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Solvation energy 3 #1469

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merged 263 commits into from
Jun 26, 2024
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b5bf7d4
Merge pull request #1408 from pyiron/fix-links
jan-janssen May 5, 2024
69e81c0
move readme file
jan-janssen May 5, 2024
df39b6c
Merge pull request #1409 from pyiron/move-readme
jan-janssen May 5, 2024
337ebc8
fix readme file
jan-janssen May 5, 2024
2ac6e0c
Merge pull request #1410 from pyiron/fix-readme
jan-janssen May 5, 2024
e09fd52
Fix readme image
jan-janssen May 5, 2024
d847236
Merge pull request #1411 from pyiron/fix-readme
jan-janssen May 5, 2024
22edac8
Update elasticmatrix.py
jan-janssen May 6, 2024
6e370a7
Merge pull request #1414 from pyiron/elasticmatrixfix
jan-janssen May 6, 2024
02414d7
Add Edit button to documentation
jan-janssen May 6, 2024
d4105f3
Merge pull request #1415 from pyiron/rtd
jan-janssen May 6, 2024
75d82b4
Add files via upload
jan-janssen May 7, 2024
128e86d
Merge pull request #1416 from pyiron/datamining-example
jan-janssen May 7, 2024
a50f198
update pyiron_base to 0.8.4
jan-janssen May 11, 2024
b3be644
Update environment-docs.yml
jan-janssen May 11, 2024
39faad2
Update environment.yml
jan-janssen May 11, 2024
01a0cbf
Update environment.yml
jan-janssen May 11, 2024
efe835b
Merge pull request #1417 from pyiron/pyiron_base
jan-janssen May 11, 2024
93082c7
add additional documentation
May 15, 2024
bde472d
Merge branch 'main' into phonopy_eigenvectors
May 15, 2024
1e35ef3
Format black
pyiron-runner May 15, 2024
2eb9f01
Bump mendeleev from 0.15.0 to 0.16.1
dependabot[bot] May 20, 2024
5f4a7a1
[dependabot skip] Update environment
github-actions[bot] May 20, 2024
9210e83
Merge pull request #1421 from pyiron/dependabot/pip/mendeleev-0.16.1
jan-janssen May 20, 2024
fac4fca
patches in default LORBIT writing
May 21, 2024
5181c4f
wrong logic before
May 21, 2024
1718c43
really annoying logic
May 21, 2024
e05b870
Format black
pyiron-runner May 21, 2024
0939b3d
Merge pull request #1424 from pyiron/magmoms_in_OUTCAR_by_default
ligerzero-ai May 21, 2024
ecc2d76
Add OutcarCollectError and catch it in Vasp.collect
pmrv Apr 19, 2024
20eb222
Format black
pyiron-runner Apr 19, 2024
edb47c2
Add tests
pmrv May 24, 2024
0ca7404
Bump mendeleev from 0.16.1 to 0.16.2
dependabot[bot] May 27, 2024
0fce260
Bump structuretoolkit from 0.0.22 to 0.0.23
dependabot[bot] May 27, 2024
5d69ac1
Bump scikit-learn from 1.4.2 to 1.5.0
dependabot[bot] May 27, 2024
599ff3d
[dependabot skip] Update environment
github-actions[bot] May 27, 2024
2c7303f
[dependabot skip] Update environment
github-actions[bot] May 27, 2024
6c6a918
[dependabot skip] Update environment
github-actions[bot] May 27, 2024
8e31f3b
Merge pull request #1427 from pyiron/dependabot/pip/mendeleev-0.16.2
jan-janssen May 27, 2024
3f6bb93
Merge pull request #1428 from pyiron/dependabot/pip/structuretoolkit-…
jan-janssen May 27, 2024
a253c48
Merge pull request #1429 from pyiron/dependabot/pip/scikit-learn-1.5.0
