Skip to content

merge developt to master #4

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
ToAmano merged 215 commits into from
Mar 8, 2026
Merged

merge developt to master #4

Changes from all commits
Commits
Show all changes
215 commits
Select commit Hold shift + click to select a range
6f7d0d3
apply code formatter test
ToAmano Mar 10, 2025
68062cc
🚧 update docstrings
ToAmano Mar 11, 2025
4e1c25a
✨ bug fix atomtype.py & move to bond/
ToAmano Mar 14, 2025
6d19770
refine README.md
ToAmano Mar 15, 2025
f58e40c
refactor diel/ -> fourier
ToAmano Mar 19, 2025
b03c102
♻️ code refactoring
ToAmano Mar 19, 2025
4d9fa4d
Update dielectric function/fouriertransform/autocorrelation
ToAmano Mar 19, 2025
67552c8
refactor dielfunction
ToAmano Mar 20, 2025
ec5914a
implemnt pytorch/numpy version WC assignment
ToAmano Mar 23, 2025
b9f85f2
♻️ refactoring
ToAmano Mar 26, 2025
0d65f12
change directory structure
ToAmano Mar 27, 2025
239a463
change directory structure
ToAmano Mar 27, 2025
cebdceb
refactor totaldipole/diel
ToAmano Mar 27, 2025
a5167e3
rename example directories
ToAmano May 7, 2025
ae90795
add CPtrain examples
ToAmano May 7, 2025
451e61d
update examles
ToAmano May 7, 2025
1e0d4ee
🐛 bug fix export_cpmd
ToAmano May 11, 2025
a52e887
🐛 fix import path for mlwc.fourier and apply formatter in cpextract
ToAmano May 11, 2025
bca93bf
🚧 apply formatter (test)
ToAmano May 11, 2025
43826fe
rename constant to Constant
ToAmano May 11, 2025
553384e
🚧 apply formatter to mlwc/include
ToAmano May 11, 2025
3bf2c27
formatter for totaldipole
ToAmano May 11, 2025
3e27d91
🚧 formatter for dielconst/gfactor
ToAmano May 11, 2025
80544c9
rename read_mol to ReadMolFile (use camel case)
ToAmano May 11, 2025
fa764a6
🚧 rename abstract class to camel case
ToAmano May 11, 2025
fa5abbd
refactor fft
ToAmano May 11, 2025
827b745
remove small.py
ToAmano May 11, 2025
2c6e314
🚧 apply formatter
ToAmano May 12, 2025
acd9f5f
remove unnecessary files
ToAmano May 12, 2025
a787f0d
remove notebooks
ToAmano May 12, 2025
2f28bdc
Remove obsolete scripts and data processing files
ToAmano May 12, 2025
983c6a6
Remove obsolete configuration and example files
ToAmano May 12, 2025
48d30ac
Merge pull request #96 from ToAmano/feature/#33_delete_unnecessary_files
ToAmano May 12, 2025
d481784
🐛 bug fix cptrain_train_new
ToAmano May 12, 2025
949f70a
🚧 refactor AverageDiel class and improve method names for clarity
ToAmano May 12, 2025
2ecccc5
fix: correct logging message casing in command_diel_dielconst function
ToAmano May 12, 2025
db176fb
fix: add missing docstring for CPextract.py diel gfactor
ToAmano May 12, 2025
8801932
refactor: simplify command_diel_plot function and remove unused class…
ToAmano May 12, 2025
8f7d187
refactor: rename class to ResampleDiel and improve method documentation
ToAmano May 12, 2025
219dcb3
fix: update handler for total_dipole parser to use command_diel_plot
ToAmano May 12, 2025
0db8d83
refactor: simplify file path construction in save methods
ToAmano May 13, 2025
76e6195
♻️ Refactor code for improved readability and consistency
ToAmano May 13, 2025
606a0e9
Add issue templates for bug reports, feature requests, and questions
