/python3.12/site-packages/pyprocar/io/vasp.py:1160, in Procar.read_phases(self) 1144 else: 1145 self.spd_phase = self.spd_phase.reshape( 1146 self.kpointsCount, 1147 self.bandsCount, (...) 1150 self.orbitalCount * 2, 1151 ) 1152 temp = np.zeros( 1153 shape=( 1154 self.spd_phase.shape[0], 1155 self.spd_phase.shape[1], 1156 self.spd_phase.shape[2], 1157 self.spd_phase.shape[3], 1158 int(self.spd_phase.shape[4] / 2) + 1, 1159 ), -> 1160 dtype=np.complex, 1161 ) 1163 for i in range(1, (self.orbitalCount) * 2 - 2, 2): 1164 temp[:, :, :, :, (i + 1) // 2].real = self.spd_phase[:, :, :, :, i]

File ~/cohenenv3.12/lib/python3.12/site-packages/numpy/init.py:397, in getattr(attr) 394 raise AttributeError(former_attrs[attr]) 396 if attr in expired_attributes: --> 397 raise AttributeError( 398 f"np.{attr} was removed in the NumPy 2.0 release. " 399 f"{expired_attributes[attr]}" 400 ) 402 if attr == "chararray": 403 warnings.warn( 404 "np.chararray is deprecated and will be removed from " 405 "the main namespace in the future. Use an array with a string " 406 "or bytes dtype instead.", DeprecationWarning, stacklevel=2)

AttributeError: np.complex_ was removed in the NumPy 2.0 release. Use np.complex128 instead.

Ronald Cohen Extreme Materials Initiative Earth and Planets Laboratory Carnegie Institution for Science 5241 Broad Branch Rd., N.W. Washington, D.C. 20015 @.***

On Mon, Jun 3, 2024 at 11:57 AM lllangWV @.***> wrote:

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.

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.

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 https://www.vasp.at/wiki/index.php/PROCAR at the bottom of the page.

The blocks represent the following are as follow:

  1. The first set is the total (absolute magnetization)
  2. The second is the x-projection of the spin
  3. The third is the y-projection
  4. The third is the z-projection

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] orbitals=[4,5,6,7,8] spins=[0] pyprocar.dosplot( code='vasp', mode='parametric', fermi=5.5962, atoms=atoms, orbitals=orbitals, spins=spins, dirname=data_dir)

Changing spins=[1] would represents the contribution of the d-orbitals of the first atom to the x-projection magnetization. Changing spins=[2] would represents the contribution of the d-orbitals of the first atom to the y-projection magnetization. Changing spins=[3] would represents the contribution of the d-orbitals of the first atom to the z-projection magnetization.

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 0.941

Logan Lang

— Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/144#issuecomment-2145576869, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5KBD5TZMBDLQ46KSW3ZFSG7PAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBVGU3TMOBWHE . You are receiving this because you authored the thread.Message ID: @.***>

recohen avatar Jun 21 '24 18:06 recohen

This is vasp. The input was:

spins=[0]

pyprocar.dosplot(code='vasp', mode='plain', elimit=[-10, 10], fermi=9.739484, orientation='horizontal', dirname='.', spins=spins, #labels=[r'$\uparrow$', r'$\downarrow$'], title=r'Total Density of States$')

When I try to run on another machine (different vasp run) I get the errors I just sent. I will try using the same output files as before on that machine. Thank you!

Sincerely,

Ron

On Jun 21, 2024, at 2:29 PM, Aldo Romero @.***> wrote:

Ron

Is this for VASP or Quantum Espresso?.... can you share the line you used?

Thanks

::::____ Prof. Aldo Humberto Romero Director Research Computing, West Virginia University Eberly Family Distinguished Professor Fellow American Physical Society Editor Physica B, Assistant Editor EPJB, Editor Frontiers in Physics Section Editor Papers in Physics Member of the Editorial Board of “Materials” and “Symmetry Physics” https://scholar.google.com/citations?user=pwte-hQAAAAJ&hl=en

Physics and Astronomy Department West Virginia University 135 Willey Street, PO Box 6315 111 White Hall Morgantown, WV 26506 Phone: 304-293-6317 Fax: 304-293-5732 email: @.***

From: Ronald Cohen @.> Date: Friday, June 21, 2024 at 2:14 PM To: romerogroup/pyprocar @.> Cc: Subscribed @.***> Subject: Re: [romerogroup/pyprocar] elk support? (Issue #144) Dear Logan Lang,

Thank you so much for this. It has been a while but I was stuck doing other things. So now if something is ferromagnetic how would one see the DOS for up and down total or along z with spin-orbit? I seem to be seeing only the majority spins. Maybe I am not understanding something major. Thank you so much,

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 Mon, Jun 3, 2024 at 11:57 AM lllangWV @.***> wrote:

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.

