diff --git a/.github/workflows/pip_install_test.yml b/.github/workflows/pip_install_test.yml index 5ae629c3..c556a88b 100644 --- a/.github/workflows/pip_install_test.yml +++ b/.github/workflows/pip_install_test.yml @@ -9,18 +9,18 @@ on: workflow_dispatch: jobs: - build-linux: - runs-on: ubuntu-latest + build: if: ${{ github.event_name == 'workflow_dispatch' || (github.event_name == 'workflow_run' && github.event.workflow_run.conclusion == 'success') }} # only run when tests have passed (or manually triggered) strategy: - max-parallel: 5 + fail-fast: false matrix: - python-version: ['3.8', '3.9', '3.10', '3.11'] + python-version: [ '3.8', '3.9', '3.10', '3.11' ] + os: [ ubuntu-latest,macos-latest,windows-latest ] - name: Python ${{ matrix.python-version }} pip install + runs-on: ${{matrix.os}} steps: - uses: actions/checkout@v2 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 2487c66f..45a8a715 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -12,16 +12,15 @@ on: workflow_dispatch: jobs: - build-linux: - runs-on: ubuntu-latest + build: strategy: - max-parallel: 5 + fail-fast: false matrix: python-version: ['3.8', '3.9', '3.10', '3.11'] + os: [ubuntu-latest,macos-latest,windows-latest] - name: Python ${{ matrix.python-version }} Test Pop - + runs-on: ${{matrix.os}} steps: - uses: actions/checkout@v2 diff --git a/CHANGELOG.rst b/CHANGELOG.rst index aac81250..b4655e05 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,6 +1,15 @@ Change Log ========== +v3.2.3 +---------- +- Ensure the sorted `pymatgen` `Structure` is created for the VASP input (fixes a rare bug in `v3.2.1` + and `v3.2.2` where for certain structures the order of elements in the POSCAR was not properly sorted, + which is usually fine, but messed with the `ROPT` `INCAR` setting). +- Plotting format updates (make legend frame more transparent to make datapoints behind it easier to see). +- Update tests +- Update docs (note about handling AFM systems) + v3.2.2 ---------- - Consolidate ``SnB``/``doped`` ``INCAR`` defaults and remove redundant settings. diff --git a/README.md b/README.md index 73a00ed4..90cd782a 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![Build status](https://github.com/SMTG-UCL/ShakeNBreak/actions/workflows/test.yml/badge.svg)](https://github.com/SMTG-UCL/ShakeNBreak/actions) +[![Build status](https://github.com/SMTG-Bham/ShakeNBreak/actions/workflows/test.yml/badge.svg)](https://github.com/SMTG-Bham/ShakeNBreak/actions) [![Documentation Status](https://readthedocs.org/projects/shakenbreak/badge/?version=latest&style=flat)](https://shakenbreak.readthedocs.io/en/latest/) [![JOSS](https://joss.theoj.org/papers/10.21105/joss.04817/status.svg)](https://doi.org/10.21105/joss.04817) [![PyPI](https://img.shields.io/pypi/v/shakenbreak)](https://pypi.org/project/shakenbreak) @@ -7,7 +7,7 @@ [![npj](https://img.shields.io/badge/npj%20Comput%20Mater%20-Mosquera--Lois%2C%20I.%2C%20Kavanagh%2C%20S.R.%2C%20Walsh%2C%20A.%20%26%20Scanlon%2C%20D.O.%20--%202023-9cf)](https://www.nature.com/articles/s41524-023-00973-1) # `ShakeNBreak` (`SnB`) - `ShakeNBreak` is a defect structure-searching method employing chemically-guided bond distortions to + `ShakeNBreak` is a defect structure-searching method employing chemically-guided bond distortions to locate ground-state and metastable structures of point defects in solid materials. [Docs here!](https://shakenbreak.readthedocs.io/en/latest/) Main features include: @@ -22,7 +22,7 @@ Main features include: The code currently supports `VASP`, `CP2K`, `Quantum-Espresso`, `CASTEP` & `FHI-aims`. Code contributions to support additional solid-state packages are welcome. -![ShakeNBreak Summary](https://raw.githubusercontent.com/SMTG-UCL/ShakeNBreak/main/docs/SnB_Supercell_Schematic_PES_2sec_Compressed.gif) +![ShakeNBreak Summary](https://raw.githubusercontent.com/SMTG-Bham/ShakeNBreak/main/docs/SnB_Supercell_Schematic_PES_2sec_Compressed.gif) ### Literature - Preview: Mosquera-Lois, I.; Kavanagh, S. R. [In Search of Hidden Defects](https://doi.org/10.1016/j.matt.2021.06.003), _Matter_ 4 (8), 2602-2605, **2021** @@ -56,7 +56,7 @@ For development work, ShakeNBreak can also be installed from a copy of the sourc 1. Download `ShakeNBreak` source code using the command: ```bash - git clone https://github.com/SMTG-UCL/ShakeNBreak + git clone https://github.com/SMTG-Bham/ShakeNBreak ``` 2. Navigate to root directory: ```bash @@ -76,7 +76,7 @@ For development work, ShakeNBreak can also be installed from a copy of the sourc ### Command line interface Alternatively, the code can be used via the command line: -![ShakeNBreak CLI](https://raw.githubusercontent.com/SMTG-UCL/ShakeNBreak/main/docs/SnB_CLI.gif) +![ShakeNBreak CLI](https://raw.githubusercontent.com/SMTG-Bham/ShakeNBreak/main/docs/SnB_CLI.gif) The functions provided include: * [`snb-generate`](https://shakenbreak.readthedocs.io/en/latest/shakenbreak.cli.html#snb-generate): Generate distorted structures for a given defect @@ -111,7 +111,7 @@ Please let us know if you have any issues with compatibility, or if you would li ## Contributing ### Bugs reports, feature requests and questions -Please use the [Issue Tracker](https://github.com/SMTG-UCL/ShakeNBreak/issues) to report bugs or request new features. +Please use the [Issue Tracker](https://github.com/SMTG-Bham/ShakeNBreak/issues) to report bugs or request new features. Contributions to extend this package are very welcome! Please use the ["Fork and Pull"](https://docs.github.com/en/get-started/quickstart/contributing-to-projects) @@ -128,9 +128,11 @@ Automatic testing is run on the master and develop branches using Github Actions ## Studies using `ShakeNBreak` We'll add papers that use `ShakeNBreak` to this list as they come out! + +- X. Wang et al. [_Physical Review B_](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134102) 2023 +- Y. Kumagai, S. R. Kavanagh et al [_PRX Energy_](http://dx.doi.org/10.1103/PRXEnergy.2.043002) 2023 - J. Willis, K. B. Spooner, D. O. Scanlon. [_ChemRxiv_](https://chemrxiv.org/engage/chemrxiv/article-details/64c29140ce23211b20a787bb) 2023 - A. T. J. Nicolson et al. [_Journal of Materials Chemistry A_](https://doi.org/10.1039/D3TA02429F) 2023 -- X. Wang et al. [_arXiv_](https://arxiv.org/abs/2302.04901) 2023 - J. Cen et al. [_Journal of Materials Chemistry A_](https://doi.org/10.1039/D3TA00532A) 2023 - J. Willis & R. Claes et al. [_ChemRxiv_](https://doi.org/10.26434/chemrxiv-2023-lttnf) 2023 - I. Mosquera-Lois & S. R. Kavanagh, A. Walsh, D. O. Scanlon [_npj Computational Materials_](https://doi.org/10.1038/s41524-023-00973-1) 2023 diff --git a/docs/Analysis.rst b/docs/Analysis.rst index d2d4677d..d176f806 100644 --- a/docs/Analysis.rst +++ b/docs/Analysis.rst @@ -246,7 +246,7 @@ manually (not recommended) or using the other defect codes listed on the As shown in the `doped `_ tutorials and docs, you may want to further analyse the behaviour and impact on material properties of your defects using advanced -defect analysis codes such as `easyunfold `_ (to analyse the +defect analysis codes such as `easyunfold `_ (to analyse the electronic structure of defects in your material), `py-sc-fermi `_ (to analyse defect concentrations, doping and Fermi level tuning), or `nonrad `_ / diff --git a/docs/Contributing.rst b/docs/Contributing.rst index b278e008..6c6dca13 100644 --- a/docs/Contributing.rst +++ b/docs/Contributing.rst @@ -4,7 +4,7 @@ Contributing Bugs reports, feature requests and questions --------------------------------------------- -Please use the `Issue Tracker `_ to report bugs or +Please use the `Issue Tracker `_ to report bugs or request new features. Contributions to extend this package are welcome! Please use the `Fork and Pull `_ workflow to do so and follow the `PEP8 `_ style guidelines. @@ -49,7 +49,7 @@ workflow to do so and follow the `PEP8 `_ sty Tests ------- -Unit tests are in the `tests `_ directory +Unit tests are in the `tests `_ directory and can be run from the top directory using ``unittest``. Automatic testing is run on the master and develop branches using `Github Actions `_. Please run tests and add new tests for any new features whenever submitting pull requests. diff --git a/docs/Generation.rst b/docs/Generation.rst index 1c2447a6..3e0943e8 100644 --- a/docs/Generation.rst +++ b/docs/Generation.rst @@ -32,7 +32,7 @@ we'll get a warning and we'll need to specify the defect site with the ``--defec .. NOTE:: To specify additional distortion parameters, we can use a - `config.yaml `_ + `config.yaml `_ file like the one below and use the ``--config`` flag to specify its path (i.e. ``snb-generate --config ./my_config.yaml``). A detailed description of all the parameters is available in the Python API section (:ref:`shakenbreak.input.Distortions class `). @@ -122,7 +122,7 @@ the following directory structures will be parsed correctly: .. NOTE:: To specify the charge state range for each defect, as well as other optional arguments, we can use a - `config.yaml `_ file + `config.yaml `_ file like the one below. A detailed description of all the parameters is available in the Python API section (:ref:`shakenbreak.input.Distortions class `). diff --git a/docs/Installation.rst b/docs/Installation.rst index a1b14d79..15bdaa51 100644 --- a/docs/Installation.rst +++ b/docs/Installation.rst @@ -41,7 +41,7 @@ For development work, ``ShakeNBreak`` can also be installed from a copy of the s .. code:: bash - git clone https://github.com/SMTG-UCL/ShakeNBreak + git clone https://github.com/SMTG-Bham/ShakeNBreak 2. Navigate to root directory: diff --git a/docs/ShakeNBreak_Example_Workflow.ipynb b/docs/ShakeNBreak_Example_Workflow.ipynb index 589c22e1..f406c968 100644 --- a/docs/ShakeNBreak_Example_Workflow.ipynb +++ b/docs/ShakeNBreak_Example_Workflow.ipynb @@ -4096,7 +4096,7 @@ "### Further Defect Analysis\n", "Once the ground state (and metastable) defect structures have been identified, we will want to compute their formation energies using our final fully-converged calculation parameters (i.e. plane-wave cutoff and k-point sampling). This can be done using [`doped`](https://doped.readthedocs.io/en/latest/), manually (not recommended) or using the other defect codes listed on the [Code Compatibility](https://shakenbreak.readthedocs.io/en/latest/Code_Compatibility.html) page.\n", "\n", - "As shown in the [`doped`](https://doped.readthedocs.io/en/latest/) examples and docs, you may want to further analyse the behaviour and impact on material properties of your defects using advanced defect analysis codes such as [`easyunfold`](https://smtg-ucl.github.io/easyunfold/) (to analyse the electronic structure of defects in your material), [`py-sc-fermi`](https://py-sc-fermi.readthedocs.io/en/latest/) (to analyse defect concentrations, doping and Fermi level tuning), or [`nonrad`](https://nonrad.readthedocs.io/en/latest/)/[`CarrierCapture.jl`](https://wmd-group.github.io/CarrierCapture.jl/dev/) (to analyse non-radiative electron-hole recombination at defects)." + "As shown in the [`doped`](https://doped.readthedocs.io/en/latest/) examples and docs, you may want to further analyse the behaviour and impact on material properties of your defects using advanced defect analysis codes such as [`easyunfold`](https://smtg-bham.github.io/easyunfold/) (to analyse the electronic structure of defects in your material), [`py-sc-fermi`](https://py-sc-fermi.readthedocs.io/en/latest/) (to analyse defect concentrations, doping and Fermi level tuning), or [`nonrad`](https://nonrad.readthedocs.io/en/latest/)/[`CarrierCapture.jl`](https://wmd-group.github.io/CarrierCapture.jl/dev/) (to analyse non-radiative electron-hole recombination at defects)." ] }, { diff --git a/docs/Tips.rst b/docs/Tips.rst index ed3ec696..dc54b97f 100644 --- a/docs/Tips.rst +++ b/docs/Tips.rst @@ -84,10 +84,33 @@ to: specified element (see next section). - Specify the total magnetic moment (``NUPDOWN`` in ``VASP``). We recommend to use a wider distortion mesh - (``delta = 0.2``) and run main ``NUPDOWN`` possibilities, e.g. if there are two extra/missing electrons run - ``NUPDOWN = 0`` (anti-parallel arrangement) and ``NUPDOWN = 2`` (parallel arrangement). + (``delta = 0.2``) and test the main ``NUPDOWN`` possibilities, e.g. if there are two extra/missing + electrons, trial ``NUPDOWN = 0`` (anti-parallel arrangement) and ``NUPDOWN = 2`` (parallel arrangement). -:code:`neighbour_elements` Use Cases +Magnetism +--------- + +If your host system is magnetic (e.g. (anti-)ferromagnetic), you should initialise the magnetic moments +(i.e. set the ``MAGMOM`` values in the ``INCAR`` files using ``user_incar_settings`` in +``Distortions.write_vasp_files()``) to match this. + +In these cases, the defect ground-state often involves a polaronic localisation which alters the local +magnetic moment(s). +Often the defect formation breaks the (magnetic) symmetry of the host, and so the choice of spin up/down +for an *anti-ferromagnetic* (AFM) system is no longer arbitrary within a ``VASP`` calculation, as the +initialisation favours spin-up as the majority spin of the system (by only allowing positive ``NUPDOWN`` +values). To account for this magnetic symmetry-breaking and thus differing localisation solutions for +different choices of AFM orderings, it is recommended to test both equivalent\ :sup:`‡` AFM orderings for +each potential polaronic defect state (i.e. when ``NUPDOWN`` is not zero). +This can be done by 'flipping' the ``MAGMOM`` values (to flip the AFM ordering) by changing the sign of +each ``MAGMOM`` value for the supercell. If doing this, it is recommended to use a wider distortion mesh +(``delta = 0.2``) to reduce the number of calculations required, as the testing of both AFM orderings +should allow sufficient coverage of the defect PES with this reduced sampling. + +:sup:`‡` = equivalent for the pristine host system, but not for the defect supercell with ``NUPDOWN`` ≠ 0. + + +``neighbour_elements`` Use Cases ------------------------------------- When generating atomic distortions with :code:`ShakeNBreak`, the :code:`neighbour_elements` optional parameter can be diff --git a/docs/conf.py b/docs/conf.py index d59de5c2..b4a09424 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -25,7 +25,7 @@ author = 'Irea Mosquera-Lois, Seán R. Kavanagh' # The full version, including alpha/beta/rc tags -release = '3.2.2' +release = '3.2.3' # -- General configuration --------------------------------------------------- @@ -89,7 +89,7 @@ # html_show_sphinx = True html_theme_options = { - "repository_url": "https://github.com/SMTG-UCL/ShakeNBreak", + "repository_url": "https://github.com/SMTG-Bham/ShakeNBreak", "repository_branch": "develop", "path_to_docs": "docs", "use_repository_button": True, @@ -99,7 +99,7 @@ # Adding “Edit Source” links on your Sphinx theme html_context = { "display_github": True, # Integrate GitHub - "github_user": "SMTG-UCL", # Username + "github_user": "SMTG-Bham", # Username "github_repo": "ShakeNBreak", # Repo name "github_version": "master", # Version "conf_py_path": "/docs/", # Path in the checkout to the docs root diff --git a/docs/docs_requirements.txt b/docs/docs_requirements.txt index 121b51f6..969029b5 100644 --- a/docs/docs_requirements.txt +++ b/docs/docs_requirements.txt @@ -1,4 +1,5 @@ sphinx +recommonmark myst-nb sphinx-book-theme sphinx_click @@ -7,7 +8,7 @@ numpy>=1.21 # needed for numpy.typing.NDArray pymatgen>2022.0.17 #==2022.10.22 pymatgen-analysis-defects #>=2022.10.28 ase -matplotlib +matplotlib>=3.6 pandas>=1.1.0 seaborn hiphive diff --git a/docs/index.rst b/docs/index.rst index c038136d..33b11b81 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -3,8 +3,8 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -.. image:: https://github.com/SMTG-UCL/ShakeNBreak/actions/workflows/test.yml/badge.svg - :target: https://github.com/SMTG-UCL/ShakeNBreak/actions +.. image:: https://github.com/SMTG-Bham/ShakeNBreak/actions/workflows/test.yml/badge.svg + :target: https://github.com/SMTG-Bham/ShakeNBreak/actions .. image:: https://readthedocs.org/projects/shakenbreak/badge/?version=latest&style=flat :target: https://shakenbreak.readthedocs.io/en/latest/ @@ -106,7 +106,7 @@ For development work, ``ShakeNBreak`` can also be installed from a copy of the s .. code:: bash - git clone https://github.com/SMTG-UCL/ShakeNBreak + git clone