jan-janssen May 27, 2024
c3c15e3
Bump scipy from 1.13.0 to 1.13.1
dependabot[bot] May 27, 2024
19ee903
[dependabot skip] Update environment
github-actions[bot] May 27, 2024
27d70ed
Update environment-docs.yml
jan-janssen May 27, 2024
170bb44
Update environment.yml
jan-janssen May 27, 2024
4aaf51c
Update environment.yml
jan-janssen May 27, 2024
8b9edbc
Update pyproject.toml
jan-janssen May 27, 2024
3c13104
[patch] use ImportAlarm from pyiron_snippets
liamhuber May 31, 2024
6174a93
Only import ImportAlarm once
liamhuber May 31, 2024
6dbb1ea
[patch] use deprecate from pyiron_snippets
liamhuber May 31, 2024
3459c45
Update environment-old.yml
jan-janssen Jun 1, 2024
089ff27
Update environment-old.yml
jan-janssen Jun 1, 2024
5fc7970
Update environment-old.yml
jan-janssen Jun 1, 2024
ae2ae3e
Update environment-old.yml
jan-janssen Jun 1, 2024
e41ed53
Update unittests_old.yml
jan-janssen Jun 1, 2024
c75c07b
Update environment-old.yml
jan-janssen Jun 1, 2024
074e921
Update environment-old.yml
jan-janssen Jun 1, 2024
7869072
Update environment-old.yml
jan-janssen Jun 1, 2024
5bc0df8
Update environment-old.yml
jan-janssen Jun 1, 2024
1ea6e41
Update environment-old.yml
jan-janssen Jun 1, 2024
c5e1c2f
Update environment-old.yml
jan-janssen Jun 1, 2024
3d03885
Update environment-old.yml
jan-janssen Jun 1, 2024
2b68109
Update environment-old.yml
jan-janssen Jun 1, 2024
bf8d466
Update environment-old.yml
jan-janssen Jun 1, 2024
9daf8f9
Update environment-old.yml
jan-janssen Jun 1, 2024
b9b0c94
Update environment-old.yml
jan-janssen Jun 1, 2024
f9d93c0
Update environment-old.yml
jan-janssen Jun 1, 2024
9d57a87
Merge pull request #1430 from pyiron/dependabot/pip/scipy-1.13.1
jan-janssen Jun 1, 2024
ea300b7
Bump pylammpsmpi from 0.2.18 to 0.2.19
dependabot[bot] Jun 3, 2024
2e5f26f
[dependabot skip] Update environment
github-actions[bot] Jun 3, 2024
aba53a8
Update environment-docs.yml
jan-janssen Jun 3, 2024
8fcad0a
Update environment.yml
jan-janssen Jun 3, 2024
d1aa2ab
Update environment.yml
jan-janssen Jun 3, 2024
0173b14
Update pyproject.toml
jan-janssen Jun 3, 2024
1725276
Merge pull request #1433 from pyiron/dependabot/pip/pylammpsmpi-0.2.19
jan-janssen Jun 3, 2024
3da4ab4
Update backwards.yml
jan-janssen Jun 3, 2024
8b3b236
Update benchmarks.yml
jan-janssen Jun 3, 2024
e45c14b
Update black.yml
jan-janssen Jun 3, 2024
4ce7d81
Update integration.yml
jan-janssen Jun 3, 2024
b86014b
Update integration_unittests.yml
jan-janssen Jun 3, 2024
6869e87
Update notebooks.yml
jan-janssen Jun 3, 2024
97cc1dd
Update pypicheck.yml
jan-janssen Jun 3, 2024
6fd7160
Update unittests.yml
jan-janssen Jun 3, 2024
25e414e
Update unittests_old.yml
jan-janssen Jun 3, 2024
c59fa84
Merge pull request #1437 from pyiron/pr_stacked
jan-janssen Jun 3, 2024
5359807
Merge branch 'main' into snippets_alarm
liamhuber Jun 3, 2024
df4f517
[patch] replace logger with snippets version
liamhuber Jun 3, 2024
dcef680
Merge pull request #1438 from pyiron/snippets_logger
jan-janssen Jun 3, 2024
454b1e9
Merge pull request #1431 from pyiron/snippets_alarm
