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Build an iterative phonon flow #306

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merged 113 commits into from
Jan 9, 2025
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6a3a342
add some drafts
JaGeo Dec 21, 2024
fc9e7a5
pre-commit auto-fixes
pre-commit-ci[bot] Dec 21, 2024
25a95b4
restructure and rely on flow instead
JaGeo Dec 21, 2024
4ca1d1c
restructure and rely on flow instead
JaGeo Dec 21, 2024
55562d5
restructure and rely on flow instead
JaGeo Dec 21, 2024
e5787c7
pre-commit auto-fixes
pre-commit-ci[bot] Dec 21, 2024
4f3d6c4
more restructuring of completeworkflow
JaGeo Dec 21, 2024
52deaa2
more restructuring of completeworkflow
JaGeo Dec 21, 2024
6ba11e0
pre-commit auto-fixes
pre-commit-ci[bot] Dec 21, 2024
855dccc
more restructuring of completeworkflow
JaGeo Dec 21, 2024
fcf0cda
bring the workflow more in shape
JaGeo Dec 22, 2024
1958654
pre-commit auto-fixes
pre-commit-ci[bot] Dec 22, 2024
3c0d6a8
fix the workflow stepwise
JaGeo Dec 22, 2024
f85baa3
pre-commit auto-fixes
pre-commit-ci[bot] Dec 22, 2024
8b54a5c
fix some more probles
JaGeo Dec 22, 2024
af16c12
pre-commit auto-fixes
pre-commit-ci[bot] Dec 22, 2024
5e09a4f
hard code displacement to 0.01 in benchmark, fix other more issues in…
JaGeo Dec 22, 2024
7094b93
pre-commit auto-fixes
pre-commit-ci[bot] Dec 22, 2024
1bd5d49
fix more logic problems
JaGeo Dec 22, 2024
295478e
make outputs nicer
JaGeo Dec 22, 2024
f7ad583
pre-commit auto-fixes
pre-commit-ci[bot] Dec 22, 2024
e17fc92
fix a bunch of tests in auto phonons after the new changes
JaGeo Dec 22, 2024
75de5db
fix more tests
JaGeo Dec 22, 2024
829e674
fix benchmark tests
JaGeo Dec 22, 2024
e2bc0eb
daza
JaGeo Dec 22, 2024
bad024c
fix more tests
JaGeo Dec 22, 2024
00e20cd
fix pre database position for all workflows
JaGeo Dec 22, 2024
c80a5ed
add more documentaion and fix number of jobs, addition of get_output
JaGeo Dec 22, 2024
9444190
pre-commit auto-fixes
pre-commit-ci[bot] Dec 22, 2024
d98727e
add more documentation
JaGeo Dec 22, 2024
215c0de
fix list comprehension
JaGeo Dec 22, 2024
1944eed
pre-commit auto-fixes
pre-commit-ci[bot] Dec 22, 2024
ec68520
mace stuff
JaGeo Dec 22, 2024
d2a1485
add to data
JaGeo Dec 23, 2024
834e175
add to data
JaGeo Dec 23, 2024
6ee7c41
add autoplex preprint to readme (#309)
JaGeo Dec 24, 2024
526580e
Update README.md (#310)
JaGeo Dec 24, 2024
3e0b5c5
Update README.md (#311)
JaGeo Dec 24, 2024
8c5aa8a
fix ranom seed for structures that are too similar
JaGeo Dec 24, 2024
13b1229
pre-commit auto-fixes
pre-commit-ci[bot] Dec 24, 2024
6eb620f
fix ranom seed for structures that are too similar
JaGeo Dec 24, 2024
bdf0c8b
fix ranom seed for structures that are too similar
JaGeo Dec 24, 2024
c59f853
pre-commit auto-fixes
pre-commit-ci[bot] Dec 24, 2024
453c75d
default random seed
JaGeo Dec 24, 2024
624f762
default random seed
JaGeo Dec 24, 2024
21f8ca2
fix write benchmark generation beyond runs in jobflow
JaGeo Dec 25, 2024
43f95d6
pre-commit auto-fixes
pre-commit-ci[bot] Dec 25, 2024
36af259
fix random seed and add strict tests
JaGeo Dec 25, 2024
a8e065b
fix lorbit problems
JaGeo Dec 25, 2024
6705f1b
fix test
JaGeo Dec 25, 2024
71c59d9
fix test
JaGeo Dec 25, 2024
82cd1e5
fix rms computation
JaGeo Dec 26, 2024
512cad7
pre-commit auto-fixes
pre-commit-ci[bot] Dec 26, 2024
1163b83
add one more test
JaGeo Dec 26, 2024
301a378
add documentation
JaGeo Dec 26, 2024
e562ce3
add hint on the default displacement
JaGeo Dec 26, 2024
74da25a
add hint on the default displacement
JaGeo Dec 26, 2024
1f89160
fix phonon data generation
JaGeo Dec 28, 2024
297de2d
pre-commit auto-fixes