https://github.com/SMTG-Bham/ShakeNBreak 2. Navigate to root directory: @@ -191,7 +191,7 @@ Contributing Bugs reports, feature requests and questions ---------------------------------------------- -Please use the `Issue Tracker `_ +Please use the `Issue Tracker `_ to report bugs or request new features. Contributions to extend this package are very welcome! Please use the @@ -213,9 +213,10 @@ Studies using ``ShakeNBreak`` We'll add papers that use `ShakeNBreak` to this list as they come out! +- X\. Wang et al. `Physical Review B `_ 2023 +- Y\. Kumagai, S. R. Kavanagh et al. `PRX Energy `__ 2023 - J\. Willis, K. B. Spooner, D. O. Scanlon. `ChemRxiv `__ 2023 - A\. T. J. Nicolson et al. `Journal of Materials Chemistry A `__ 2023 -- X\. Wang et al. `arXiv`_ 2023 - J\. Cen et al. `Journal of Materials Chemistry A`_ 2023 - J\. Willis & R. Claes et al. `ChemRxiv `__ 2023 - I\. Mosquera-Lois & S. R. Kavanagh, A. Walsh, D. O. Scanlon `npj Computational Materials`_ 2023 @@ -234,7 +235,6 @@ We'll add papers that use `ShakeNBreak` to this list as they come out! .. Kat YTOS .. Squires (and mention benchmark test against AIRSS? See Slack message) -.. _arXiv: https://arxiv.org/abs/2302.04901 .. _Journal of Materials Chemistry A: https://doi.org/10.1039/D3TA00532A .. _npj Computational Materials: https://www.nature.com/articles/s41524-023-00973-1 .. _Nature Communications: https://www.nature.com/articles/s41467-022-32669-3 @@ -257,7 +257,7 @@ You may also find this Preview paper useful, which discusses the general problem - Mosquera-Lois, I.; Kavanagh, S. R. `In Search of Hidden Defects`_. *Matter* 4 (8), 2602-2605, **2021** -``BibTeX`` entries for these papers are provided in the repository `CITATIONS.md `_ file. +``BibTeX`` entries for these papers are provided in the repository `CITATIONS.md `_ file. .. _ShakeNBreak\: Navigating the defect configurational landscape: https://doi.org/10.21105/joss.04817 .. _Journal of Open Source Software: https://doi.org/10.21105/joss.04817 @@ -298,4 +298,4 @@ Requirements Code_Compatibility Contributing changelog_link - ShakeNBreak on GitHub \ No newline at end of file + ShakeNBreak on GitHub \ No newline at end of file diff --git a/setup.py b/setup.py index d2138bae..5247c8ce 100644 --- a/setup.py +++ b/setup.py @@ -130,7 +130,7 @@ def package_files(directory): setup( name="shakenbreak", - version="3.2.2", + version="3.2.3", description="Package to generate and analyse distorted defect structures, in order to " "identify ground-state and metastable defect configurations.", long_description=long_description, @@ -163,7 +163,7 @@ def package_files(directory): "numpy", # >=1.21.2" needed for numpy.typing.NDArray? "pymatgen>=2022.10.22", "pymatgen-analysis-defects>=2022.10.28", - "matplotlib", + "matplotlib>=3.6", "ase", "pandas>=1.1.0", "seaborn", @@ -228,7 +228,7 @@ def package_files(directory): "Homepage": "https://shakenbreak.readthedocs.io/en/latest/index.html", "Documentation": "https://shakenbreak.readthedocs.io/en/latest/index.html", "Package": "https://pypi.org/project/shakenbreak/", - "Repository": "https://github.com/SMTG-UCL/shakenbreak", + "Repository": "https://github.com/SMTG-Bham/shakenbreak", }, ) diff --git a/shakenbreak/analysis.py b/shakenbreak/analysis.py index 0a5623e0..7c59adf4 100644 --- a/shakenbreak/analysis.py +++ b/shakenbreak/analysis.py @@ -801,7 +801,7 @@ def compare_structures( Minimum atomic displacement threshold to include in atomic displacements sum (in Å, default 0.1 Å). display_df (:obj:`bool`): - Whether or not to display the structure comparison DataFrame + Whether to display the structure comparison DataFrame interactively in Jupyter/Ipython (Default: True). verbose (:obj:`bool`): Whether to print information message about structures being compared. diff --git a/shakenbreak/input.py b/shakenbreak/input.py index ba93654b..33625b70 100755 --- a/shakenbreak/input.py +++ b/shakenbreak/input.py @@ -203,8 +203,8 @@ def _create_vasp_input( Dictionary of user VASP INCAR settings, to overwrite/update the `doped` defaults. user_potcar_functional (str): - POTCAR functional to use. Default is "PBE" and if this fails, - tries "PBE_52", then "PBE_54". + POTCAR functional to use. Default is "PBE" and if this fails, + tries "PBE_52", then "PBE_54". user_potcar_settings (:obj:`dict`): Dictionary of user VASP POTCAR settings, to overwrite/update the `doped` defaults (e.g. {'Fe': 'Fe_pv', 'O': 'O'}}). Highly @@ -256,31 +256,47 @@ def _create_vasp_input( if matching_dirs: # defect species with same name already present # check if Unperturbed structures match - match_found = False + + match_found = True + for dir in matching_dirs: - with contextlib.suppress( - Exception - ): # if Unperturbed structure could not be parsed / - # compared to distorted_defect_dict, then pass - prev_unperturbed_struc = Structure.from_file( - f"{output_path}/{dir}/Unperturbed/POSCAR" - ) - current_unperturbed_struc = distorted_defect_dict["Unperturbed"][ - "Defect Structure" - ].copy() - for i in [prev_unperturbed_struc, current_unperturbed_struc]: - i.remove_oxidation_states() - if prev_unperturbed_struc == current_unperturbed_struc: - warnings.warn( - f"The previously-generated defect folder {dir} in " - f"{os.path.basename(os.path.abspath(output_path))} " - f"has the same Unperturbed defect structure as the current " - f"defect species: {defect_name}. ShakeNBreak files in {dir} will " - f"be overwritten." + if any( + x in i + for i in os.listdir(dir) + for x in ["Unperturbed", "Rattled", "Bond_Distortion"] + ): + # if any SnB folder found in matching_dirs, then we need to check if structures match, + # otherwise we can write to this same folder + match_found = False + break + + if ( + not match_found + ): # SnB folders in matching_dirs, so check if Unperturbed structures match + for dir in matching_dirs: + with contextlib.suppress( + Exception + ): # if Unperturbed structure could not be parsed / + # compared to distorted_defect_dict, then pass + prev_unperturbed_struc = Structure.from_file( + f"{output_path}/{dir}/Unperturbed/POSCAR" ) - defect_name = dir - match_found = True - break + current_unperturbed_struc = distorted_defect_dict["Unperturbed"][ + "Defect Structure" + ].copy() + for i in [prev_unperturbed_struc, current_unperturbed_struc]: + i.remove_oxidation_states() + if prev_unperturbed_struc == current_unperturbed_struc: + warnings.warn( + f"The previously-generated defect distortions folder {dir} in " + f"{os.path.basename(os.path.abspath(output_path))} " + f"has the same Unperturbed defect structure as the current " + f"defect species: {defect_name}. ShakeNBreak files in {dir} will " + f"be overwritten." + ) + defect_name = dir + match_found = True + break if not match_found: # no matching structure found, assume inequivalent defects last_letter = [ @@ -304,7 +320,7 @@ def _create_vasp_input( f"{charge_state}" ) warnings.warn( - f"A previously-generated defect folder {prev_dir_name} exists in " + f"A previously-generated defect distortions folder {prev_dir_name} exists in " f"{os.path.basename(os.path.abspath(output_path))}, " f"and the Unperturbed defect structure could not be matched to the " f"current defect species: {defect_name}. These are assumed to be " @@ -324,7 +340,7 @@ def _create_vasp_input( f"_{'+' if charge_state > 0 else ''}{charge_state}" ) warnings.warn( - f"Previously-generated defect folders ({prev_dir_name}...) exist in " + f"Previously-generated defect distortions folders ({prev_dir_name}...) exist in " f"{os.path.basename(os.path.abspath(output_path))}, " f"and the Unperturbed defect structures could not be matched to the " f"current defect species: {defect_name}. These are assumed to be " @@ -362,10 +378,10 @@ def _create_vasp_input( for ( distortion, single_defect_dict, - ) in ( - distorted_defect_dict.items() - ): # for each distortion, create sub-subfolder folder - dds._structure = single_defect_dict["Defect Structure"] + ) in distorted_defect_dict.items(): # for each distortion, create subfolder + dds._structure = single_defect_dict[ + "Defect Structure" + ].get_sorted_structure() # ensure sorted dds.poscar_comment = single_defect_dict.get("POSCAR Comment", None) try: @@ -1157,45 +1173,64 @@ def _get_defects_dict_from_defects_entries(defect_entries): """ Return a dictionary in the SnB format: {"defect_name_wout_charge": [DefectEntry, ...]