feat:add support to pass kpoints np.array to get band eigenvalues. #145
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* Dev (#125) * update workflow and install method. * build(deps): update pyproject.toml * build(deps): update pyproject.toml * chore: delete release-check.md * ci: update publish-to-pypi.yml * Update pyproject.toml * Update pyproject.toml * update mix.ep50.pth, mix.iter500.pth and train_config.json (#126) * update h-BN example, ckpt and the related doc. (#127) * update mix.ep50.pth, mix.iter500.pth and train_config.json * update hBN example * docs: update hands_on.md * update run.py: (#128) * update run.py: support change device and dtype when postprocess the model * update argcheck.py * update argcheck.py * add E3 features (node/edge) to hamiltonian/density blocks (#129) * stack changes * fix test ham to feature * update write block function in command line (#132) * update write block * update task naming for each mdoel * feat(dftb): add support sk params from dftb skf files . (#133) * add xitorch interp1d * feat: create dptb/utils/_xitorch/__init__.py * update C_chain example * add sk * read skfile and load sk para * update sk_param.py * update onsite.py: add support load onsite E from the dftb skf files. * update sk_param.py * update sk_param.py * add hopping dptb * add core for dftb support. * update sk_param.py: make the outof skparams in the same format as nnsk model parameters. * update dftbsk.py： make the skparas from skf files in the same style of nnsk. * update hopping_dptb.py * update onsite.py * update dftbsk.py and nnsk.py * add new mix type: dftb + nnenv * update build.py * update build.py and dftbsk.py * update deeptb.py * add build_model for dftbsk and dftbsk+nnenv two new mode. * add hBN dftb example * fix(SKParam): Update SKParam class to handle missing keys in skdict and raise appropriate errors. Add unit tests for SKParam class. * feat(train): Add skints loss function for training with nnsk model * test(hopping_dptb): Update dftb/hopping_dptb.py and add test_dftbsk.py * test(build_model): Update deeptb.py and test_build_model.py with dftbsk changes * test: Refactor test_build_model.py to remove unnecessary blank lines and add validation for model_options in test_build_model_failure() * update deeptb.py * test(test_sktb): to add new tests for dftbsk and nnsk models * 📃 docs(dftb): Update hBN_dftb example with new data and input files * Update deeptb.py * Update SE2Aggregation class in se2.py to use the last 4 columns of x instead of the last 3 columns. Update _SE2Descriptor class in se2.py to set the flow parameter to "target_to_source". and add radial info into env matrix (#135) * feat(command): add cskf command to collect the skfiles into a pth database (#134) * add xitorch interp1d * feat: create dptb/utils/_xitorch/__init__.py * update C_chain example * add sk * read skfile and load sk para * update sk_param.py * update onsite.py: add support load onsite E from the dftb skf files. * update sk_param.py * update sk_param.py * add hopping dptb * add core for dftb support. * update sk_param.py: make the outof skparams in the same format as nnsk model parameters. * update dftbsk.py： make the skparas from skf files in the same style of nnsk. * update hopping_dptb.py * update onsite.py * update dftbsk.py and nnsk.py * add new mix type: dftb + nnenv * update build.py * update build.py and dftbsk.py * update deeptb.py * add build_model for dftbsk and dftbsk+nnenv two new mode. * add hBN dftb example * fix(SKParam): Update SKParam class to handle missing keys in skdict and raise appropriate errors. Add unit tests for SKParam class. * feat(train): Add skints loss function for training with nnsk model * test(hopping_dptb): Update dftb/hopping_dptb.py and add test_dftbsk.py * test(build_model): Update deeptb.py and test_build_model.py with dftbsk changes * test: Refactor test_build_model.py to remove unnecessary blank lines and add validation for model_options in test_build_model_failure() * update deeptb.py * test(test_sktb): to add new tests for dftbsk and nnsk models * 📃 docs(dftb): Update hBN_dftb example with new data and input files * 🦄 refactor(SKParam): Update SKParam class to include HubdU and Occu in skdict * Update deeptb.py * ✨ feat(cskf): Add collectskf.py to collect sktb params from sk files * 🧪 test(csfk): update test_skparam to add unit test for cskf command * 📃 docs(dftb): add docs about dftb example into index.rst * Fix bugs in SE2Aggregation and _SE2Descriptor classes * add example mos2 * update hBN example * fix(se2): update the smooth function in getting env descriptor (#136) * 🐞 fix(se2): update the smooth function in getting env descriptor * test: update test_emb_se2.py * test: update test_emb_se2.py * Update version 2.0.1 in pyproject.toml * Fix(nnsk): NNSK class in nnsk.py to use the get() method when accessing the full orbital (#139) * Update NNSK class in nnsk.py to use the get() method when accessing values in the full_basis_to_basis dictionary. * fix digital error in test_emb_se2 * temp * Update(nnsk): automatic orthogonalization (#141) * fix(data): fix the bug in dm parse (#142) * Update(nnsk): automatic orthogonalization * update DM parse * feat:add support to pass kpoints np.array to get band eigenvalues. (#145) * feat: create toskint.ipynb * feat:add support to pass kpoints nparray to get band eigenvalues. * feat(curve_fitting.py): develop a curve fitting function that converts the dftb model to nnsk (#146) * update fitting dftb * add(dftb2nnsk): develop fitting class for converting dftb to nnsk model * remove(curve-fitting.ipynb): remove the notebook for development * fix test split * add(test_dftb2nnsk): add simple test for dftb2nnsk class * temp * fix test * fix(nnsk): fix device type errpr in to json function * rename hopping_dptb to hopping_dftb * temp * align inferences * update decaying function * remove rc from dftb2nnsk * fix test nrl * fix test nrl * update argcheck * update dftb2nnsk.py * update argcheck * update read_NRL_tojson.py --------- Co-authored-by: qqgu <guqq_phy@qq.com> * feat(data): add parse md trajectory of abacus (#144) * update abacus parse md * fix(default_dataset): The natom and nframe default setting * shift the 'pos‘ position in test default dataset * fix lattice constant transform * update parse_abacus_md * update abacus.py * update abacus.py * update parse abacus scf lattice constant --------- Co-authored-by: qqgu <guqq_phy@qq.com> * style: optmize the import of each submodule (#154) * data import * optimize imports * fix: idp(data) in nnsk and deeptb, and refactor soc switch in hr2hk (#152) * refactor: plotting code in dftb2nnsk.py fix push_decay method and update push options (#156) * Refactor plotting code in dftb2nnsk.py * refactor(nnsk): Refactor NNSK class in nnsk.py to fix push_decay method and update push options * update saver.py to save ckpt with name of ovlp * fix: update nnsk from reference and change the sign of ovp_thr * update saver.py * update mos2 example * Update test_sktb.py with new model weights and fix init_model path in test_md * docs: Update dftb.md with hBN model training steps and fix formatting (#157) * docs: Update dftb.md with hBN model training steps and fix formatting * Bump actions/setup-python from 4 to 5 (#131) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#130) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * feat: add -v to get dptb version, and update the version.py to load version number and git version (#158) * Refactor plotting code in dftb2nnsk.py * refactor(nnsk): Refactor NNSK class in nnsk.py to fix push_decay method and update push options * update saver.py to save ckpt with name of ovlp * fix: update nnsk from reference and change the sign of ovp_thr * update saver.py * update mos2 example * Update test_sktb.py with new model weights and fix init_model path in test_md * docs: Update dftb.md with hBN model training steps and fix formatting * Refactor main.py to add version flag and handle unknown version * Update pyproject.toml to add toml dependency * feat: update pyproject.toml and __init__.py to automatically get the version number. (#160) * Refactor plotting code in dftb2nnsk.py * refactor(nnsk): Refactor NNSK class in nnsk.py to fix push_decay method and update push options * update saver.py to save ckpt with name of ovlp * fix: update nnsk from reference and change the sign of ovp_thr * update saver.py * update mos2 example * Update test_sktb.py with new model weights and fix init_model path in test_md * docs: Update dftb.md with hBN model training steps and fix formatting * Refactor main.py to add version flag and handle unknown version * Update pyproject.toml to add toml dependency * update pyproject.toml and add -v command * update ut.sh * update unit_test.yml and ut.sh * ci: update unit_test.yml * ci: update unit_test.yml * ci: update unit_test.yml * ci: update unit_test.yml * ci: update unit_test.yml * ci: update unit_test.yml * build(deps): update 2 files and delete 1 file * ci: update devcontainer.yml * ci: update devcontainer.yml * ci: update devcontainer.yml * ci: update devcontainer.yml * ci: update devcontainer.yml * back to main * Update devcontainer.yml and unit_test.yml workflows --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Yinzhanghao Zhou <64253517+floatingCatty@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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