ToAmano May 13, 2025
d8da171
Add pull request template for improved contribution guidelines
ToAmano May 13, 2025
35aef44
Add Dependabot configuration for GitHub Actions updates
ToAmano May 13, 2025
8c672af
Add labeler configuration for automated file labeling
ToAmano May 13, 2025
29c1354
Merge pull request #99 from ToAmano/feature/pr_template
ToAmano May 13, 2025
842b67d
♻️ refactor totaldipole/moldipole parser
ToAmano May 13, 2025
5e6b901
refactor: add mypy configuration and package data for type checking
ToAmano May 14, 2025
aaa99bc
♻️ Refactor CPextract Diel Module
ToAmano May 15, 2025
db6cdb5
♻️ refactor: improve logging and enhance readability in ReadMolFile c…
ToAmano May 15, 2025
4e00aa4
♻️ refactor: remove unnecessary files
ToAmano May 16, 2025
948b417
♻️ refactor: add bondtype definitions in input.yaml
ToAmano May 16, 2025
d52a5a6
✨ new feature
ToAmano May 17, 2025
d33730c
♻️ Remove unnecesary old files
ToAmano May 17, 2025
a61249d
♻️ refactor: using isort&black
ToAmano May 17, 2025
da49b2e
♻️ refactor pbc_mol.py (isort, black, and mother small changes)
ToAmano May 17, 2025
58af5c4
♻️ refactor: add deprecation warning to compute_distances function
ToAmano May 17, 2025
3de50b5
♻️ refactor: fix variable name in error message and clean up comments…
ToAmano May 17, 2025
10d1d55
♻️ refactor: remove unused class and functions
ToAmano May 17, 2025
8d0ef81
♻️ refactor: change log level from info to debug for bond length check
ToAmano May 17, 2025
381d2ab
♻️ refactor: update type annotations and improve logging in cptrain_p…
ToAmano May 17, 2025
3c2dcf7
♻️ add CPtrain example
ToAmano May 26, 2025
513a3cb
♻️ refactor: improve logging format and clean up unused imports in cp…
ToAmano May 26, 2025
6764f3b
Refactor dataset and model classes for improved clarity and structure
ToAmano May 26, 2025
33ad902
Refactor tests for bond center and PBC calculations
ToAmano May 26, 2025
3c25a89
♻️ refactor: update bond index references and improve methanol bond f…
ToAmano May 26, 2025
8ffcfc9
♻️ refactor: standardize function names and improve type hints across…
ToAmano May 26, 2025
6d161b4
♻️ refactor: improve logging format and clean up unused imports in Tr…
ToAmano May 26, 2025
dc6936b
♻️ refactor: improve type hints and variable naming in logging setup …
ToAmano May 26, 2025
9497674
♻️ refactor: clean up imports and improve code organization in multip…
ToAmano May 26, 2025
f5863b7
♻️ refactor: update import statements and clean up unused variables i…
ToAmano May 26, 2025
e71af99
♻️ refactor: remove unused _format_name_length function to clean up code
ToAmano May 26, 2025
8fbc326
Merge branch 'develop' into feature/#30_refactoring
ToAmano May 26, 2025
309ffa9
Merge pull request #100 from ToAmano/feature/#30_refactoring
ToAmano May 26, 2025
0a9f9f8
Remove unnecessary examples
ToAmano May 26, 2025
974397c
Remove notebook/ directory
ToAmano May 26, 2025
3b8db3c
♻️ Remove unnecessary test files
ToAmano May 26, 2025
7d43c49
♻️ Remove unnecessary files at root
ToAmano May 26, 2025
e274444
♻️ Remove recipe/
ToAmano May 26, 2025
fb8891e
♻️ Remove src/quadrupple
ToAmano May 26, 2025