} for the given defect_entries list. + + If the DefectEntry.name attribute is set for all DefectEntrys in defect_entries, + then these are used to obtain 'defect_name_wout_charge', otherwise the names are + set to the default doped defect names. """ - # defect_entries is a list of DefectEntry objects which likely has duplicate DefectEntry's of the - # same type but different charge state. So get list of included charge states for each - # DefectEntry.defect base name: - charge_state_dict = { - defect_entry.defect.name: [ - entry.charge_state - for entry in defect_entries - if entry.defect.name == defect_entry.defect.name - ] - for defect_entry in defect_entries - } + # check if all defect_entries have a name attribute set: + if all(getattr(defect_entry, "name", False) for defect_entry in defect_entries): + snb_defects_dict = { + defect_entry.name.rsplit("_", 1)[0]: [ # defect names without charge + def_entry + for def_entry in defect_entries + if def_entry.name.rsplit("_", 1)[0] + == defect_entry.name.rsplit("_", 1)[0] + ] + for defect_entry in defect_entries + } - # subselect defect_entries to those with a unique defect.defect_structure to avoid duplicates: - sm = StructureMatcher() - defect_entry_list = [] - for defect_entry in defect_entries: - if not any( - sm.fit(defect_entry.defect.defect_structure, entry.defect.defect_structure) - for entry in defect_entry_list - ): - # ensure sc_defect_frac_coords defined: - _find_sc_defect_coords(defect_entry) - defect_entry_list.append(defect_entry) - - defect_entries_dict = name_defect_entries( - defect_entry_list - ) # DefectsGenerator.defect_entries - # format: {"defect_species": DefectEntry} -> convert: - snb_defects_dict = { - defect_entry_name_wout_charge: [] - for defect_entry_name_wout_charge in defect_entries_dict - } + else: + # defect_entries is a list of DefectEntry objects which likely has duplicate DefectEntry's of the + # same type but different charge state. So get list of included charge states for each + # DefectEntry.defect base name: + charge_state_dict = { + defect_entry.defect.name: [ + entry.charge_state + for entry in defect_entries + if entry.defect.name == defect_entry.defect.name + ] + for defect_entry in defect_entries + } + + # sub-select defect_entries to those with a unique defect.defect_structure to avoid duplicates: + sm = StructureMatcher() + defect_entry_list = [] + for defect_entry in defect_entries: + if not any( + sm.fit( + defect_entry.defect.defect_structure, entry.defect.defect_structure + ) + for entry in defect_entry_list + ): + # ensure sc_defect_frac_coords defined: + _find_sc_defect_coords(defect_entry) + defect_entry_list.append(defect_entry) + + defect_entries_dict = name_defect_entries( + defect_entry_list + ) # DefectsGenerator.defect_entries + # format: {"defect_species": DefectEntry} -> convert: + snb_defects_dict = { + defect_entry_name_wout_charge: [] + for defect_entry_name_wout_charge in defect_entries_dict + } - for name_wout_charge, defect_entry in defect_entries_dict.items(): - for charge in charge_state_dict[defect_entry.defect.name]: - charged_defect_entry = copy.deepcopy(defect_entry) - charged_defect_entry.charge_state = charge - snb_defects_dict[name_wout_charge].append(charged_defect_entry) + for name_wout_charge, defect_entry in defect_entries_dict.items(): + for charge in charge_state_dict[defect_entry.defect.name]: + charged_defect_entry = copy.deepcopy(defect_entry) + charged_defect_entry.charge_state = charge + snb_defects_dict[name_wout_charge].append(charged_defect_entry) return snb_defects_dict @@ -1590,7 +1625,8 @@ def __init__( set equal to `defect_species` (with charge states included). If a list or single `DefectEntry` object is provided, the defect folder names will be set equal to `DefectEntry.name` if the `name` - attribute is set, otherwise generated according to the `doped` convention + attribute is set for all input `DefectEntry`s, otherwise generated + according to the `doped` convention (see: https://doped.readthedocs.io/en/latest/dope_workflow_example.html). Defect charge states (from which bond distortions are determined) are @@ -2270,7 +2306,7 @@ def apply_distortions( **self._mc_rattle_kwargs, ) - # Remove distortions with interatomic distances less than 1 Angstrom if Hydrogen + # Remove distortions with inter-atomic distances less than 1 Angstrom if Hydrogen # not present for dist, struct in list( defect_distorted_structures["distortions"].items() diff --git a/shakenbreak/plotting.py b/shakenbreak/plotting.py index 24eaa4ff..9bd0eb55 100644 --- a/shakenbreak/plotting.py +++ b/shakenbreak/plotting.py @@ -1436,7 +1436,9 @@ def plot_colorbar( handles = [(im, line_handle)] + handles labels = [line_label] + labels - plt.legend(handles, labels, scatteryoffsets=[0.5], frameon=True).set_zorder( + plt.legend( + handles, labels, scatteryoffsets=[0.5], frameon=True, framealpha=0.3 + ).set_zorder( 100 ) # make sure it's on top of the other points @@ -1544,16 +1546,15 @@ def plot_datasets( as a mpl.figure.Figure object """ # Validate input - if dataset_labels is not None: - if len(datasets) != len(dataset_labels): - raise ValueError( - f"Number of datasets and labels must match! " - f"You gave me {len(datasets)} datasets and" - f" {len(dataset_labels)} labels." - ) - else: + if dataset_labels is None: dataset_labels = ["Distortions"] * len(datasets) + elif len(datasets) != len(dataset_labels): + raise ValueError( + f"Number of datasets and labels must match! " + f"You gave me {len(datasets)} datasets and" + f" {len(dataset_labels)} labels." + ) _install_custom_font() # Set up figure with plt.style.context(f"{MODULE_DIR}/shakenbreak.mplstyle"): @@ -1654,10 +1655,9 @@ def plot_datasets( label="Rattled", ) - if ( - len(sorted_distortions) > 0 - and len([key for key in dataset["distortions"] if key != "Rattled"]) > 0 - ): # more than just Rattled + if len(sorted_distortions) > 0 and [ + key for key in dataset["distortions"] if key != "Rattled" + ]: # more than just Rattled if imported_indices: # Exclude datapoints from other charge states non_imported_sorted_indices = [ i @@ -1682,11 +1682,11 @@ def plot_datasets( if imported_indices: other_charges = len( - list( + [ list(dataset["distortions"].keys())[i].split("_")[-1] for i in imported_indices - ) - ) # number of other charge states whose distortions have been imported + ] # number of other charge states whose distortions have been imported + ) for i, j in zip(imported_indices, range(other_charges)): other_charge_state = int( list(dataset["distortions"].keys())[i].split("_")[-1] @@ -1766,17 +1766,17 @@ def plot_datasets( # If several datasets, check min & max energy are included if len(datasets) > 1: min_energy = min( - [min(list(dataset["distortions"].values())) for dataset in datasets] + min(list(dataset["distortions"].values())) for dataset in datasets ) max_energy = max( - [max(list(dataset["distortions"].values())) for dataset in datasets] + max(list(dataset["distortions"].values())) for dataset in datasets ) ax.set_ylim( min_energy - 0.1 * (max_energy - min_energy), max_energy + 0.1 * (max_energy - min_energy), ) - ax.legend(frameon=True).set_zorder( + ax.legend(frameon=True, framealpha=0.3).set_zorder( 100 ) # show legend on top of all other datapoints diff --git a/tests/__init__.py b/tests/__init__.py old mode 100755 new mode 100644 diff --git a/tests/data/Ag_Sb_Cs_Te2.90_-2.json b/tests/data/Ag_Sb_Cs_Te2.90_-2.json new file mode 100644 index 00000000..193b9b98 --- /dev/null +++ b/tests/data/Ag_Sb_Cs_Te2.90_-2.json @@ -0,0 +1 @@ +{"defect": {"@module": "doped.core", "@class": "Substitution", "structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0, "lattice": {"matrix": [[6.2637, -5.902343, 5.902343], [0.0, -3.01562, -3.01562], [6.28679, 5.914443, -5.914443]], "pbc": [true, true, true], "a": 10.435959154255922, "b": 4.264730702963553, "c": 10.46350804006945, "alpha": 90.0, "beta": 106.18615257482439, "gamma": 90.0, "volume": 447.2350678640466}, "properties": {}, "sites": [{"species": [{"element": "Ag", "occu": 