Aiida-quantumespresso

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4.4.0

This minor release mainly includes documentation changes, but also a small breaking change in [[a389629](https://github.com/aiidateam/aiida-quantumespresso/commit/a389629387b74805ffe2f4d6515ac05b8f62b4d5)].
Work chains that wrap the `PwBaseWorkChain` for an `nscf` or `bands` calculation and add the `parent_folder` during runtime would have to adapt the `validator` for the `pw` name space as follows to avoid warnings:

python
spec.inputs['nscf']['pw'].validator = PwCalculation.validate_inputs_base


Now, the validator that checks for the presence of the `parent_folder` in the inputs is adapted so it checks if the `parent_folder` port is in the name space.
If not, the validation is skipped.
So work chains that wrap the `PwBaseWorkChain` to run an `nscf` or `bands` calculation can simply exclude the `parent_folder` port in the `pw` name space:

python
spec.expose_inputs(
PwBaseWorkChain,
namespace='nscf',
exclude=('clean_workdir', 'pw.structure', 'pw.parent_folder'),
namespace_options={
'help': 'Inputs for the `PwBaseWorkChain` of the `nscf` calculation.',
'validator': validate_nscf
}
)


A new calculation function `create_magnetic_configuration` is added, which can be used to create a new `StructureData` with the required kinds for a specific magnetic configuration.
For example, for an HCP structure with two Co sites:

python
In [1]: from aiida import orm

In [2]: from ase.build import bulk
...: structure = orm.StructureData(ase=bulk('Co', 'hcp', 2.5, 4.06))


The `create_magnetic_configuration` can be used to quickly create a new `StructureData` with two different kinds:

python
In [3]: from aiida_quantumespresso.calculations.functions.create_magnetic_configuration import create_magnetic_configuration
...:
...: results = create_magnetic_configuration(structure, [-2, 2])

In [4]: results['structure'].sites
Out[4]:
[<Site: kind name 'Co0' -2.7755575615629e-17,1.4433756729741,2.03>,
<Site: kind name 'Co1' 0.0,0.0,0.0>]

In [5]: results['magnetic_moments'].get_dict()
Out[5]: {'Co0': 2, 'Co1': -2}


For more information, see the tutorial on how to work with magnetic systems:

https://aiida-quantumespresso.readthedocs.io/en/latest/tutorials/magnetism.html

The release also makes an important change in the dependencies related to a bug introduced in `pydantic`, see:

https://github.com/pydantic/pydantic/issues/5821

Hence the version of `pydantic` is adapted to `1.10.8`, where this bug is fixed.

‼️ Breaking changes

* `PwCalculation`: refactor `parent_folder` validation [[a389629](https://github.com/aiidateam/aiida-quantumespresso/commit/a389629387b74805ffe2f4d6515ac05b8f62b4d5)]

✨ New features

* Add the `create_magnetic_configuration` function [[d9b18a7](https://github.com/aiidateam/aiida-quantumespresso/commit/d9b18a7c20ce023018755c202f8d06cbf8bd27c5)]

👌 Improvements

* `PpParser`: Include exception in `ERROR_OUTPUT_DATAFILE_PARSE` message [[72f114e](https://github.com/aiidateam/aiida-quantumespresso/commit/72f114e4b05b45297abf0954b6334f5a461ed17e)]

🐛 Bug Fixes

* `PwParser`: Fix case when `settings` are not provided [[5d4a7d9](https://github.com/aiidateam/aiida-quantumespresso/commit/5d4a7d9405b757e2ecf65a72c1ee92aa2fb36a39)]

📚 Documentation

* Small improvements to "Installation" page [[90ad1d6](https://github.com/aiidateam/aiida-quantumespresso/commit/90ad1d6026d3c4b557970d6cc7626e85195ca4dc)]
* Switch to `sphinx-book-theme` from `pydata_sphinx_theme` [[3578a9d](https://github.com/aiidateam/aiida-quantumespresso/commit/3578a9d08af5e8cdd0851f852185bce2f2c7bd51)]
* Switch to using MyST Markdown [[37d2a14](https://github.com/aiidateam/aiida-quantumespresso/commit/37d2a14256480785491429c4ca424ebdc258ae34)]
* Add how-to for `PwCalculationTools.get_scf_accuracy` [[29b4db9](https://github.com/aiidateam/aiida-quantumespresso/commit/29b4db9e5c0d225331aba58981663ad4af641640)]
* Bump Python version for RTD build [[483d99b](https://github.com/aiidateam/aiida-quantumespresso/commit/483d99b77ca26ce4c607440922b432e39c16d1cf)]
* Fix breaking changes `CHANGELOG.md` [[7f4c4a1](https://github.com/aiidateam/aiida-quantumespresso/commit/7f4c4a108b09c31cfc9ee252d7e8fbe574ea477f)]