jan-janssen Jun 3, 2024
3e1e67c
Merge pull request #1432 from pyiron/snippets_deprecate
jan-janssen Jun 3, 2024
0f7e810
Update pyproject.toml
jan-janssen Jun 4, 2024
342458b
Update environment-docs.yml
jan-janssen Jun 4, 2024
42d39d4
Update environment.yml
jan-janssen Jun 4, 2024
f74ddac
Update environment.yml
jan-janssen Jun 4, 2024
233478c
Merge pull request #1439 from pyiron/pyiron_base
jan-janssen Jun 4, 2024
56c473d
Update pyproject.toml
jan-janssen Jun 5, 2024
15d9ab7
Update environment.yml
jan-janssen Jun 5, 2024
42118df
Update environment-docs.yml
jan-janssen Jun 5, 2024
321fcde
Update environment.yml
jan-janssen Jun 5, 2024
351fed5
Merge pull request #1442 from pyiron/mendeleev_update
jan-janssen Jun 5, 2024
7e9bf1a
remove setting calculation mode
samwaseda Jun 6, 2024
0929733
Merge pull request #1443 from pyiron/elastic_remove_minimize
samwaseda Jun 6, 2024
c7d0374
remove initial magnetic moments
samwaseda Jun 6, 2024
8e2d4f7
backward compatibility
samwaseda Jun 6, 2024
46cf158
Merge pull request #1444 from pyiron/bugfix_sphinx_tests
samwaseda Jun 6, 2024
0b7a4a1
Remove unnecessary init overloads
pmrv May 24, 2024
2c14bcb
Remove unnecessary DFTOutput subclass
pmrv May 24, 2024
6e4c122
Remove unnecessary GenericOutput subclass
pmrv May 24, 2024
47c851b
Pull Output.dft_output to base class
pmrv May 24, 2024
9ea7b60
Remove now unnecessary Output subclass and leave a warning comment
pmrv May 24, 2024
5c5d3de
Update pyproject.toml
jan-janssen Jun 7, 2024
62aa9d6
Update environment.yml
jan-janssen Jun 7, 2024
013688a
Update environment-docs.yml
jan-janssen Jun 7, 2024
0f76f7b
Update environment.yml
jan-janssen Jun 7, 2024
18420ce
Do not access files accidentely in interactive output
pmrv Feb 28, 2024
dbe84d8
Same for generic outputs
pmrv Feb 28, 2024
7f91818
From none the exception to keep trace clean.
pmrv Mar 1, 2024
a551838
Use .content for Sphinx
pmrv Jun 4, 2024
b77877a
Fix sphinx unit test
pmrv Jun 4, 2024
5f5402b
Issue a warning when silencing not found output
pmrv Jun 4, 2024
8ac546d
Format black
pyiron-runner Jun 7, 2024
64dc14d
Merge pull request #1445 from pyiron/pyiron_base
jan-janssen Jun 9, 2024
d205a0c
LAMMPS: Add get_input_file_dict()
jan-janssen Jun 10, 2024
c20e99b
Merge remote-tracking branch 'refs/remotes/origin/main' into lammps_c…
jan-janssen Jun 10, 2024
619d5e3
LAMMPS: use get_input_file_dict() in write_input()
jan-janssen Jun 10, 2024
79b7173
Format black
pyiron-runner Jun 10, 2024
9c8f747
Update base.py
jan-janssen Jun 10, 2024
e09eca5
Update base.py
jan-janssen Jun 10, 2024
4e324f7
VASP: Implement get_input_file_dict()
jan-janssen Jun 10, 2024
dfff0c6
Format black
pyiron-runner Jun 10, 2024
02f6ce5
Bump phonopy from 2.23.1 to 2.24.2
dependabot[bot] Jun 10, 2024
7362624
[dependabot skip] Update environment
github-actions[bot] Jun 10, 2024
78206c3
Merge pull request #1450 from pyiron/dependabot/pip/phonopy-2.24.2
jan-janssen Jun 10, 2024
34c930b
Use input file dict from base
jan-janssen Jun 10, 2024
8a1c535
Add _store_output()
jan-janssen Jun 10, 2024
19ea6e0
Format black