1.0}], "abc": [0.74486, 0.0, 0.267088], "xyz": [6.344705749519999, -2.816742454996, 2.816742454996], "properties": {}, "label": "Ag"}, {"species": [{"element": "Ag", "occu": 1.0}], "abc": [0.492432, 0.0, 0.51769], "xyz": [6.3390546335, 0.15534542849400035, -0.15534542849400035], "properties": {}, "label": "Ag"}, {"species": [{"element": "Ag", "occu": 1.0}], "abc": [0.254265, 0.0, 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{"species": [{"element": "Te", "occu": 1.0}], "abc": [0.770366, 0.0, 0.745295], "xyz": [9.51085466725, -0.13895957185299954, 0.13895957185299954], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1.0}], "abc": [0.504096, 0.0, 0.98061], "xyz": [9.3223952571, 2.8244144533020004, -2.8244144533020004], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1.0}], "abc": [0.254273, 0.0, 0.241633], "xyz": [3.11178571817, -0.07168185622000021, 0.07168185622000021], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1.0}], "abc": [0.120607, 0.5, 0.871302], "xyz": [6.23313876648, 2.9335921325850003, -5.949212132585], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1.0}], "abc": [0.017267, 0.0, 0.504083], "xyz": [3.2772192714699995, 2.879454414188, -2.879454414188], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1.0}], "abc": [0.860954, 0.5, 0.133502], "xyz": [6.23205660838, 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{}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.0, 0.5, 0.0], "xyz": [0.0, 6.540652, 0.0], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.25, 0.7499999999999999, 0.0], "xyz": [3.270326, 9.810977999999999, 0.0], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.0, 0.25, 0.25], "xyz": [0.0, 3.270326, 3.270326], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.25, 0.5, 0.25], "xyz": [3.270326, 6.540652, 3.270326], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.5, 0.7499999999999999, 0.25], "xyz": [6.540652, 9.810977999999999, 3.270326], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.0, 0.0, 0.5], "xyz": [0.0, 0.0, 6.540652], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.25, 0.25, 0.5], "xyz": [3.270326, 3.270326, 6.540652], 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3.270326], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.0, 0.5, 0.5], "xyz": [0.0, 6.540652, 6.540652], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.25, 0.7499999999999999, 0.5], "xyz": [3.270326, 9.810977999999999, 6.540652], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.0, 0.25, 0.7499999999999999], "xyz": [0.0, 3.270326, 9.810977999999999], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.25, 0.5, 0.7499999999999999], "xyz": [3.270326, 6.540652, 9.810977999999999], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.5, 0.7499999999999999, 0.7499999999999999], "xyz": [6.540652, 9.810977999999999, 9.810977999999999], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.0, 0.7499999999999999, 0.7499999999999999], "xyz": [0.0, 9.810977999999999, 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0.37499999999999994, 0.625], "xyz": [11.446140999999999, 4.905488999999999, 8.175815], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.875, 0.125, 0.875], "xyz": [11.446140999999999, 1.635163, 11.446140999999999], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.125, 0.625, 0.125], "xyz": [1.635163, 8.175815, 1.635163], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.37499999999999994, 0.875, 0.125], "xyz": [4.905488999999999, 11.446140999999999, 1.635163], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.125, 0.37499999999999994, 0.37499999999999994], "xyz": [1.635163, 4.905488999999999, 4.905488999999999], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.37499999999999994, 0.625, 0.37499999999999994], "xyz": [4.905488999999999, 8.175815, 4.905488999999999], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.625, 0.875, 0.37499999999999994], "xyz": [8.175815, 11.446140999999999, 4.905488999999999], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.125, 0.125, 0.625], "xyz": [1.635163, 1.635163, 8.175815], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.37499999999999994, 0.37499999999999994, 0.625], "xyz": [4.905488999999999, 4.905488999999999, 8.175815], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.625, 0.625, 0.625], "xyz": [8.175815, 8.175815, 8.175815], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.875, 0.875, 0.625], "xyz": [11.446140999999999, 11.446140999999999, 8.175815], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.37499999999999994, 0.125, 0.875], "xyz": [4.905488999999999, 1.635163, 11.446140999999999], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.625, 0.37499999999999994, 0.875], "xyz": [8.175815, 4.905488999999999, 11.446140999999999], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.875, 0.625, 0.875], "xyz": [11.446140999999999, 8.175815, 11.446140999999999], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.125, 0.875, 0.37499999999999994], "xyz": [1.635163, 11.446140999999999, 4.905488999999999], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.125, 0.625, 0.625], "xyz": [1.635163, 8.175815, 8.175815], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.37499999999999994, 0.875, 0.625], "xyz": [4.905488999999999, 11.446140999999999, 8.175815], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.125, 0.37499999999999994, 0.875], "xyz": [1.635163, 4.905488999999999, 11.446140999999999], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.37499999999999994, 0.625, 0.875], "xyz": [4.905488999999999, 8.175815, 11.446140999999999], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.625, 0.875, 0.875], "xyz": [8.175815, 11.446140999999999, 11.446140999999999], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.125, 0.875, 0.875], "xyz": [1.635163, 11.446140999999999, 11.446140999999999], "properties": {}, "label": "Te"}], "@version": null}, "_element_list": ["Cd", "Te"], "conventional_structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0, "lattice": {"matrix": [[6.540652, 0.0, 0.0], [0.0, 6.540652, 0.0], [0.0, 0.0, 6.540652]], "pbc": [true, true, true], "a": 6.540652, "b": 6.540652, "c": 6.540652, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 279.8099335904176}, "properties": {}, "sites": [{"species": [{"element": "Cd", "occu": 1}], "abc": [0.0, 0.0, 0.0], "xyz": [0.0, 0.0, 0.0], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.0, 0.5, 0.5], "xyz": [0.0, 3.270326, 3.270326], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.5, 0.0, 0.5], "xyz": [3.270326, 0.0, 3.270326], "properties": {}, "label": "Cd"}, {"species": [{"element": "Cd", "occu": 1}], "abc": [0.5, 0.5, 0.0], "xyz": [3.270326, 3.270326, 0.0], "properties": {}, "label": "Cd"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.25, 0.25, 0.25], "xyz": [1.635163, 1.635163, 1.635163], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.25, 0.7499999999999999, 0.7499999999999999], "xyz": [1.635163, 4.905488999999999, 4.905488999999999], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.7499999999999999, 0.25, 0.7499999999999999], "xyz": [4.905488999999999, 1.635163, 4.905488999999999], "properties": {}, "label": "Te"}, {"species": [{"element": "Te", "occu": 1}], "abc": [0.7499999999999999, 0.7499999999999999, 0.25], "xyz": [4.905488999999999, 4.905488999999999, 1.635163], "properties": {}, "label": "Te"}], "@version": null}, "_BilbaoCS_conv_cell_vector_mapping": [0, 1, 2], "@version": null} \ No newline at end of file diff --git a/tests/test_cli.py b/tests/test_cli.py index 30fc1f23..b55e2688 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -125,18 +125,10 @@ def tearDown(self): for i in os.listdir("."): if "distortion_metadata" in i: os.remove(i) - elif ( - "Vac_Cd" in i - or "Int_Cd" in i - or "Wally_McDoodle" in i - or "pesky_defects" in i - or "vac_1_Cd" in i - or "v_Cd" in i - or "v_Te" in i - or "Cd_i" in i - or "_defect_folder" in i - or "Te_Cd" in i - ): + elif any(x in i for x in [ + "Vac_Cd", "Int_Cd", "Wally_McDoodle", "pesky_defects", "vac_1_Cd", "v_Cd", "v_Te", "Cd_i", + "_defect_folder", "Te_Cd", "Te_i_Td_Te2.83" + ]): shutil.rmtree(i) for defect in os.listdir(self.EXAMPLE_RESULTS): @@ -154,11 +146,11 @@ def tearDown(self): elif os.path.isfile(f"{self.EXAMPLE_RESULTS}/{defect}"): os.remove(f"{self.EXAMPLE_RESULTS}/{defect}") - if_present_rm(f"{self.EXAMPLE_RESULTS}/pesky_defects/") - if_present_rm(f"{self.EXAMPLE_RESULTS}/vac_1_Ti_0_defect_folder") - if_present_rm(f"{self.EXAMPLE_RESULTS}/v_Ti_0_defect_folder") + for i in os.listdir(f"{self.EXAMPLE_RESULTS}"): + if any(x in i for x in ["pesky_defects", "vac_1_Ti_0_defect_folder", "v_Ti_0_defect_folder", + "test_groundstate_all", "Te_i_Td_Te2.83"]): + if_present_rm(f"{self.EXAMPLE_RESULTS}/{i}") if_present_rm(f"{self.EXAMPLE_RESULTS}/v_Ti_0/Bond_Distortion_20.0%") - if_present_rm(f"{self.EXAMPLE_RESULTS}/test_groundstate_all") # Remove re-generated files folder = "Bond_Distortion_-60.0%_from_0" @@ -3272,6 +3264,41 @@ def test_plot(self): if "yaml" in file or "png" in file ] + # test with new doped naming + defect = "Te_i_Td_Te2.83_+2" + shutil.copytree(f"{self.EXAMPLE_RESULTS}/v_Ti_0", f"{self.EXAMPLE_RESULTS}/{defect}") + with warnings.catch_warnings(record=True) as w: + result = runner.invoke( + snb, + [ + "plot", + "-d", + defect, + "-p", + self.EXAMPLE_RESULTS, + "-v", + ], + ) + self.assertIn( + f"{defect}: Energy difference between minimum, found with -0.4 bond distortion, " + "and unperturbed: -3.26 eV.", + result.output, + ) # verbose output + self.assertIn( + f"Plot saved to {defect}/{defect}.png", result.output + ) + self.assertEqual(w[0].category, UserWarning) + self.assertEqual( + f"Path {self.EXAMPLE_RESULTS}/distortion_metadata.json or {self.EXAMPLE_RESULTS}/" + f"{defect}/distortion_metadata.json not found. Will not parse " + "its contents (to specify which neighbour atoms were distorted in plot text).", + str(w[0].message), + ) + self.assertTrue( + os.path.exists(os.path.join(self.EXAMPLE_RESULTS, defect, defect + ".png")) + ) + self.tearDown() + # Test --all option, with the distortion_metadata.json file present to parse number of # distorted neighbours and their identities defect = "v_Ti_0" diff --git a/tests/test_input.py b/tests/test_input.py old mode 100755 new mode 100644 index 49020693..33fc2386 --- a/tests/test_input.py +++ b/tests/test_input.py @@ -13,7 +13,7 @@ from ase.build import bulk, make_supercell from ase.calculators.aims import Aims from doped import _ignore_pmg_warnings -from doped.vasp import _test_potcar_functional_choice +from doped.vasp import _test_potcar_functional_choice, DefectRelaxSet from monty.serialization import dumpfn, loadfn from pymatgen.analysis.defects.generators import VacancyGenerator from pymatgen.analysis.defects.thermo import DefectEntry @@ -113,9 +113,12 @@ def setUp(self): os.path.join(self.VASP_CDTE_DATA_DIR, "CdTe_Bulk_Supercell_POSCAR") ) - self.cdte_doped_defect_dict = loadfn( + self.cdte_doped_defect_dict = loadfn( # old doped defects dict os.path.join(self.VASP_CDTE_DATA_DIR, "CdTe_defects_dict.json") ) + self.cdte_doped_reduced_defect_gen = loadfn( + os.path.join(self.VASP_CDTE_DATA_DIR, "reduced_CdTe_defect_gen.json") + ) self.cdte_defects = {} # Refactor to dict of DefectEntrys objects, with doped/PyCDT names for defects_type, defect_dict_list in self.cdte_doped_defect_dict.items(): @@ -404,6 +407,10 @@ def setUp(self): # Get the current locale setting self.original_locale = locale.getlocale(locale.LC_CTYPE) # should be UTF-8 + self.Ag_Sb_AgSbTe2_m2_defect_entry = loadfn( + f"{self.DATA_DIR}/Ag_Sb_Cs_Te2.90_-2.json" + ) + def tearDown(self) -> None: # reset locale: locale.setlocale(locale.LC_CTYPE, self.original_locale) # should be UTF-8 @@ -412,7 +419,9 @@ def tearDown(self) -> None: for i in self.cdte_defect_folders_old_names + self.cdte_defect_folders: if_present_rm(i) for i in os.listdir(): - if os.path.isdir(i) and ("v_Te" in i or "v_Cd" in i or "vac_1_Cd" in i): + if os.path.isdir(i) and any( + x in i for x in ["v_Te", "v_Cd", "vac_1_Cd", "Ag_Sb"] + ): if_present_rm(i) for fname in os.listdir("./"): if fname.endswith("json"): # distortion_metadata and parsed_defects_dict @@ -979,7 +988,7 @@ def test_create_vasp_input(self): ) self._check_V_Cd_folder_renaming( w, - "A previously-generated defect folder vac_1_Cd_0 exists in ", + "A previously-generated defect distortions folder vac_1_Cd_0 exists in ", ", and the Unperturbed defect structure could not be matched to the current defect species: " "vac_1_Cd_0. These are assumed to be inequivalent defects, so the previous vac_1_Cd_0 will " "be renamed to vac_1_Cda_0 and ShakeNBreak files for the current defect will be saved to " @@ -1084,8 +1093,9 @@ def test_create_vasp_input(self): ) self._check_V_Cd_folder_renaming( w, - "The previously-generated defect folder vac_1_Cdb_0 in ", - " has the same Unperturbed defect structure as the current defect species: vac_1_Cd_0. ShakeNBreak files in vac_1_Cdb_0 will be overwritten.", + "The previously-generated defect distortions folder vac_1_Cdb_0 in ", + " has the same Unperturbed defect structure as the current defect species: vac_1_Cd_0. " + "ShakeNBreak files in vac_1_Cdb_0 will be overwritten.", ) if not _potcars_available(): # test POTCAR warning assert any( @@ -1101,6 +1111,9 @@ def test_create_vasp_input(self): self.assertFalse(os.path.exists("vac_1_Cdc_0")) V_Cd_POSCAR = Poscar.from_file("vac_1_Cdb_0/Unperturbed/POSCAR") self.assertEqual(V_Cd_POSCAR.comment, "V_Cd Unperturbed, Overwritten") + self.assertEqual( + len(V_Cd_POSCAR.site_symbols), len(set(V_Cd_POSCAR.site_symbols)) + ) # no duplicates self.assertEqual(V_Cd_POSCAR.structure, self.V_Cd_struc) # 3. Unperturbed structures are present, but don't match. "a" and "b" present, @@ -1118,14 +1131,20 @@ def test_create_vasp_input(self): ) self._check_V_Cd_folder_renaming( w, - "Previously-generated defect folders (vac_1_Cdb_0...) exist in ", + "Previously-generated defect distortions folders (vac_1_Cdb_0...) exist in ", ", and the Unperturbed defect structures could not be matched to the current defect species: vac_1_Cd_0. These are assumed to be inequivalent defects, so ShakeNBreak files for the current defect will be saved to vac_1_Cdc_0 to prevent overwriting.", ) self.assertTrue(os.path.exists("vac_1_Cdc_0")) self.assertFalse(os.path.exists("vac_1_Cdd_0")) V_Cd_prev_POSCAR = Poscar.from_file("vac_1_Cdb_0/Unperturbed/POSCAR") + self.assertEqual( + len(V_Cd_prev_POSCAR.site_symbols), len(set(V_Cd_prev_POSCAR.site_symbols)) + ) # no duplicates self.assertEqual(V_Cd_prev_POSCAR.comment, "V_Cd Unperturbed, Overwritten") V_Cd_new_POSCAR = Poscar.from_file("vac_1_Cdc_0/Unperturbed/POSCAR") + self.assertEqual( + len(V_Cd_new_POSCAR.site_symbols), len(set(V_Cd_new_POSCAR.site_symbols)) + ) # no duplicates self.assertEqual(V_Cd_new_POSCAR.comment, "V_Cd Rattled, New Folder") self.assertEqual(V_Cd_new_POSCAR.structure, self.V_Cd_minus0pt5_struc_rattled) @@ -1135,12 +1154,14 @@ def test_with_non_UTF_8_encoding(self): locale.setlocale(locale.LC_CTYPE, "en_US.US-ASCII") self.test_create_vasp_input() - def _check_V_Cd_rattled_poscar(self, defect_dir): - result = Poscar.from_file(f"{defect_dir}/POSCAR") - self.assertEqual(result.comment, "V_Cd Rattled") - self.assertEqual(result.structure, self.V_Cd_minus0pt5_struc_rattled) - return result + poscar = Poscar.from_file(f"{defect_dir}/POSCAR") + self.assertEqual( + len(poscar.site_symbols), len(set(poscar.site_symbols)) + ) # no duplicates + self.assertEqual(poscar.comment, "V_Cd Rattled") + self.assertEqual(poscar.structure, self.V_Cd_minus0pt5_struc_rattled) + return poscar def _check_V_Cd_folder_renaming(self, w, top_dir, defect_dir): self.assertTrue( @@ -1357,10 +1378,16 @@ def test_Distortions_single_atom_primitive(self): defect_entry, ] ) - mock_print.assert_called_once_with( - "Oxidation states were not explicitly set, thus have been guessed as " - "{'Cu': 0}. If this is unreasonable you should manually set oxidation_states" + oxi_state_warning_message = ( + "Oxidation states were not explicitly set, thus have been guessed as {'Cu': 0.0}. If " + "this is unreasonable you should manually set oxidation_states" ) + try: + mock_print.assert_called_once_with(oxi_state_warning_message) + except AssertionError: + mock_print.assert_any_call( + oxi_state_warning_message.replace("0.0", "0") + ) self.assertEqual(dist.oxidation_states, {"Cu": 