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.

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 https://www.vasp.at/wiki/index.php/PROCAR at the bottom of the page.

The blocks represent the following are as follow:

  1. The first set is the total (absolute magnetization)
  2. The second is the x-projection of the spin
  3. The third is the y-projection
  4. The third is the z-projection

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] orbitals=[4,5,6,7,8] spins=[0] pyprocar.dosplot( code='vasp', mode='parametric', fermi=5.5962, atoms=atoms, orbitals=orbitals, spins=spins, dirname=data_dir)

Changing spins=[1] would represents the contribution of the d-orbitals of the first atom to the x-projection magnetization. Changing spins=[2] would represents the contribution of the d-orbitals of the first atom to the y-projection magnetization. Changing spins=[3] would represents the contribution of the d-orbitals of the first atom to the z-projection magnetization.

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 0.941

Logan Lang

— Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/144#issuecomment-2145576869, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5KBD5TZMBDLQ46KSW3ZFSG7PAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBVGU3TMOBWHE . You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHubhttps://github.com/romerogroup/pyprocar/issues/144#issuecomment-2183218296, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB24DTIHPZZWAI33LY5DV3DZIRUO7AVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBTGIYTQMRZGY. You are receiving this because you are subscribed to this thread.Message ID: @.***> — Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/144#issuecomment-2183254620, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5N7G6R4ZDECCVVEI6DZIRWHTAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBTGI2TINRSGA. You are receiving this because you authored the thread.

recohen avatar Jun 21 '24 18:06 recohen

It's not a problem with my installation. The run that ran on the other machine runs on this one. Here are the files that are not working now: https://www.dropbox.com/scl/fi/xh8514n3lcixnr9e7fqkl/HSE06FMdos.tar.gz?rlkey=3yg6mv1jrrqi979t0rfqa60wa&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 Fri, Jun 21, 2024 at 2:29 PM Aldo Romero @.***> wrote:

Ron

Is this for VASP or Quantum Espresso?.... can you share the line you used?

Thanks

::::____

Prof. Aldo Humberto Romero Director Research Computing, West Virginia University Eberly Family Distinguished Professor Fellow American Physical Society Editor Physica B, Assistant Editor EPJB, Editor Frontiers in Physics Section Editor Papers in Physics Member of the Editorial Board of “Materials” and “Symmetry Physics” https://scholar.google.com/citations?user=pwte-hQAAAAJ&hl=en

Physics and Astronomy Department West Virginia University 135 Willey Street, PO Box 6315 111 White Hall Morgantown, WV 26506 Phone: 304-293-6317 Fax: 304-293-5732 email: @.***

From: Ronald Cohen @.> Date: Friday, June 21, 2024 at 2:14 PM To: romerogroup/pyprocar @.> Cc: Subscribed @.***> Subject: Re: [romerogroup/pyprocar] elk support? (Issue #144) Dear Logan Lang,

Thank you so much for this. It has been a while but I was stuck doing other things. So now if something is ferromagnetic how would one see the DOS for up and down total or along z with spin-orbit? I seem to be seeing only the majority spins. Maybe I am not understanding something major. Thank you so much,

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 Mon, Jun 3, 2024 at 11:57 AM lllangWV @.***> wrote:

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.

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.

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 https://www.vasp.at/wiki/index.php/PROCAR at the bottom of the page.