74c4784
Merge pull request #105 from ToAmano/feature/#34_delete_unnecessary_f…
ToAmano May 26, 2025
d73bfd2
Merge pull request #107 from ToAmano/feature/#34_delete_unnecessary_f…
ToAmano May 26, 2025
bada4c6
✨ Add pre-commit configuration and workflow for automated code checks
ToAmano May 26, 2025
f781ac7
♻️ Apply black/isort formatter
ToAmano May 26, 2025
d36d733
✨ apply flake8 in src/ (comment outed)
ToAmano May 26, 2025
1ef1168
Merge pull request #108 from ToAmano/feature/#35_apply_formatter
ToAmano May 26, 2025
c1e0463
✨ Add Pull Request Labeler workflow
ToAmano May 26, 2025
76c0d5f
Merge pull request #109 from ToAmano/feature/#36_pr_labeler
ToAmano May 26, 2025
37d5a5e
✨ Refactor: Rename read_itp class to ReadItpFile for consistency
ToAmano May 26, 2025
cadef83
✨ Add BondType and BondDefinition classes; enhance MolecularInfo stru…
ToAmano May 27, 2025
815ceaf
♻️ activate flake8/mypy/pylint for extractor_rdkit.py
ToAmano May 27, 2025
790beda
🚧 add reference implementation for atomtype
ToAmano May 27, 2025
dfef553
♻️ Refactor: move ReadItpFile to extractor_itp.py
ToAmano May 28, 2025
fd965a9
✨ extractor_rdkit for converting bond info from RDKit
ToAmano May 28, 2025
5759597
✨ update test for atomtype
ToAmano May 28, 2025
dc74038
♻️ update import path for atomtype
ToAmano May 28, 2025
ce253ba
✨ Bug fix for _coc_build_data
ToAmano Jun 8, 2025
99a6e2d
♻️ Update type annotations for positions_skelton and index_tmp in Mol…
ToAmano Jun 8, 2025
8ddea59
♻️ Refactor type hints and improve bond-related methods in ReadMolFile
ToAmano Jun 8, 2025
90ff10d
✨ Implement bond and atomic type parsing in ReadItpFile
ToAmano Jun 8, 2025
720b51c
✨ Add documentation for chemical bond treatment and MolecularInfo class
ToAmano Jun 9, 2025
b97727a
♻️ Refactor MolecularInfo class
ToAmano Jun 9, 2025
908d4c8
♻️ Refactor MolecularDataExtractor and ReadMolFile
ToAmano Jun 9, 2025
3b5c571
♻️ Refactor BondAnalyze
ToAmano Jun 9, 2025
4f240e7
♻️ Refactor MolecularDataExtractor
ToAmano Jun 9, 2025
6fdfd94
📝 Fix typos and improve clarity in atomtype documentation
ToAmano Jun 11, 2025
4fd8ce2
✨ Add workflow to test command line scripts
ToAmano Jun 11, 2025
62ee714
✨ Fix working directory for dependency installation in workflow
ToAmano Jun 11, 2025
f9f3b35
🚧 debug workflow
ToAmano Jun 11, 2025
dca5f90
✨ Add initial setup.py for package configuration
ToAmano Jun 11, 2025
8a98a7c
rename requirements.txt
ToAmano Jun 11, 2025
ffdb39b
Remove unnecessary 'ls' command from dependency installation step
ToAmano Jun 11, 2025
1918acf
🐛 [Bug Fix] fix import error in CPextract.py cpmd dipole
ToAmano Jun 11, 2025
fe8c42b
🐛 [Bug Fix] import bug fix in Cpextract.py
ToAmano Jun 11, 2025
1c29728
🐛 Import path fix in epextract_cpmd.dipole
ToAmano Jun 11, 2025
a637889
🐛 import path fix CPmake.py
ToAmano Jun 11, 2025
bb1a82d
🐛 add captum in requirements.txt
ToAmano Jun 11, 2025
1047f08
🐛 add captum in setup.cfg
ToAmano Jun 11, 2025
3bd3802
🐛 add sklearn
ToAmano Jun 11, 2025
bcd01c9
🐛 fix package name from 'sklearn' to 'scikit-learn' in requirements
ToAmano Jun 11, 2025
7961dde
Merge pull request #113 from ToAmano/feature/#37_add_cmdline_test_pr