🔧 Maintenance

* Catch warning in `restart_mode` test for `PwBaseWorkChain` [[45e1907](https://github.com/aiidateam/aiida-quantumespresso/commit/45e19072f28d30fb4d6df1bbc489f38ce94cd1be)]
* Update `tox` configuration [[0702152](https://github.com/aiidateam/aiida-quantumespresso/commit/0702152c1dc18fd8d04cbf44f99a15761be955fe)]
* Add script to update `CHANGELOG.md` [[b21076c](https://github.com/aiidateam/aiida-quantumespresso/commit/b21076cdd1773fe3b7de18bc83e89ec7b367d837)]
* Remove Python 3.8 from the nightly workflow matrix [[0859d0a](https://github.com/aiidateam/aiida-quantumespresso/commit/0859d0a05c495c8a92208d118da6066f385600a7)]

⬆️ Update dependencies

* Restrict `pydantic` to at least `1.10.8` [[f430139](https://github.com/aiidateam/aiida-quantumespresso/commit/f430139e36723f73253efa66a6444018123760d2)]

♻️ Refactor

* `BasePwCpInputGenerator`: Remove superfluous validation [[0b6476c](https://github.com/aiidateam/aiida-quantumespresso/commit/0b6476c6c8379a0ea6575f4323979d136f7220aa)]
* Move basic parsing into `BaseParser` class [[1c223c7](https://github.com/aiidateam/aiida-quantumespresso/commit/1c223c78f0a2eda38089a08d9f21626f49d2fd6b)]

4.3.0

Release version `4.3.0` comes with a lot of new features, improvements and bug fixes.
Although this is technically a minor release, this new version does come with some _minor_ breaking changes:

* The default value of `clean_workdir` was changed from `True` to `False`.
* The `automatic_parallelization` feature of the `PwBaseWorkChain` was removed, as this was badly broken with no clear path to fixing it. Moreover, [v7.1 of Quantum ESPRESSO](https://gitlab.com/QEF/q-e/-/releases/qe-7.1) has implemented some basic automated parallelization for `pw.x` when no parallelization flags are specified.
* Work chains no longer set/override static inputs inside the steps of their outline. All defaults are moved to the protocol files instead, and it is recommended to always use the `get_builder_from_protocol()` method to run a work chain. For more details, [see the corresponding PR](https://github.com/aiidateam/aiida-quantumespresso/pull/902).

Support for Quantum ESPRESSO v7.2 `pw.x` parsing was added, as well as the `HubbardStructureData` data plugin and corresponding implementation in the `PwCalculation` plugin to support the [new input syntax for using Hubbard corrections](https://gitlab.com/QEF/q-e/-/releases/qe-7.1#incompatible-changes-in-71-version) in the `pw.x` code.

For `ph.x`, the symmetry labels printed in the `stdout` after the mode frequencies are now parsed for each q-point.
In the case of restarts in the `PhBaseWorkChain`, care has been taken to properly parse these symmetry labels from the separate output files and merge them, so the `output_parameters` are the same with or without restarts.

The `XpsWorkChain` has been added to compute the XPS spectra using core-hole pseudo potentials and the `pw.x` code. The work chain can handle both molecules and crystals. The chemical shifts, as well as the cole-level binding energy can be obtained.

Finally, improved error handling for the `PwBaseWorkChain` was implemented for several typical failure modes of the `pw.x` code, and the `CRASH` file is now also retrieved, as this will be the default location of error messages from Quantum ESPRESSO v7.2 onwards.