The blocks represent the following are as follow:

  1. The first set is the total (absolute magnetization)
  2. The second is the x-projection of the spin
  3. The third is the y-projection
  4. The third is the z-projection

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] orbitals=[4,5,6,7,8] spins=[0] pyprocar.dosplot( code='vasp', mode='parametric', fermi=5.5962, atoms=atoms, orbitals=orbitals, spins=spins, dirname=data_dir)

Changing spins=[1] would represents the contribution of the d-orbitals of the first atom to the x-projection magnetization. Changing spins=[2] would represents the contribution of the d-orbitals of the first atom to the y-projection magnetization. Changing spins=[3] would represents the contribution of the d-orbitals of the first atom to the z-projection magnetization.

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 0.941

Logan Lang

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recohen avatar Jun 21 '24 19:06 recohen

Hey Ron!

Thank you so much for this. It has been a while, but I was stuck doing other things. So now, if something is ferromagnetic, how would one see the DOS for up and down total or along z with spin-orbit? I seem to be seeing only the majority spins. Maybe I am not understanding something major. Thank you so much.

If your calculation is a collinear spin-polarized one (without spin-orbit coupling), you can use the spins keyword argument. spins=[0] corresponds to spin up, and spins=[1] corresponds to spin down.

For calculations that include spin-orbit coupling (which implies non-collinear spins), you would still use the spins keyword argument. In non-collinear spin calculations, spins=[0] plots the spin density magnitude, while spins=[1,2,3] corresponds to spins oriented along the $S_x$, $S_y$, and $S_z$ directions, respectively.

Regarding the error:

AttributeError: np.complex_ was removed in the NumPy 2.0 release. Use np.complex128 instead.

It appears that NumPy updated their methods. This is an easy fix. In our code, we use np.complex to handle the phase factor of the projections, which occurs when LORBIT > 11 is set. Currently, we only use these phase factors for band unfoldings, so you can set LORBIT = 11 and still plot the spin projections.

I apologize I can't fix this immediately as I am away from my main computer this weekend, but I will get to it on Monday!

Logan Lang

lllangWV avatar Jun 21 '24 22:06 lllangWV

Thank you! I didn’t realize that is the important error. I hate the way python makes incompatible changes. I can try to fix that too. Ron—On Jun 21, 2024, at 18:37, Logan Lang @.***> wrote: Hey Ron!

Thank you so much for this. It has been a while, but I was stuck doing other things. So now, if something is ferromagnetic, how would one see the DOS for up and down total or along z with spin-orbit? I seem to be seeing only the majority spins. Maybe I am not understanding something major. Thank you so much.

If your calculation is a collinear spin-polarized one (without spin-orbit coupling), you can use the spins keyword argument. spins=[0] corresponds to spin up, and spins=[1] corresponds to spin down. For calculations that include spin-orbit coupling (which implies non-collinear spins), you would still use the spins keyword argument. In non-collinear spin calculations, spins=[0] plots the spin density magnitude, while spins=[1,2,3] corresponds to spins oriented along the $S_x$, $S_y$, and $S_z$ directions, respectively. Regarding the error:

AttributeError: np.complex_ was removed in the NumPy 2.0 release. Use np.complex128 instead.

It appears that NumPy updated their methods. This is an easy fix. In our code, we use np.complex to handle the phase factor of the projections, which occurs when LORBIT > 11 is set. Currently, we only use these phase factors for band unfoldings, so you can set LORBIT = 11 and still plot the spin projections. I apologize I can't fix this immediately as I am away from my main computer this weekend, but I will get to it on Monday! Logan Lang

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

recohen avatar Jun 23 '24 03:06 recohen

Dear Logan,

Thank you again. I tried editing all the uses of complex_ in the source and installed it again, but when I import pyprocar it still gives the same error and is not seeing the edited version. I tried pip install --upgrade --force-reinstall . but still the same. I am sorry this must be a very stupid question!

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, Jun 21, 2024 at 6:37 PM Logan Lang @.***> wrote:

Hey Ron!

Thank you so much for this. It has been a while, but I was stuck doing other things. So now, if something is ferromagnetic, how would one see the DOS for up and down total or along z with spin-orbit? I seem to be seeing only the majority spins. Maybe I am not understanding something major. Thank you so much.

If your calculation is a collinear spin-polarized one (without spin-orbit coupling), you can use the spins keyword argument. spins=[0] corresponds to spin up, and spins=[1] corresponds to spin down.