pre-commit-ci[bot] Dec 28, 2024
899bd4e
clean up
JaGeo Dec 28, 2024
52175df
fix references
JaGeo Dec 29, 2024
c5f2ae7
add test for stratisfied split
JaGeo Dec 30, 2024
519b6d3
Merge branch 'iterative_phonon_flow.py' of github.com:autoatml/autopl…
JaGeo Dec 30, 2024
941ad78
fix doc issues and data issues
JaGeo Dec 30, 2024
2d456ac
pre-commit auto-fixes
pre-commit-ci[bot] Dec 30, 2024
ddb51c8
fix doc issues and data issues
JaGeo Dec 30, 2024
5530cd6
pre-commit auto-fixes
pre-commit-ci[bot] Dec 30, 2024
c3f87a4
fix import issues
JaGeo Dec 30, 2024
aff293d
Merge branch 'iterative_phonon_flow.py' of github.com:autoatml/autopl…
JaGeo Dec 30, 2024
1f2c72f
pre-commit auto-fixes
pre-commit-ci[bot] Dec 30, 2024
76e21e6
fix import issues
JaGeo Dec 30, 2024
937dec6
pre-commit auto-fixes
pre-commit-ci[bot] Dec 30, 2024
b61c4a7
add test for pre-database
JaGeo Dec 30, 2024
25085a7
deactivate filter* on test data
JaGeo Dec 31, 2024
44fc621
pre-commit auto-fixes
pre-commit-ci[bot] Dec 31, 2024
20ce3a0
Add tests for test file sizes
JaGeo Dec 31, 2024
6ee13d0
pre-commit auto-fixes
pre-commit-ci[bot] Dec 31, 2024
abe61bb
remove definition
JaGeo Dec 31, 2024
ed9d7ec
fix output of do_
JaGeo Dec 31, 2024
145c354
pre-commit auto-fixes
pre-commit-ci[bot] Dec 31, 2024
4e1c3c7
extend test to more generations and fix dft reference passing
JaGeo Jan 2, 2025
9b23188
conflicts
JaGeo Jan 2, 2025
1ad1d9c
pre-commit auto-fixes
pre-commit-ci[bot] Jan 2, 2025
ea15f67
fix doc
JaGeo Jan 2, 2025
22e1f88
Merge branch 'iterative_phonon_flow.py' of github.com:autoatml/autopl…
JaGeo Jan 2, 2025
9d9c514
fix doc
JaGeo Jan 2, 2025
79d2067
fix doc
JaGeo Jan 2, 2025
b6a7668
fix doc
JaGeo Jan 2, 2025
f768aad
pre-commit auto-fixes
pre-commit-ci[bot] Jan 2, 2025
4ea17d1
try increasing myst heading anchors
naik-aakash Jan 2, 2025
4d6b226
try adding back _all__ block
naik-aakash Jan 3, 2025
b7bf3a1
add try except block in rmse calculation
JaGeo Jan 4, 2025
2e05227
Merge branch 'iterative_phonon_flow.py' of github.com:autoatml/autopl…
JaGeo Jan 4, 2025
e582522
pre-commit auto-fixes
pre-commit-ci[bot] Jan 4, 2025
db273a1
fix some more None issues
JaGeo Jan 4, 2025
6781beb
Merge branch 'iterative_phonon_flow.py' of github.com:autoatml/autopl…
JaGeo Jan 4, 2025
2b4fd49
pre-commit auto-fixes
pre-commit-ci[bot] Jan 4, 2025
9d4036c
fix some more None issues
JaGeo Jan 4, 2025
9c83e05
Merge branch 'iterative_phonon_flow.py' of github.com:autoatml/autopl…
JaGeo Jan 4, 2025
3cfb845
fix some more None issues
JaGeo Jan 4, 2025
aa3cc7b
pre-commit auto-fixes
pre-commit-ci[bot] Jan 4, 2025
7924bed
test iterative_phonon_flow.py
JaGeo Jan 6, 2025
8d3fda8
test iterative_phonon_flow.py fix
JaGeo Jan 6, 2025
a8b6142
fix format
JaGeo Jan 6, 2025
2984c2a
fix confusing list outputs
JaGeo Jan 6, 2025
d3a87df
pre-commit auto-fixes
pre-commit-ci[bot] Jan 6, 2025
ab6b53b
very small fixes
QuantumChemist Jan 8, 2025
24ff6bb
extend gluexml unit test
QuantumChemist Jan 8, 2025
6dc3e2f
Update src/autoplex/data/common/jobs.py
QuantumChemist Jan 8, 2025
820b133
pre-commit auto-fixes
pre-commit-ci[bot] Jan 8, 2025
03c1790
fix linting
QuantumChemist Jan 8, 2025
7799531
Merge branch 'iterative_phonon_flow.py' of https://github.com/autoatm…
QuantumChemist Jan 8, 2025
a24ec5b
improve function name and decription, improve the related unit test
QuantumChemist Jan 9, 2025
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1 change: 1 addition & 0 deletions src/autoplex/auto/phonons/jobs.py
Original file line number Diff line number Diff line change
@@ -30,6 +30,7 @@
from pymatgen.phonon.dos import PhononDos



@job(
data=[
PhononBSDOSDoc,
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