Jdftx coords #1
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Jdftx coords #1
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* Support pymatgen Species in FHI-aims control.in * Simplify building geometry.in file * A bug fixed
…erialsproject#4093) * Correctly compute rotational symmetry number for D*h point group Correct value is 2 * pre-commit auto-fixes * Add docs * pre-commit auto-fixes --------- Co-authored-by: Sasha Fonari <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…sproject#4105) * `pre-commit migrate-config` * `pre-commit autoupdate` * Replace deprecated `ExpCellFilter` with `FrechetCellFilter` * Fix test for new `FrechetCellFilter` * `dos2unix` --------- Co-authored-by: Shyue Ping Ong <[email protected]>
…ences" method in pmg Element class
Periodic table edits
Jeiters rename
Co-authored-by: Shyue Ping Ong <[email protected]>
Fix for Species class's valence(s) property
… conflict with unexpected minimization keywords
JDFTXOutfileSlice __getattr__ fix
…or pDOS/pCOHP analysis
…void any issues with using a JOutStructure in place of a Structure, adding eigenvals and bandProjections to JDFTXOutputs
…ucture objects), added a "constant_lattice" bool attribute to JDFTXOutfileSlice for creating a Trajectory, changed the "_get_trajectory" method for JDFTXOutfile to instead concatenate the "trajectory" attributes of the JDFTXOutfileSlice's
…e, removing test for ValueError no longer raised in _set_trajectory in JDFTXOutfileSlice
…e validation methods to AbstractTag for validations that are called multiple times, cleaned up cluttered tests and added comments to make it more clear what is being tested
…-8 (materialsproject#4219) * explicit mode for zopen * fix bad mode for cifwrite * remove tag * remove an unnecessary cast to int * TODO: test monty zopen change * fix implicit mode * Revert "TODO: test monty zopen change" This reverts commit c9bf970. * Revert "Revert "TODO: test monty zopen change"" This reverts commit be411a0. * Revert "Revert "Revert "TODO: test monty zopen change""" This reverts commit e75c196. * explicit text mode for stout * some explicit utf-8 for zopen * TO BE REVERTED: test monty pr * add the rest encoding * Revert "TO BE REVERTED: test monty pr" This reverts commit d899c87.
* pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.2 → v0.8.1](astral-sh/ruff-pre-commit@v0.7.2...v0.8.1) - [github.com/MarcoGorelli/cython-lint: v0.16.2 → v0.16.6](MarcoGorelli/cython-lint@v0.16.2...v0.16.6) - [github.com/igorshubovych/markdownlint-cli: v0.42.0 → v0.43.0](igorshubovych/markdownlint-cli@v0.42.0...v0.43.0) - [github.com/kynan/nbstripout: 0.8.0 → 0.8.1](kynan/nbstripout@0.8.0...0.8.1) - [github.com/RobertCraigie/pyright-python: v1.1.387 → v1.1.389](RobertCraigie/pyright-python@v1.1.387...v1.1.389) * pre-commit auto-fixes * Convert to f-syntax to satisfy ruff Signed-off-by: Matthew Horton <[email protected]> --------- Signed-off-by: Matthew Horton <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Matthew Horton <[email protected]>
…project#4217) * increase warning stacklevel * unignore b028 ruff rule * fix some * fix more in apps, command_line and ext * remove unnecessary explicit UserWarning * replace explicit stacklevel 1 * fix io * fix entries * fix electronic_structure * avoid manual deprecation warning * fix core * fix analysis * futurewarning for legacy mprester
…sproject#4205) * clean up comment and docstring * change reference to stable doc instead of latest * fix assert_str_content_equal and add test * clean up assert_str_content_equal usage * make error msg more detailed * don't force positional as err msg contains expected and actual tag * fix quote * make assert_msonable staticmethod * sort methods alphabetically * add list of methods * comment out test_symmetry_ops * skip failing tests * only comment out assert to reduce change * simplify single file module * make module dir private * remove test for module dir * add test for non existent structure * add more tests * more human readable err msg and test
…lsproject#4210) * fix uv pip install from bdist usage * use uv to build wheels * add single quote for macos * add single quote for macos * try ATAT3 install, it should fail * Revert "try ATAT3 install, it should fail" This reverts commit 3f63f4b. * modest verbose level * use mamba native env name and py ver
* add NBANDS parser * add unit test * test more vasp versions * remove repeat default arg * add overridden test
* update link * add markdown check hook * try to migrate the lint workflow * Revert "add markdown check hook" This reverts commit 2786a73. * comment out ruff for now * try linkspector * fall back to markdown-link-check * revert md-link-check
…nation_environments` (materialsproject#4194) * fix index in 32bit system * pre-commit auto-fixes --------- Co-authored-by: Haoyu Yang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…` as UTF…" (materialsproject#4221) This reverts commit b2a5e0f.
…ct` for `io.abinit.pseudos` (materialsproject#4223)
* Modify FHI-aims inputs to not use species string FHI-aims does not read spin from the species and that causes issues with magnetic calculations * Add the option for oxidation state to still be in species Issue is only with spin * Fix lint errors --------- Signed-off-by: Shyue Ping Ong <[email protected]> Co-authored-by: Shyue Ping Ong <[email protected]>
…2 in CI (materialsproject#4224) * skip another test * fix import * update reason * what? looks like the latest monty doesn't pack reverse readline fix? * Revert "what? looks like the latest monty doesn't pack reverse readline fix?" This reverts commit b891244.
…thin a for-loop now, adding "forces" as an attribute passed upstread to JDFTXOutfile
…when reading initial coordinates in joustructures.py (_get_initial_coords), added missing 1/bohr_to_ang when creating a JDFTXInfile from a pmg Structure, added specification of coords-type when creating JDFTXInfile from a pmg Structure, added keyword argument for from_structure to store ion position tags as fractional or cartesian coordinates
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