For calculations that include spin-orbit coupling (which implies non-collinear spins), you would still use the spins keyword argument. In non-collinear spin calculations, spins=[0] plots the spin density magnitude, while spins=[1,2,3] corresponds to spins oriented along the $S_x$, $S_y$, and $S_z$ directions, respectively.

Regarding the error:

AttributeError: np.complex_ was removed in the NumPy 2.0 release. Use np.complex128 instead.

It appears that NumPy updated their methods. This is an easy fix. In our code, we use np.complex to handle the phase factor of the projections, which occurs when LORBIT > 11 is set. Currently, we only use these phase factors for band unfoldings, so you can set LORBIT = 11 and still plot the spin projections.

I apologize I can't fix this immediately as I am away from my main computer this weekend, but I will get to it on Monday!

Logan Lang

— Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/144#issuecomment-2183547927, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5OFM2CZ34YEWXRGVPTZISTLVAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBTGU2DOOJSG4 . You are receiving this because you authored the thread.Message ID: @.***>

recohen avatar Jun 24 '24 15:06 recohen

Hey Ron,

I am back to my my main computer and looking into the issue now! I just checked, the new version of numpy was literally released last week, so that explains why I have not seen this error before. A temporary fix would be to install pyprocar, then uninstall and reinstall numpy with an older version.

I am showing you what I normally do when I install pyprocar. I usually like to create anaconda virtual environment to make sure the dependencies are right.

conda create -n pyprocar_6.1.10 python==3.8
conda activate pyprocar_6.1.10

pip install pyprocar
pip uninstall numpy
pip install numpy==1.26.4

I am going to update, the way we handle these dependencies. Currently we just grab the most updated version, but this method is obviously not going to work. I'll push the updated version later today.

Logan Lang

lllangWV avatar Jun 24 '24 16:06 lllangWV

Thank you! I wonder why just editing the file did not work for me. I use virtual environments without conda. Conda caused me trouble,

Thanks!

Ron

On Jun 24, 2024, at 12:46 PM, Logan Lang @.***> wrote:

Hey Ron,

I am back to my my main computer and looking into the issue now! I just checked, the new version of numpy was literally released last week, so that explains why I have not seen this error before. A temporary fix would be to install pyprocar, then uninstall and reinstall numpy with an older version.

I am showing you what I normally do when I install pyprocar. I usually like to create anaconda virtual environment to make sure the dependencies are right.

conda create -n pyprocar_6.1.10 python==3.8 conda activate pyprocar_6.1.10

pip install pyprocar pip uninstall numpy pip install numpy==1.26.4 I am going to update, the way we handle these dependencies. Currently we just grab the most updated version, but this method is obviously not going to work. I'll push the updated version later today.

Logan Lang

— Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/144#issuecomment-2186996546, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5MWR3NCYNZPX53VSGTZJBEQDAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBWHE4TMNJUGY. You are receiving this because you authored the thread.

recohen avatar Jun 24 '24 16:06 recohen

I am just curious, I have a few questions.

How do you install pyprocar? Is it by pip install pyprocar or do you clone the repository

git clone [email protected]:romerogroup/pyprocar.git
cd pyprocar 
pip install .

When you say you are editing the file, are you editing the version in located in your site-packages inside your virtual environment or the file in the main pyprocar directory pyprocar/pyprocar/io/vasp.py?

lllangWV avatar Jun 24 '24 17:06 lllangWV

I clones from github and then did the cd and pip install . I edited the version in the github clone and redid the install.

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 Mon, Jun 24, 2024 at 1:22 PM Logan Lang @.***> wrote:

I am just curious, I have a few questions.

How do you install pyprocar? Is it by pip install pyprocar or do you clone the repository

git clone @.***:romerogroup/pyprocar.gitcd pyprocar pip install .

When you say you are editing the file, are you editing the version in located in your site-packages inside your virtual environment or the file in the main pyprocar directory pyprocar/pyprocar/io/vasp.py?

— Reply to this email directly, view it on GitHub https://github.com/romerogroup/pyprocar/issues/144#issuecomment-2187054692, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABA2R5KTG6UKKRHCPFJP4YTZJBIULAVCNFSM6AAAAABGEPFZXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBXGA2TINRZGI . You are receiving this because you authored the thread.Message ID: @.***>

recohen avatar Jun 24 '24 17:06 recohen