ToAmano Jun 11, 2025
c7b7285
🐛 fix command line detection to check script name from sys.argv[0]
ToAmano Jun 11, 2025
cc6058f
✨ Add workflow to test command line scripts
ToAmano Jun 11, 2025
a1be663
✨ Fix working directory for dependency installation in workflow
ToAmano Jun 11, 2025
5e962b6
🚧 debug workflow
ToAmano Jun 11, 2025
b1699b8
✨ Add initial setup.py for package configuration
ToAmano Jun 11, 2025
d0482e5
rename requirements.txt
ToAmano Jun 11, 2025
89d90ec
Remove unnecessary 'ls' command from dependency installation step
ToAmano Jun 11, 2025
150c68b
🐛 [Bug Fix] fix import error in CPextract.py cpmd dipole
ToAmano Jun 11, 2025
6de5b8f
🐛 [Bug Fix] import bug fix in Cpextract.py
ToAmano Jun 11, 2025
c232d20
🐛 Import path fix in epextract_cpmd.dipole
ToAmano Jun 11, 2025
b196776
🐛 import path fix CPmake.py
ToAmano Jun 11, 2025
2ee14c5
🐛 add captum in requirements.txt
ToAmano Jun 11, 2025
8c04d90
🐛 add captum in setup.cfg
ToAmano Jun 11, 2025
3307399
🐛 add sklearn
ToAmano Jun 11, 2025
24a119e
🐛 fix package name from 'sklearn' to 'scikit-learn' in requirements
ToAmano Jun 11, 2025
eb17cab
Merge pull request #112 from ToAmano/feature/#36_refactor_atomtype
ToAmano Jun 11, 2025
74f887b
Merge pull request #114 from ToAmano/feature/#38_fix_logger_setting
ToAmano Jun 12, 2025
038fb7f
✨ Support ase Trajectory
ToAmano Jun 12, 2025
7e0e608
♻️ add comment for ase.io.read
ToAmano Jun 15, 2025
6590383
✨ Refactor trajectory loading and validation functions into cptrain_c…
ToAmano Jun 15, 2025
b53f976
Merge pull request #129 from ToAmano/feature/support_for_trajectory_a…
ToAmano Jun 15, 2025
246beb2
🐛 Bug Fix assign_wcs_torch for double bond
ToAmano Jun 17, 2025
1e31636
✨ Support for triple bond and N in make_atoms_with_wc
ToAmano Jun 17, 2025
ae4cd52
✨ Add Timer context manager and decorator for logging execution time
ToAmano Jun 18, 2025
abba069
🐛 Bug Fix: use library logger
ToAmano Jun 18, 2025
1317244
✨ Add timer decorator to trajectory loading functions for performance…
ToAmano Jun 18, 2025
1e13073
✨ Add automatic torch device detector
ToAmano Jun 18, 2025
68939d0
✨ Add logging for script start time and version in CPmake.py and CPtr…
ToAmano Jun 18, 2025
e530944
♻️ Improve logging format
ToAmano Jun 18, 2025
c987e5e
♻️ Use logging and remove print
ToAmano Jun 18, 2025
585a481
♻️ Refactor trajectory loading function
ToAmano Jun 24, 2025
7632e7c
♻️ Refactor: add type annotation
ToAmano Jun 24, 2025
59587fa
♻️ Refactor: use str for return in get_device
ToAmano Jun 24, 2025
010ba5a
♻️ Refactor ml/train for flake8
ToAmano Jun 25, 2025
e643851
♻️ Remove unnecessary function
ToAmano Jun 25, 2025
e9ae3ae
♻️ Refactor ml/ for flake8
ToAmano Jun 25, 2025
d1c2f76
uncomment flake8 in precommit
ToAmano Jun 26, 2025
bf142a0
add # flake8: noqa for old file
ToAmano Jun 26, 2025
84b8126
increase logger visivility
ToAmano Jun 26, 2025
1843336
Add # flake8: noqa for old files
ToAmano Jul 16, 2025
f3344d4
Add # flake8: nowa for model files
ToAmano Jul 16, 2025
ca42ea5
Ignore E203(space before : ) in flake8
ToAmano Jul 16, 2025
d9c86a2
Minor update windowfunction
ToAmano Jul 16, 2025
cca669d
