Added methods to compute and compare DOS fingerprints #2772
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…into dos_fingerprinting
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…into dos_fingerprinting git pull
JaGeo
reviewed
Dec 13, 2022
JaGeo
reviewed
Dec 13, 2022
pymatgen/electronic_structure/dos.py
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| "some error in the spelling." | ||
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| def _fp_to_dict(self, fp): |
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Yes, It could be. Will make the changes. Thanks for the feedback 😃
JaGeo
approved these changes
Dec 14, 2022
Thanks for the review @JaGeo 😄 |
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Hi @janosh , This PR is ready to be merge. |
janosh
requested changes
Dec 15, 2022
pymatgen/electronic_structure/dos.py
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| @@ -1165,6 +1166,150 @@ def get_upper_band_edge( | |||
| upper_band_edge = energies[np.argmax(densities)] | |||
| return upper_band_edge | |||
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| def get_dos_fp(self, type="summed_pdos", binning=True, min_e=None, max_e=None, nbins=256, normalize=True): | |||
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Would be good to add type annotations here.
def get_dos_fp(self, type: str = "summed_pdos", binning: bool = True, ...There was a problem hiding this comment.
Thanks for the suggestions , I have made the requested changes.
pymatgen/electronic_structure/dos.py
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| type (str): Specify fingerprint type needed can accept 's/p/d/f/summed_pdos/tdos' | ||
| min_e (float): The minimum mode energy to include in the fingerprint | ||
| max_e (float): The maximum mode energy to include in the fingerprint | ||
| nbins (int): Number of bins to be used in the fingerprint |
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Can we rename this to n_bins for proper snake casing?
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Remove unnecessary file
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Hi @janosh , all suggestions have been incorporated now. And tests seems to pass as well. 😄 |
janosh
requested changes
Dec 19, 2022
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@naik-aakash Thanks, looks great! Just a few more nitpicks.
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Hi @janosh , thank you for the really useful tips and suggestions. 😃 |
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Hi @janosh , I do not know why so many tests are failing. I looked at Failed tests and they do not have anything to do with this PR. I hope it could still be merged. |
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@naik-aakash Sorry for the delay here. Back from traveling now. PR looks good! Made a few last changes. Failures like you said are unrelated. Ready to merge. |
janosh
approved these changes
Dec 24, 2022
@janosh No worries! Thank you. Happy Holidays |
lbluque
pushed a commit
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that referenced
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Jan 5, 2023
…ct#2772) * added dos_fingerprint and similarity index methods * Added test cases and reformatted and cleaned code * added binwidth ,renamed states to densities in fp obj,updated tests * added source link * changed get_dos_fp_similarity and fp_to_dict methods to static * Delete Test.py, unnecessary file * simplified dict updating, added missing type annotations * NamedTuple return type fixed * small clean up * document get_dos_fp() and get_dos_fp_similarity() raise conditions in doc str * add types for fp1,fp2 and update doc str * update exception tests Co-authored-by: anaik <anaik@sv2218.zit.bam.de> Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
lbluque
pushed a commit
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that referenced
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May 23, 2023
…ct#2772) * added dos_fingerprint and similarity index methods * Added test cases and reformatted and cleaned code * added binwidth ,renamed states to densities in fp obj,updated tests * added source link * changed get_dos_fp_similarity and fp_to_dict methods to static * Delete Test.py, unnecessary file * simplified dict updating, added missing type annotations * NamedTuple return type fixed * small clean up * document get_dos_fp() and get_dos_fp_similarity() raise conditions in doc str * add types for fp1,fp2 and update doc str * update exception tests Co-authored-by: anaik <anaik@sv2218.zit.bam.de> Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
lbluque
pushed a commit
to lbluque/pymatgen
that referenced
this pull request
May 25, 2023
…ct#2772) * added dos_fingerprint and similarity index methods * Added test cases and reformatted and cleaned code * added binwidth ,renamed states to densities in fp obj,updated tests * added source link * changed get_dos_fp_similarity and fp_to_dict methods to static * Delete Test.py, unnecessary file * simplified dict updating, added missing type annotations * NamedTuple return type fixed * small clean up * document get_dos_fp() and get_dos_fp_similarity() raise conditions in doc str * add types for fp1,fp2 and update doc str * update exception tests Co-authored-by: anaik <anaik@sv2218.zit.bam.de> Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
janosh
added a commit
that referenced
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May 26, 2023
* added dos_fingerprint and similarity index methods * Added test cases and reformatted and cleaned code * added binwidth ,renamed states to densities in fp obj,updated tests * added source link * changed get_dos_fp_similarity and fp_to_dict methods to static * Delete Test.py, unnecessary file * simplified dict updating, added missing type annotations * NamedTuple return type fixed * small clean up * document get_dos_fp() and get_dos_fp_similarity() raise conditions in doc str * add types for fp1,fp2 and update doc str * update exception tests Co-authored-by: anaik <anaik@sv2218.zit.bam.de> Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
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Compute and compare fingerprints of project and total density of states.
This functionality could be really useful to compare the DOS of materials from different softwares (eg:- LOBSTER and VASP ) or versions (Eg:- VASP v5 and VASP v6)