pyiron-runner Jun 10, 2024
e377501
Remove write_input() and use write_input() from base
jan-janssen Jun 10, 2024
e20d94a
VASP: Encapsulate the output parser in the parse_vasp_output() function
jan-janssen Jun 10, 2024
ee6a6de
Vasp: Refactor bader analysis
jan-janssen Jun 10, 2024
ccdc846
Format black
pyiron-runner Jun 10, 2024
86d1e7f
Format black
pyiron-runner Jun 10, 2024
c7ee56e
Merge remote-tracking branch 'refs/remotes/origin/vasp_refactor_bader…
jan-janssen Jun 10, 2024
54deaf4
Merge remote-tracking branch 'refs/remotes/origin/vasp_refactor_outpu…
jan-janssen Jun 10, 2024
bd4d300
Use super() call in get_input_file_dict()
jan-janssen Jun 10, 2024
4758969
Format black
pyiron-runner Jun 10, 2024
159394a
Merge pull request #1453 from pyiron/vasp_refactor_bader
jan-janssen Jun 10, 2024
60a609c
Merge remote-tracking branch 'refs/remotes/origin/main' into vasp_ref…
jan-janssen Jun 11, 2024
17ec7a8
Add docstring
jan-janssen Jun 11, 2024
9b36fca
Add docstring
jan-janssen Jun 11, 2024
4882d8c
Add DocStrings
jan-janssen Jun 11, 2024
8b5ae63
Update pyiron_atomistics/lammps/base.py
jan-janssen Jun 11, 2024
4128044
Update pyiron_atomistics/vasp/base.py
jan-janssen Jun 11, 2024
7b524f7
Format black
pyiron-runner Jun 12, 2024
2addb4b
Format black
pyiron-runner Jun 12, 2024
66ee8b4
Format black
pyiron-runner Jun 12, 2024
7e19a13
Merge pull request #1452 from pyiron/vasp_refactor_output_parser
jan-janssen Jun 12, 2024
3d4aae2
Merge branch 'main' into vasp_calculate
jan-janssen Jun 12, 2024
b6185f9
Merge branch 'vasp_calculate' into vasp_calculate_base
jan-janssen Jun 12, 2024
9d3a599
Update base.py
jan-janssen Jun 12, 2024
69bd794
Merge pull request #1454 from pyiron/vasp_calculate_base
jan-janssen Jun 12, 2024
e5e9e1d
Merge pull request #1455 from pyiron/main
jan-janssen Jun 12, 2024
79a02e6
Merge branch 'lammps_calculate' into lammps_calculate_with_base
jan-janssen Jun 12, 2024
36ac077
Merge pull request #1456 from pyiron/main
jan-janssen Jun 12, 2024
26de0f8
Merge branch 'lammps_calculate' into lammps_calculate_with_base
jan-janssen Jun 12, 2024
89a5a09
Merge pull request #1451 from pyiron/lammps_calculate_with_base
jan-janssen Jun 12, 2024
88b456f
Merge pull request #1418 from pyiron/phonopy_eigenvectors
raynol-dsouza Jun 12, 2024
c9d5280
remove calc_static from DFT
samwaseda Jun 12, 2024
ee12fcf
remove calc_static from Sphinx
samwaseda Jun 12, 2024
dfc3991
re-introduce calc_static in sphinx
samwaseda Jun 12, 2024
fe51fb4
remove args from calc_static in VASP
samwaseda Jun 12, 2024
fe0b5af
remove fix_symmetry from calc_minimize
samwaseda Jun 12, 2024
c3151a3
restore calc_static following Marvin's recommendation and remove non-…
samwaseda Jun 12, 2024
7703874
remove non-generic terms from vasp
samwaseda Jun 12, 2024
11ad7b6
remove non generic parameters from sphinx
samwaseda Jun 12, 2024
3d2af86
remove die-hard parameters
samwaseda Jun 12, 2024
c1e079a
Correct test which was always wrong
samwaseda Jun 12, 2024
83add11
remove algorithm
samwaseda Jun 12, 2024
7efe4bc
restore args because codacy complains