limit pre-commit to src/ directory
ToAmano Aug 26, 2025
eb4d0f0
limit mypy and flake8 in pre-commits to a few files
ToAmano Aug 26, 2025
0441bbc
limit flake8 in pre-commit to a few files
ToAmano Aug 26, 2025
f99f9bb
refactor cptrain_train
ToAmano Aug 26, 2025
70182ae
minor refactor
ToAmano Aug 26, 2025
3814c8c
refactor cptrain_test
ToAmano Aug 26, 2025
081fb40
refactor cpmake_smile.py
ToAmano Aug 26, 2025
6c662ea
refactor assign_wcs_torch
ToAmano Aug 26, 2025
86b4f26
rename UNITCELL_VECTOR to unitcell_vector
ToAmano Aug 26, 2025
5cda83d
Merge pull request #135 from ToAmano/feature/test_acetone
ToAmano Aug 26, 2025
4dd7113
✨ implement multiple initial seeds for models
ToAmano Aug 26, 2025
dc6b925
Merge pull request #136 from ToAmano/feature/multiplemodel-differents…
ToAmano Aug 27, 2025
d96d004
extend print_parameters in the model
ToAmano Aug 29, 2025
82d0dfe
implement model evaluation in cptrain_core
ToAmano Aug 29, 2025
10e69ca
Use a function to evaluate model in cptrain_train
ToAmano Aug 29, 2025
3b62662
Use a function to evaluate model in cptrain_test
ToAmano Aug 29, 2025
0f13ca0
minor refacor
ToAmano Aug 30, 2025
af353df
refator cptrain_core
ToAmano Aug 30, 2025
a788b9d
add cptrain files to pre-commit
ToAmano Aug 30, 2025
c94f6dd
update pre-commit
ToAmano Aug 30, 2025
b65697f
change cptrain file structure
ToAmano Aug 30, 2025
60a775f
upse sklearn mse
ToAmano Aug 30, 2025
4fe92da
remove unused numpy
ToAmano Aug 30, 2025
b58d461
fix import path
ToAmano Aug 30, 2025
0af4002
Separate graphics functions into include/
ToAmano Sep 1, 2025
5c82b64
minor bug fix cptrain_pred
ToAmano Sep 1, 2025
ca62067
implement metrics calculation
ToAmano Sep 1, 2025
0a865c4
add save figure functin in cptrain_core
ToAmano Sep 1, 2025
ba3eedb
Use functions in cptrain_core
ToAmano Sep 1, 2025
9ee4258
use functions in cptrain_core
ToAmano Sep 1, 2025
3720908
minor update
ToAmano Sep 4, 2025
465d7e4
Remove device variable from model
ToAmano Sep 4, 2025
b7498cd
fix figure label
ToAmano Sep 5, 2025
0130eb8
fix figure label
ToAmano Sep 5, 2025
75a731a
refactor cptrain_train_io
ToAmano Mar 8, 2026
eee9c76
replace traced torchscript model for c++ inference with scripted torc…
ToAmano Mar 8, 2026
4ad54e7
remove / for os.path.join
ToAmano Mar 8, 2026
e802894
update tutorial 1 (liquid methanol)
ToAmano Mar 8, 2026
39c5efb
refactor cptrain_train.py
ToAmano Mar 8, 2026
ddd043a
update cptrain example input
ToAmano Mar 8, 2026
f9480ba
update cptrain example input
ToAmano Mar 8, 2026
e33baf8
update tutorial input
ToAmano Mar 8, 2026
59f67be
add pytorch dataset
ToAmano Mar 8, 2026
9d5f269
add pytorch dataset for gnn
ToAmano Mar 8, 2026
4afd086
comment out schnet in cptrain_train.py
ToAmano Mar 8, 2026
11355c3
add transforms
ToAmano Mar 8, 2026
a88c5dd
comment out schnet transform
ToAmano Mar 8, 2026
0d5d138
Merge pull request #1 from ToAmano/feature/refactor-cptraintrain
ToAmano Mar 8, 2026
e06830b
bug fix tutorial doc
ToAmano Mar 8, 2026
d1743a4
Merge pull request #2 from ToAmano/feature/refactor-cptraintrain
ToAmano Mar 8, 2026

Sorry, this diff is taking too long to generate.

It may be too large to display on GitHub.