‼️ Breaking changes

* Protocols: Set `clean_workdir` default to `False` [[f8e512f](https://github.com/aiidateam/aiida-quantumespresso/commit/f8e512f9cb5404d702aa1d721e2369c7257f977f)]
* `PwBaseWorkChain`: Remove `automatic_parallelization` input [[5cae75f](https://github.com/aiidateam/aiida-quantumespresso/commit/5cae75ff671268dc1e5684e1c84f801a10839e0b)]
* Protocols: Move all static work chain inputs to protocol [[01f1470](https://github.com/aiidateam/aiida-quantumespresso/commit/01f14701e6846338f84db25bf7e654fcdfb6f927)]

✨ New features

* `PwBaseWorkChain`: Add `ERROR_IONIC_INTERRUPTED_PARTIAL_TRAJECTORY` handler [[9291f84](https://github.com/aiidateam/aiida-quantumespresso/commit/9291f841445800fa2b38d97b6957e98a2818b624)]
* `PwCalculation`: Add exit code and handler for `scale_h` error [[d350d7e](https://github.com/aiidateam/aiida-quantumespresso/commit/d350d7eb5b7bfcf4682ee8f635c721708be1d1d7)]
* `PwParser`: Add retrieval and parsing of `CRASH` file [[7f53c96](https://github.com/aiidateam/aiida-quantumespresso/commit/7f53c96bf744ed622fe7b1d13b0f7e9198ed5656)]
* Add the `HubbardStructureData` data plugin [[355020c](https://github.com/aiidateam/aiida-quantumespresso/commit/355020ca9ea63db0803ecc5746f93a879f488696)]
* `PwParser`: Add support for QE v7.2 [[57f5f8f](https://github.com/aiidateam/aiida-quantumespresso/commit/57f5f8ffa359ed5f5d937c43ae1f53cbc55eb314)]
* `PhParser`: parse symmetry labels from the `stdout` of `ph.x` [[8a9950a](https://github.com/aiidateam/aiida-quantumespresso/commit/8a9950aa870a26badb24b572910f7b8526236f37)]
* Add Feature: `XpsWorkChain` [[a9d124e](https://github.com/aiidateam/aiida-quantumespresso/commit/a9d124e2cfa5a5a5891affbe40515d38d1dd3913)]
* Add Feature: `XspectraCrystalWorkChain` [[01e7593](https://github.com/aiidateam/aiida-quantumespresso/commit/01e759319552645072b7a89dd0347225ab14d635)]
* Add `OpenGridCalculation` [[361ff04](https://github.com/aiidateam/aiida-quantumespresso/commit/361ff0413659b23f895747e04f8448f574811958)]
* Feature/get xspectra structures [[bc63d56](https://github.com/aiidateam/aiida-quantumespresso/commit/bc63d5661a6e79e3cf599ada3fdfc8eb3cb8193d)]

👌 Improvements

* ``PwBaseWorkChain``: improve diagonalization handler [[cc29488](https://github.com/aiidateam/aiida-quantumespresso/commit/cc29488c9e450bac5af7d28ee3f79ab8bcb01b6a)]
* `PwCalculation`: Add `ERROR_IONIC_INTERRUPTED_PARTIAL_TRAJECTORY` code [[92a6c6f](https://github.com/aiidateam/aiida-quantumespresso/commit/92a6c6fb00c02ace0f8afc0d06d8f938a0e2d221)]
* `PwParser`: Keep scheduler parser error unless more specific available [[b8d6a3a](https://github.com/aiidateam/aiida-quantumespresso/commit/b8d6a3a489c8d24a06cfc58956a97b121ad92316)]
* Protocols: consider `pbc` of `StructureData` [[ef21642](https://github.com/aiidateam/aiida-quantumespresso/commit/ef21642ba8c715b384e726628f866f7a3df63890)]
* CLI: Simplify `cli.utils.validate_hubbard_parameters` and add tests [[74d25d1](https://github.com/aiidateam/aiida-quantumespresso/commit/74d25d1782cddb2801781999e6c708191f1cdae7)]
* `PwCalculation`: Add exit codes, mostly related to diagonalization [[159b83e](https://github.com/aiidateam/aiida-quantumespresso/commit/159b83e5a96db258697fa821b48746adfbacd2ad)]
* `PwParser`: Include path in exception when XML schema not found [[56fdb57](https://github.com/aiidateam/aiida-quantumespresso/commit/56fdb57643fa44e7bcff82640d9cbcb26f7759b3)]

🐛 Bug Fixes

* `PwCalculation`: Fix restart validation for `nscf`/`bands` [[29a0dfa](https://github.com/aiidateam/aiida-quantumespresso/commit/29a0dfa3257863f73de17a0347dfa578da5d292e)]
* `PwParser`: Correct the `disk_io` type for all XML schemas [[89d39a4](https://github.com/aiidateam/aiida-quantumespresso/commit/89d39a47d4eae0f9b39ef93fe07404a5102c6ee7)]
* `PwParser`: Fix trajectory verification for `fixed_coords` [[105670f](https://github.com/aiidateam/aiida-quantumespresso/commit/105670fd145c572213bb750069679ef6fca7a80d)]
* `XspectraCoreWorkChain`: Ensure `overrides` respected in `get_builder_from_protocol()` [[7b2d701](https://github.com/aiidateam/aiida-quantumespresso/commit/7b2d701cb7f61719efa5a14f762b8f85078fb4dd)]
* `PhCalculation`: Fix exception when `parent_folder` is on different computer [[24b3779](https://github.com/aiidateam/aiida-quantumespresso/commit/24b3779e0df2d30378898f89dd884b69593218e9)]