samwaseda Jun 12, 2024
90df2d8
I feel someone throwing maple sirup on my face for not using pycharm
samwaseda Jun 12, 2024
2216726
Format black
pyiron-runner Jun 12, 2024
90d6988
remove redundant doc
samwaseda Jun 12, 2024
3b99eac
Merge branch 'fix_spx_symmetry' of github.com:pyiron/pyiron_atomistic…
samwaseda Jun 12, 2024
e48de5b
Merge pull request #1457 from pyiron/fix_spx_symmetry
samwaseda Jun 12, 2024
12b2d26
Change index error in electronic structure to warning
samwaseda Jun 20, 2024
4995d40
Merge remote-tracking branch 'refs/remotes/origin/main' into lammps_c…
jan-janssen Jun 20, 2024
2edc692
Update LAMMPS interface to be compatible to latest changes in pyiron_…
jan-janssen Jun 20, 2024
1a0fc0a
Merge remote-tracking branch 'origin/lammps_calculate' into lammps_ca…
jan-janssen Jun 20, 2024
e50a801
fix pandas import
jan-janssen Jun 20, 2024
638274f
Format black
pyiron-runner Jun 20, 2024
93d81d4
Update pyproject.toml
jan-janssen Jun 20, 2024
a53fa87
Update environment.yml
jan-janssen Jun 20, 2024
94259ba
Update pyproject.toml
jan-janssen Jun 20, 2024
200f280
Update environment-docs.yml
jan-janssen Jun 20, 2024
bec9d36
Update environment.yml
jan-janssen Jun 20, 2024
7b88402
Update environment-docs.yml
jan-janssen Jun 20, 2024
f948918
Update environment.yml
jan-janssen Jun 20, 2024
1f0a6ba
Update pyproject.toml
jan-janssen Jun 20, 2024
0e97492
Update environment.yml
jan-janssen Jun 20, 2024
c9cc501
Update unittests.yml
jan-janssen Jun 20, 2024
3f9a49f
Update environment-docs.yml
jan-janssen Jun 20, 2024
d949ecb
Update environment.yml
jan-janssen Jun 20, 2024
73c5e8e
Update environment.yml
jan-janssen Jun 20, 2024
b004abd
Update pyproject.toml
jan-janssen Jun 20, 2024
6bdc87c
write_input() - call super() to copy restart files
jan-janssen Jun 21, 2024
4fc2ae6
Merge pull request #1460 from pyiron/pyiron_base
jan-janssen Jun 21, 2024
762fa8d
Merge remote-tracking branch 'refs/remotes/origin/main' into lammps_c…
jan-janssen Jun 21, 2024
470f2af
Fix bugs
jan-janssen Jun 21, 2024
f4420c6
Merge remote-tracking branch 'refs/remotes/origin/main' into vasp_cal…
jan-janssen Jun 21, 2024
cdf0abb
Compatibility to calculate function()
jan-janssen Jun 21, 2024
b469bb3
Format black
pyiron-runner Jun 21, 2024
e7915e6
Remove super().write_input() call
jan-janssen Jun 21, 2024
bc4f428
Format black
pyiron-runner Jun 21, 2024
86e398e
Update environment-old.yml
jan-janssen Jun 21, 2024
1920be2
Update environment-old.yml
jan-janssen Jun 21, 2024
06f452d
Fix import of existing calculation
jan-janssen Jun 21, 2024
48c3d4e
Format black
pyiron-runner Jun 21, 2024
2aa7627
VASP fix restart
jan-janssen Jun 21, 2024
00177f7
Merge pull request #1446 from pyiron/lammps_calculate
jan-janssen Jun 21, 2024
f241ab8
Merge remote-tracking branch 'refs/remotes/origin/main' into vasp_cal…
jan-janssen Jun 21, 2024
f512ea5
Merge pull request #1447 from pyiron/vasp_calculate
jan-janssen Jun 21, 2024
c093cb7
Update pyproject.toml
jan-janssen Jun 21, 2024
36fac69
Update environment.yml
jan-janssen Jun 21, 2024
a94e928
Update environment-docs.yml
