Added methods to compute and compare DOS fingerprints #2772

naik-aakash · 2022-12-13T11:18:33Z

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)

Added method to compute fingerprints
Added method to compare two DOS fingerprints (tanimoto index and dot product)
Added test cases for the corresponding methods

…into dos_fingerprinting

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…into dos_fingerprinting git pull

coveralls · 2022-12-13T11:39:37Z

Coverage: 46.362% (-0.5%) from 46.884% when pulling 8309b1b on naik-aakash:dos_fingerprinting into b566980 on materialsproject:master.

pymatgen/electronic_structure/dos.py

JaGeo · 2022-12-13T13:32:00Z

pymatgen/electronic_structure/dos.py

+                "some error in the spelling."
+            )
+
+    def _fp_to_dict(self, fp):


It could be static, I assume

Yes, It could be. Will make the changes. Thanks for the feedback 😃

JaGeo

You could replace one "finger print" with fingerprint in the documentation but otherwise it looks fine from my side.

naik-aakash · 2022-12-14T15:42:05Z

You could replace one "finger print" with fingerprint in the documentation but otherwise it looks fine from my side.

Thanks for the review @JaGeo 😄

naik-aakash · 2022-12-14T16:06:06Z

Hi @janosh , This PR is ready to be merge.

janosh

Thanks @naik-aakash! I left some comments.

janosh · 2022-12-15T01:59:50Z

pymatgen/electronic_structure/dos.py

@@ -1165,6 +1166,150 @@ def get_upper_band_edge(
        upper_band_edge = energies[np.argmax(densities)]
        return upper_band_edge

+    def get_dos_fp(self, type="summed_pdos", binning=True, min_e=None, max_e=None, nbins=256, normalize=True):


Would be good to add type annotations here.

def get_dos_fp(self, type: str = "summed_pdos", binning: bool = True, ...

Thanks for the suggestions , I have made the requested changes.

pymatgen/electronic_structure/dos.py

janosh · 2022-12-15T02:02:30Z

pymatgen/electronic_structure/dos.py

+            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


Can we rename this to n_bins for proper snake casing?

… methods

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Remove unnecessary file

naik-aakash · 2022-12-15T13:17:38Z

Hi @janosh , all suggestions have been incorporated now. And tests seems to pass as well. 😄

janosh

@naik-aakash Thanks, looks great! Just a few more nitpicks.

pymatgen/electronic_structure/dos.py

naik-aakash · 2022-12-19T09:58:44Z

Hi @janosh , thank you for the really useful tips and suggestions. 😃

naik-aakash · 2022-12-20T21:09:01Z

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.

… doc str

janosh · 2022-12-24T00:56:03Z

@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.

naik-aakash · 2022-12-24T08:57:43Z

@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 No worries! Thank you. Happy Holidays

…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>

* 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>

naik-aakash and others added 11 commits December 5, 2022 18:09

added dos_fingerprint and similarity index methods

177a7a9

Added test cases and reformatted and cleaned code

e9669d1

added binwidth ,renamed states to densities in fp obj,updated tests

6a52d42

Merge branch 'materialsproject:master' into dos_fingerprinting

04b4ec7

remove redundant comment

876eefe

Merge branch 'dos_fingerprinting' of github.com:naik-aakash/pymatgen …

b7b2296

…into dos_fingerprinting

Merge branch 'materialsproject:master' into dos_fingerprinting

e5e1c10

added source link

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fix liniting error

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Merge branch 'dos_fingerprinting' of github.com:naik-aakash/pymatgen …

2a4c76f

…into dos_fingerprinting git pull

naik-aakash added 2 commits December 13, 2022 14:03

fix line length linting error

0ee33dd

fix line lenghts

d5468ef

JaGeo reviewed Dec 13, 2022

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pymatgen/electronic_structure/dos.py Outdated Show resolved Hide resolved

JaGeo reviewed Dec 13, 2022

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changed get_dos_fp_similarity and fp_to_dict methods to static

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naik-aakash requested a review from JaGeo December 13, 2022 14:38

fixed typo in doc string

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JaGeo approved these changes Dec 14, 2022

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fixed doc string suggestion

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janosh suggested changes Dec 15, 2022

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naik-aakash and others added 6 commits December 15, 2022 10:00

Updated doc strings based on suggestion, added type annotation to the…

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… methods

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Merge branch 'materialsproject:master' into dos_fingerprinting

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mypy fixes

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fix flake8

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naik-aakash and others added 4 commits December 15, 2022 12:10

mypy error fix

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mypy error fix

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Delete Test.py

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janosh suggested changes Dec 19, 2022

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naik-aakash and others added 4 commits December 19, 2022 09:44

simplified dict updating, added missing type annotations

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mypy error fixes

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NamedTuple return type fixed

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Merge branch 'materialsproject:master' into dos_fingerprinting

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Merge branch 'materialsproject:master' into dos_fingerprinting

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janosh added 4 commits December 23, 2022 16:51

small clean up

c589945

document get_dos_fp() and get_dos_fp_similarity() raise conditions in…

1c2dbc4

… doc str

add types for fp1,fp2 and update doc str

a8216c7

update exception tests

8309b1b

janosh approved these changes Dec 24, 2022

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janosh merged commit 4847ec7 into materialsproject:master Dec 24, 2022

naik-aakash deleted the dos_fingerprinting branch January 10, 2024 12:23

naik-aakash mentioned this pull request Jul 22, 2024

DOS Fingerprints enhancements #3946

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Added methods to compute and compare DOS fingerprints #2772

Added methods to compute and compare DOS fingerprints #2772

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Added methods to compute and compare DOS fingerprints #2772

Added methods to compute and compare DOS fingerprints #2772

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naik-aakash commented Dec 13, 2022

Compute and compare fingerprints of project and total density of states.

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