📚 Documentation

* Fix the intersphinx URL of the AiiDA documentation [[08532d8](https://github.com/aiidateam/aiida-quantumespresso/commit/08532d8f69d87bd1853bb2a9010854efbc6bbaee)]
* `README.md`: Fix Build Status badge to point to `ci` action [[1e9c345](https://github.com/aiidateam/aiida-quantumespresso/commit/1e9c3454174807e115f48eb7667f928680a11dfc)]
* Add developer section to README [[146bc57](https://github.com/aiidateam/aiida-quantumespresso/commit/146bc57d74b76a11d7205a0f8449ae39c7675110)]

🔧 Maintenance

* DevOps: Symlink `CRASH` and `data-file.xml` files, and reduce fixture file contents [[0a48533](https://github.com/aiidateam/aiida-quantumespresso/commit/0a48533f40e276e5423428e0ca9745bd0b789121)]

⬆️ Update dependencies
* Symlink `CRASH` and `data-file.xml` files, and reduce fixture file contents [[0a48533](https://github.com/aiidateam/aiida-quantumespresso/commit/0a48533f40e276e5423428e0ca9745bd0b789121)]
* Devops: Update `pylint` version [[9f4142d](https://github.com/aiidateam/aiida-quantumespresso/commit/9f4142d4713b0d1c32042b3ca35905d725954bf4)]

♻️ Refactor
* Update `pylint` version [[9f4142d](https://github.com/aiidateam/aiida-quantumespresso/commit/9f4142d4713b0d1c32042b3ca35905d725954bf4)]

4.2.0

Features
- Add the `XspectraBaseWorkChain` [[854]](https://github.com/aiidateam/aiida-quantumespresso/pull/854)
- Add the `XspectraCoreWorkChain` [[872]](https://github.com/aiidateam/aiida-quantumespresso/pull/872)

Changes
- Protocols: Use v1.2 of SSSP and PBEsol by default for pw.x protocols [[884]](https://github.com/aiidateam/aiida-quantumespresso/pull/884)

Fixes
- `PwBandsWorkChain`: Fix `nbnd` for spin-polarised calculations [[875]](https://github.com/aiidateam/aiida-quantumespresso/pull/875)

Dependencies
- Update requirement `aiida-pseudo~=1.0` [[882]](https://github.com/aiidateam/aiida-quantumespresso/pull/882)
- Update pre-commit requirement `isort==5.12.0` [[883]](https://github.com/aiidateam/aiida-quantumespresso/pull/883)

Devops
- Fix nightly build tests [[870]](https://github.com/aiidateam/aiida-quantumespresso/pull/870)

Documentation
- Add various `settings` parameters for `PwCalculation` [[869]](https://github.com/aiidateam/aiida-quantumespresso/pull/869)

4.1.0

New

- Add the `options` argument to all `get_builder_from_protocol` [[846]](https://github.com/aiidateam/aiida-quantumespresso/pull/846)
- `XspectraParser`: Parse parameters from `CalcJob` inputs [[853]](https://github.com/aiidateam/aiida-quantumespresso/pull/853)

Fixes

- `XspectraCalculation`/`XspectraParser`: various improvements and fixes [[837]](https://github.com/aiidateam/aiida-quantumespresso/pull/837)
- CLI: update to be compatible with `aiida-core==2.1` [[855]](https://github.com/aiidateam/aiida-quantumespresso/pull/855)
- Fix bug in `wrap_bare_dict_inputs` [[860]](https://github.com/aiidateam/aiida-quantumespresso/pull/860)
- `PwBaseWorkChain`: Fix kpoints override in `get_builder_from_protocol` [[862]](https://github.com/aiidateam/aiida-quantumespresso/pull/862)
- `BasePwCpInputGenerator`: do not require pseudos in `validate_inputs` [[866]](https://github.com/aiidateam/aiida-quantumespresso/pull/866)
- `PwBaseWorkChain`: Set `restart_mode` in `parameters` if `parent_folder` [[867]](https://github.com/aiidateam/aiida-quantumespresso/pull/867)