jan-janssen Jun 21, 2024
b9fa90b
Update environment-old.yml
jan-janssen Jun 21, 2024
f936b1c
Update environment.yml
jan-janssen Jun 21, 2024
d94f596
Merge pull request #1459 from pyiron/safer_electronic_structure
samwaseda Jun 21, 2024
7811613
Merge pull request #1462 from pyiron/pyiron_base
jan-janssen Jun 21, 2024
68fdd20
Bump phonopy from 2.24.2 to 2.24.3
dependabot[bot] Jun 24, 2024
607905a
[dependabot skip] Update environment
github-actions[bot] Jun 24, 2024
4736bdc
Merge pull request #1464 from pyiron/dependabot/pip/phonopy-2.24.3
jan-janssen Jun 24, 2024
eeb347d
Update pyproject.toml
jan-janssen Jun 26, 2024
a54c81e
Update environment.yml
jan-janssen Jun 26, 2024
4ef68c8
Update environment-docs.yml
jan-janssen Jun 26, 2024
5ac66f2
Update environment.yml
jan-janssen Jun 26, 2024
d2a6459
Update environment.yml
jan-janssen Jun 26, 2024
dc55646
Update environment-docs.yml
jan-janssen Jun 26, 2024
9da9e18
Update pyproject.toml
jan-janssen Jun 26, 2024
194f7e7
Update report.py
jan-janssen Jun 26, 2024
c5c54a2
Merge pull request #1466 from pyiron/scipy-1
jan-janssen Jun 26, 2024
8efbad2
Update pyproject.toml
jan-janssen Jun 26, 2024
24b3a10
Update environment-docs.yml
jan-janssen Jun 26, 2024
124870d
Update environment.yml
jan-janssen Jun 26, 2024
db7107b
Update environment.yml
jan-janssen Jun 26, 2024
1c03c8a
Update environment-docs.yml
jan-janssen Jun 26, 2024
ac821ac
Update environment.yml
jan-janssen Jun 26, 2024
bd3fe0e
Update environment.yml
jan-janssen Jun 26, 2024
c8331d9
Update pyproject.toml
jan-janssen Jun 26, 2024
17dfcfa
Merge pull request #1467 from pyiron/pint
jan-janssen Jun 26, 2024
11fb1da
Merge remote-tracking branch 'refs/remotes/origin/main' into solvatio…
jan-janssen Jun 26, 2024
714b95d
parse ediel_sol from OUTCAR
jan-janssen Jun 26, 2024
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2 changes: 1 addition & 1 deletion .ci_support/environment-docs.yml
Original file line number Diff line number Diff line change
@@ -11,7 +11,7 @@ dependencies:
- defusedxml =0.7.1
- h5py =3.11.0
- matplotlib-base =3.8.4
- mendeleev =0.15.0
- mendeleev =0.16.1
- mp-api =0.41.2
- numpy =1.26.4
- pandas =2.2.2
2 changes: 1 addition & 1 deletion .ci_support/environment.yml
Original file line number Diff line number Diff line change
@@ -9,7 +9,7 @@ dependencies:
- defusedxml =0.7.1
- h5py =3.11.0
- matplotlib-base =3.8.4
- mendeleev =0.15.0
- mendeleev =0.16.1
- mp-api =0.41.2
- numpy =1.26.4
- pandas =2.2.2
2 changes: 1 addition & 1 deletion binder/environment.yml
Original file line number Diff line number Diff line change
@@ -7,7 +7,7 @@ dependencies:
- defusedxml =0.7.1
- h5py =3.11.0
- matplotlib-base =3.8.4
- mendeleev =0.15.0
- mendeleev =0.16.1
- mp-api =0.41.2
- numpy =1.26.4
- pandas =2.2.2
2 changes: 1 addition & 1 deletion pyproject.toml
Original file line number Diff line number Diff line change
@@ -29,7 +29,7 @@ dependencies = [
"defusedxml==0.7.1",
"h5py==3.11.0",
"matplotlib==3.8.4",
"mendeleev==0.15.0",
"mendeleev==0.16.1",
"mp-api==0.41.2",
"numpy==1.26.4",
"pandas==2.2.2",