Deprecation

- Remove obsolete and broken TCOD related code [[850]](https://github.com/aiidateam/aiida-quantumespresso/pull/850)

Devops

- DevOps: Add a job with integration tests to the CI workflow

Dependencies

- Dependencies: Add support for Python 3.11 [[857]](https://github.com/aiidateam/aiida-quantumespresso/pull/857)

4.0.1

Fixes
- `PwCalculation/PhCalculation`: Add validation for `pseudos` port [[839]](https://github.com/aiidateam/aiida-quantumespresso/pull/839)
- `Q2rParser`: Set `filename` for `force_constants` [[827]](https://github.com/aiidateam/aiida-quantumespresso/pull/827)
- Docs: Update the `Get Started` example for `PhCalculation` [[829]](https://github.com/aiidateam/aiida-quantumespresso/pull/829)
- DevOps: Add `AIIDA_WARN_V3` environment variable to CI and address all deprecation warnings [[836]](https://github.com/aiidateam/aiida-quantumespresso/pull/836)

Dependencies
- Add lower requirement `aiida-core>=2.0.4`, fixes error in `NamelistCalculation` restarting from `FolderData` [[841]](https://github.com/aiidateam/aiida-quantumespresso/pull/841)

4.0.0

This major release mainly provides support for `aiida-core` v2.0, as well as the `xspectra.x` code of Quantum ESPRESSO.
Version 7.1 of Quantum ESPRESSO is also now supported.
Note that in line with our new [compatibility policy](https://github.com/aiidateam/aiida-quantumespresso#compatibility-matrix), from this major version onwards we will no longer be supporting Quantum ESPRESSO versions below v6.6.

New

- `PhBaseWorkChain`: Add a first draft for the protocols [[810]](https://github.com/aiidateam/aiida-quantumespresso/pull/810)
- Add the `XspectraCalculation` and `XspectraParser` plugins [[815]](https://github.com/aiidateam/aiida-quantumespresso/pull/815)

Improvements

- `PwCalculation`: allow regex patterns in detect_important_message [[771]](https://github.com/aiidateam/aiida-quantumespresso/pull/771)
- Parsers: add exception title to `ERROR_UNEXPECTED_PARSER_EXCEPTION` [[793]](https://github.com/aiidateam/aiida-quantumespresso/pull/793)
- `CalcJob`: simplify `parent_folder` handling [[805]](https://github.com/aiidateam/aiida-quantumespresso/pull/805)
- `MatDynCalculation`: use validator to check `flfrc` input [[814]](https://github.com/aiidateam/aiida-quantumespresso/pull/814)
- `CpParser`: add stresses and fix for QE v7.0 [[786]](https://github.com/aiidateam/aiida-quantumespresso/pull/786)
- `PwParser`: Add support for QE v7.1 [[822]](https://github.com/aiidateam/aiida-quantumespresso/pull/822)

Bug Fixes

- `PhCalculation`: Fix bug when `only_initialization=True` [[813]](https://github.com/aiidateam/aiida-quantumespresso/pull/813)

Devops

- Devops: fix the nightly build [[784]](https://github.com/aiidateam/aiida-quantumespresso/pull/784)
- DevOps: Move the source directory into `src/` [[812]](https://github.com/aiidateam/aiida-quantumespresso/pull/812)
- DevOps: update nightly to show as failed on error [[817]](https://github.com/aiidateam/aiida-quantumespresso/pull/817)
- DevOps: only run Slack notification if tests failed [[819]](https://github.com/aiidateam/aiida-quantumespresso/pull/819)
- DevOps: address deprecation warnings [[820]](https://github.com/aiidateam/aiida-quantumespresso/pull/820)

Dependencies

- Dependencies: put upper limit markupsafe<2.1 [[790]](https://github.com/aiidateam/aiida-quantumespresso/pull/790)
- Dependencies: Update Python requirements [[803]](https://github.com/aiidateam/aiida-quantumespresso/pull/803)
- Dependencies: Update requirement for `aiida-core~=2.0` [[804]](https://github.com/aiidateam/aiida-quantumespresso/pull/804)
- Refactor: Additional compatibility for `aiida-core` v2.0 [[806]](https://github.com/aiidateam/aiida-quantumespresso/pull/806)
- Remove the use of deprecated distutils package [[808]](https://github.com/aiidateam/aiida-quantumespresso/pull/808)

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