0}) self.assertAlmostEqual(dist.stdev, 0.2529625487091717) @@ -1489,6 +1516,9 @@ def test_write_vasp_files(self): V_Cd_Bond_Distortion_folder = "vac_1_Cd_0/Bond_Distortion_-50.0%" self.assertTrue(os.path.exists(V_Cd_Bond_Distortion_folder)) V_Cd_POSCAR = Poscar.from_file(f"{V_Cd_Bond_Distortion_folder}/POSCAR") + self.assertEqual( + len(V_Cd_POSCAR.site_symbols), len(set(V_Cd_POSCAR.site_symbols)) + ) # no duplicates self.assertEqual( V_Cd_POSCAR.comment, "-50.0% N(Distort)=2 ~[0.0,0.0,0.0]", @@ -1530,6 +1560,9 @@ def test_write_vasp_files(self): Int_Cd_2_Bond_Distortion_folder = "Int_Cd_2_0/Bond_Distortion_-60.0%" self.assertTrue(os.path.exists(Int_Cd_2_Bond_Distortion_folder)) Int_Cd_2_POSCAR = Poscar.from_file(f"{Int_Cd_2_Bond_Distortion_folder}/POSCAR") + self.assertEqual( + len(Int_Cd_2_POSCAR.site_symbols), len(set(Int_Cd_2_POSCAR.site_symbols)) + ) # no duplicates self.assertEqual( Int_Cd_2_POSCAR.comment, "-60.0% N(Distort)=2 ~[0.8,0.2,0.8]", @@ -1583,6 +1616,10 @@ def test_write_vasp_files(self): V_Cd_minus0pt5_POSCAR = Poscar.from_file( "vac_1_Cd_0/Bond_Distortion_-50.0%/POSCAR" ) + self.assertEqual( + len(V_Cd_minus0pt5_POSCAR.site_symbols), + len(set(V_Cd_minus0pt5_POSCAR.site_symbols)), + ) # no duplicates self.assertEqual( V_Cd_minus0pt5_POSCAR.structure, self.V_Cd_minus0pt5_struc_rattled ) @@ -1631,6 +1668,10 @@ def test_write_vasp_files(self): V_Cd_kwarged_POSCAR = Poscar.from_file( "vac_1_Cd_0/Bond_Distortion_-50.0%/POSCAR" ) + self.assertEqual( + len(V_Cd_kwarged_POSCAR.site_symbols), + len(set(V_Cd_kwarged_POSCAR.site_symbols)), + ) # no duplicates self.assertEqual( V_Cd_kwarged_POSCAR.structure, self.V_Cd_minus0pt5_struc_kwarged ) @@ -1842,6 +1883,9 @@ def test_write_vasp_files(self): _int_Cd_2_POSCAR = Poscar.from_file( "Int_Cd_2_+1/Unperturbed/POSCAR" ) # test POSCAR loaded fine + self.assertEqual( + len(_int_Cd_2_POSCAR.site_symbols), len(set(_int_Cd_2_POSCAR.site_symbols)) + ) # no duplicates kpoints = Kpoints.from_file("Int_Cd_2_+1/Unperturbed/KPOINTS") self.assertEqual(kpoints.kpts, [[1, 1, 1]]) @@ -1951,12 +1995,373 @@ def test_write_vasp_files(self): V_Cd_kwarged_POSCAR = Poscar.from_file( "test_path/vac_1_Cd_0/Bond_Distortion_-50.0%/POSCAR" ) + self.assertEqual( + len(V_Cd_kwarged_POSCAR.site_symbols), + len(set(V_Cd_kwarged_POSCAR.site_symbols)), + ) # no duplicates self.assertEqual( V_Cd_kwarged_POSCAR.structure, self.V_Cd_minus0pt5_struc_kwarged ) + def test_write_vasp_files_from_doped_defect_gen(self): + """Test Distortions() class with (new) doped DefectsGenerator input""" + dist = input.Distortions( + self.cdte_doped_reduced_defect_gen, + stdev=0.25, # old default + seed=42, # old default + ) + with patch("builtins.print") as mock_print: + with warnings.catch_warnings(record=True) as w: + _, distortion_metadata = dist.write_vasp_files( + user_incar_settings={"IVDW": 12}, + verbose=False, + ) + + # check if expected folders were created: + for key in self.cdte_doped_reduced_defect_gen.keys(): + self.assertTrue(os.path.exists(f"{key}")) + self.assertTrue(os.path.exists(f"{key}/Unperturbed")) + self.assertTrue(os.path.exists(f"{key}/Unperturbed/POSCAR")) + self.assertTrue(os.path.exists(f"{key}/Unperturbed/KPOINTS")) + if _potcars_available(): + self.assertTrue(os.path.exists(f"{key}/Unperturbed/INCAR")) + self.assertTrue(os.path.exists(f"{key}/Unperturbed/POTCAR")) + + # check expected info printing: + mock_print.assert_any_call( + "Applying ShakeNBreak...", + "Will apply the following bond distortions:", + "['-0.6', '-0.5', '-0.4', '-0.3', '-0.2', '-0.1', '0.0', '0.1', '0.2', '0.3', '0.4', '0.5', " + "'0.6'].", + "Then, will rattle with a std dev of 0.25 Å \n", + ) + mock_print.assert_any_call( + "\033[1m" + "\nDefect: v_Cd" + "\033[0m" + ) # bold print + mock_print.assert_any_call( + "\033[1m" + "Number of missing electrons in neutral state: 2" + "\033[0m" + ) + mock_print.assert_any_call( + "\nDefect v_Cd in charge state: -2. Number of distorted neighbours: 0" + ) + mock_print.assert_any_call( + "\nDefect v_Cd in charge state: -1. Number of distorted neighbours: 1" + ) + mock_print.assert_any_call( + "\nDefect v_Cd in charge state: 0. Number of distorted neighbours: 2" + ) + # test correct distorted neighbours based on oxidation states: + mock_print.assert_any_call( + "\nDefect v_Te in charge state: -1. Number of distorted neighbours: 3" + ) + mock_print.assert_any_call( + "\nDefect Cd_Te in charge state: +4. Number of distorted neighbours: 0" + ) + mock_print.assert_any_call( + "\nDefect Te_Cd in charge state: +1. Number of distorted neighbours: 3" + ) + mock_print.assert_any_call( + "\nDefect Cd_i_C3v in charge state: 0. Number of distorted neighbours: 2" + ) + mock_print.assert_any_call( + "\nDefect Te_i_Td_Te2.83 in charge state: -2. Number of distorted neighbours: 0" + ) + + # check if correct files were created: + V_Cd_Bond_Distortion_folder = "v_Cd_0/Bond_Distortion_-50.0%" + self.assertTrue(os.path.exists(V_Cd_Bond_Distortion_folder)) + V_Cd_POSCAR = Poscar.from_file(f"{V_Cd_Bond_Distortion_folder}/POSCAR") + self.assertEqual( + len(V_Cd_POSCAR.site_symbols), len(set(V_Cd_POSCAR.site_symbols)) + ) # no duplicates + self.assertEqual( + V_Cd_POSCAR.comment, + "-50.0% N(Distort)=2 ~[0.5,0.5,0.5]", # closest to middle + ) # default + kpoints = Kpoints.from_file(f"{V_Cd_Bond_Distortion_folder}/KPOINTS") + self.assertEqual(kpoints.kpts, [[1, 1, 1]]) + + if _potcars_available(): + assert not filecmp.cmp( # INCAR settings changed now + f"{V_Cd_Bond_Distortion_folder}/INCAR", self.V_Cd_INCAR_file + ) + assert self.V_Cd_INCAR != Incar.from_file( + f"{V_Cd_Bond_Distortion_folder}/INCAR" + ) + kwarged_INCAR = self.V_Cd_INCAR.copy() + kwarged_INCAR.update({"IVDW": 12}) + assert kwarged_INCAR == Incar.from_file( + f"{V_Cd_Bond_Distortion_folder}/INCAR" + ) + + # check if POTCARs have been written: + potcar = Potcar.from_file(f"{V_Cd_Bond_Distortion_folder}/POTCAR") + assert set(potcar.as_dict()["symbols"]) == { + input.default_potcar_dict["POTCAR"][el_symbol] + for el_symbol in V_Cd_POSCAR.structure.symbol_set + } + else: # test POTCAR warning + assert any( + str(warning.message) + == "POTCAR directory not set up with pymatgen (see the doped docs Installation page: " + "https://doped.readthedocs.io/en/latest/Installation.html for instructions on setting " + "this up). This is required to generate `POTCAR` files and set `NELECT` (i.e. charge " + "state) and `NUPDOWN` in the `INCAR` files!\nNo `POTCAR` files will be written, and " + "`NELECT` and `NUPDOWN` will not be set in `INCAR`s. Beware!" + for warning in w + ) + + Int_Cd_2_Bond_Distortion_folder = "Cd_i_C3v_0/Bond_Distortion_-60.0%" + self.assertTrue(os.path.exists(Int_Cd_2_Bond_Distortion_folder)) + Int_Cd_2_POSCAR = Poscar.from_file(f"{Int_Cd_2_Bond_Distortion_folder}/POSCAR") + self.assertEqual( + len(Int_Cd_2_POSCAR.site_symbols), len(set(Int_Cd_2_POSCAR.site_symbols)) + ) # no duplicates + self.assertEqual( + Int_Cd_2_POSCAR.comment, + "-60.0% N(Distort)=2 ~[0.3,0.4,0.4]", # closest to middle + ) + kpoints = Kpoints.from_file(f"{Int_Cd_2_Bond_Distortion_folder}/KPOINTS") + self.assertEqual(kpoints.kpts, [[1, 1, 1]]) + + if _potcars_available(): + assert not filecmp.cmp( # INCAR settings changed now + f"{Int_Cd_2_Bond_Distortion_folder}/INCAR", self.V_Cd_INCAR_file + ) + kwarged_INCAR = self.V_Cd_INCAR.copy() + kwarged_INCAR.update({"IVDW": 12}) + kwarged_INCAR.pop("NELECT") # different NELECT for Cd_i_+2 + Int_Cd_2_INCAR = Incar.from_file(f"{Int_Cd_2_Bond_Distortion_folder}/INCAR") + Int_Cd_2_INCAR.pop("NELECT") + assert kwarged_INCAR == Int_Cd_2_INCAR + + # check if POTCARs have been written: + potcar = Potcar.from_file(f"{Int_Cd_2_Bond_Distortion_folder}/POTCAR") + assert set(potcar.as_dict()["symbols"]) == { + input.default_potcar_dict["POTCAR"][el_symbol] + for el_symbol in V_Cd_POSCAR.structure.symbol_set + } + + def _check_agsbte2_files(self, folder_name, mock_print, w, charge_state=-2): + # check if expected folders were created: + self.assertTrue(os.path.exists(f"{folder_name}")) + if charge_state == -2: + folder_list = ["Rattled", "Unperturbed"] + else: + folder_list = [ + "Unperturbed", + "Bond_Distortion_-50.0%", + "Bond_Distortion_20.0%", + ] # just + # check sub-sample + + for i in folder_list: + self.assertTrue(os.path.exists(f"{folder_name}/{i}")) + self.assertTrue(os.path.exists(f"{folder_name}/{i}/POSCAR")) + self.assertTrue(os.path.exists(f"{folder_name}/{i}/KPOINTS")) + if _potcars_available(): + self.assertTrue(os.path.exists(f"{folder_name}/{i}/INCAR")) + self.assertTrue(os.path.exists(f"{folder_name}/{i}/POTCAR")) + + # check expected info printing: + mock_print.assert_any_call( + "Applying ShakeNBreak...", + "Will apply the following bond distortions:", + "['-0.6', '-0.5', '-0.4', '-0.3', '-0.2', '-0.1', '0.0', '0.1', '0.2', '0.3', '0.4', '0.5', " + "'0.6'].", + "Then, will rattle with a std dev of 0.29 Å \n", + ) + defect_wout_charge = folder_name.rsplit("_", 1)[0] + mock_print.assert_any_call( + "\033[1m" + f"\nDefect: {defect_wout_charge}" + "\033[0m" + ) # bold print + mock_print.assert_any_call( + "\033[1m" + "Number of missing electrons in neutral state: 2" + "\033[0m" + ) + mock_print.assert_any_call( + f"\nDefect {defect_wout_charge} in charge state: {int(charge_state)}. Number of distorted " + f"neighbours: {int(2 + charge_state)}" + ) + + # check if correct files were created: + distortion_folder = "Rattled" if charge_state == -2 else "Unperturbed" + poscar = Poscar.from_file(f"{folder_name}/{distortion_folder}/POSCAR") + self.assertEqual( + poscar.comment, + f"{distortion_folder} N(Distort)={int(2 + charge_state)} ~[0.5,0.9,0.6]", + ) # closest to middle default + + # check correct element ordering in POSCAR: + self.assertEqual( + len(poscar.site_symbols), len(set(poscar.site_symbols)) + ) # no duplicates + + kpoints = Kpoints.from_file(f"{folder_name}/{distortion_folder}/KPOINTS") + self.assertEqual(kpoints.kpts, [[1, 1, 1]]) + + if _potcars_available(): + # check if POTCARs have been written: + potcar = Potcar.from_file(f"{folder_name}/{distortion_folder}/POTCAR") + assert set(potcar.as_dict()["symbols"]) == { + input.default_potcar_dict["POTCAR"][el_symbol] + for el_symbol in poscar.structure.symbol_set + } + else: # test POTCAR warning + assert any( + str(warning.message) + == "POTCAR directory not set up with pymatgen (see the doped docs Installation page: " + "https://doped.readthedocs.io/en/latest/Installation.html for instructions on setting " + "this up). This is required to generate `POTCAR` files and set `NELECT` (i.e. charge " + "state) and `NUPDOWN` in the `INCAR` files!\nNo `POTCAR` files will be written, and " + "`NELECT` and `NUPDOWN` will not be set in `INCAR`s. Beware!" + for warning in w + ) + + def test_write_vasp_files_from_doped_defect_entry(self): + """ + Test Distortions() class with (new) doped DefectEntry input. + If the DefectEntry.name attribute is set, then this should be + used as the folder name for the defect. + """ + dist = input.Distortions( + self.Ag_Sb_AgSbTe2_m2_defect_entry, + ) + with patch("builtins.print") as mock_print: + with warnings.catch_warnings(record=True) as w: + _, distortion_metadata = dist.write_vasp_files( + user_incar_settings={"IVDW": 12}, + verbose=True, + ) + + self._check_agsbte2_files( + self.Ag_Sb_AgSbTe2_m2_defect_entry.name, mock_print, w + ) + + def test_write_vasp_files_from_doped_defect_entry_wout_name(self): + """ + Test Distortions() class with (new) doped DefectEntry input. + Here the DefectEntry.name attribute is not set (e.g. manual + DefectEntry generation from the user), and so the doped + defect name is regenerated. + """ + defect_entry = copy.deepcopy(self.Ag_Sb_AgSbTe2_m2_defect_entry) + delattr(defect_entry, "name") + dist = input.Distortions( + defect_entry, + ) + with patch("builtins.print") as mock_print: + with warnings.catch_warnings(record=True) as w: + _, distortion_metadata = dist.write_vasp_files() + + self._check_agsbte2_files("Ag_Sb_-2", mock_print, w) + + def test_write_vasp_files_from_doped_defect_entry_list(self): + """ + Test Distortions() class with input of doped DefectEntry list. + Here the DefectEntry.name attributes are set in all cases, so + these should be used as the folder names for the defects. + + Note that here we test all name attributes set for DefectEntry + list, the next test ("w_incomplete_names") tests with only some + name attributes set, and then `test_write_vasp_files_from_list` + tests no name attributes set. + """ + Ag_Sb_AgSbTe2_neutral_defect_entry = copy.deepcopy( + self.Ag_Sb_AgSbTe2_m2_defect_entry + ) + Ag_Sb_AgSbTe2_neutral_defect_entry.charge_state = 0 + Ag_Sb_AgSbTe2_neutral_defect_entry.name = ( + Ag_Sb_AgSbTe2_neutral_defect_entry.name.rsplit("_", 1)[0] + "_0" + ) + + dist = input.Distortions( + [self.Ag_Sb_AgSbTe2_m2_defect_entry, Ag_Sb_AgSbTe2_neutral_defect_entry], + ) + with patch("builtins.print") as mock_print: + with warnings.catch_warnings(record=True) as w: + _, distortion_metadata = dist.write_vasp_files( + user_incar_settings={"IVDW": 12}, + verbose=True, + ) + + self._check_agsbte2_files( + self.Ag_Sb_AgSbTe2_m2_defect_entry.name, mock_print, w, charge_state=-2 + ) + self._check_agsbte2_files( + Ag_Sb_AgSbTe2_neutral_defect_entry.name, mock_print, w, charge_state=0 + ) + + def test_write_vasp_files_from_doped_defect_entry_list_w_incomplete_names(self): + """ + Test Distortions() class with input of doped DefectEntry list. + Here the DefectEntry.name attributes are not set in all cases, so + the doped defect names are regenerated and used as folder names. + """ + Ag_Sb_AgSbTe2_neutral_defect_entry = copy.deepcopy( + self.Ag_Sb_AgSbTe2_m2_defect_entry + ) + Ag_Sb_AgSbTe2_neutral_defect_entry.charge_state = 0 + delattr(Ag_Sb_AgSbTe2_neutral_defect_entry, "name") + + dist = input.Distortions( + [self.Ag_Sb_AgSbTe2_m2_defect_entry, Ag_Sb_AgSbTe2_neutral_defect_entry], + ) + with patch("builtins.print") as mock_print: + with warnings.catch_warnings(record=True) as w: + _, distortion_metadata = dist.write_vasp_files( + user_incar_settings={"IVDW": 12}, + verbose=True, + ) + + # reset to doped names: + self._check_agsbte2_files("Ag_Sb_-2", mock_print, w, charge_state=-2) + self._check_agsbte2_files("Ag_Sb_0", mock_print, w, charge_state=0) + + def test_write_vasp_files_overwriting(self): + """ + Test that no warnings are thrown when the defect folder already + exists, but no SnB distortion folders in it (i.e. if doped + defect folder already generated). + """ + drs = DefectRelaxSet(self.Ag_Sb_AgSbTe2_m2_defect_entry) + drs.write_all(unperturbed_poscar=True) + + self.assertTrue(os.path.exists(f"{self.Ag_Sb_AgSbTe2_m2_defect_entry.name}")) + self.assertTrue( + os.path.exists(f"{self.Ag_Sb_AgSbTe2_m2_defect_entry.name}/vasp_std") + ) + self.assertTrue( + os.path.exists(f"{self.Ag_Sb_AgSbTe2_m2_defect_entry.name}/vasp_std/POSCAR") + ) + self.assertTrue( + os.path.exists( + f"{self.Ag_Sb_AgSbTe2_m2_defect_entry.name}/vasp_std/KPOINTS" + ) + ) + self.assertTrue( + os.path.exists(f"{self.Ag_Sb_AgSbTe2_m2_defect_entry.name}/vasp_ncl") + ) + self.assertTrue( + os.path.exists(f"{self.Ag_Sb_AgSbTe2_m2_defect_entry.name}/vasp_nkred_std") + ) + + dist = input.Distortions(self.Ag_Sb_AgSbTe2_m2_defect_entry) + with patch("builtins.print") as mock_print: + with warnings.catch_warnings(record=True) as w: + _, distortion_metadata = dist.write_vasp_files( + user_incar_settings={"IVDW": 12}, + verbose=True, + ) + + self.assertEqual( + len([warning for warning in w if warning.category == UserWarning]), 0 + ) + self._check_agsbte2_files( + self.Ag_Sb_AgSbTe2_m2_defect_entry.name, mock_print, w, charge_state=-2 + ) + def test_write_vasp_files_from_doped_dict(self): - """Test Distortion() class with doped dict input""" + """Test Distortions() class with doped dict input""" # Test normal behaviour vacancies = { "vacancies": [ @@ -2077,7 +2482,11 @@ def test_write_vasp_files_from_doped_dict(self): self.assertIn(no_bulk_error, e.exception) def test_write_vasp_files_from_list(self): - """Test Distortion() class with Defect list input""" + """ + Test Distortion() class with DefectEntry list input. + Here, the DefectEntry.name attributes are not set, and + so the doped defect names are regenerated. + """ # Test normal behaviour with patch("builtins.print") as mock_print: dist = input.Distortions(self.cdte_defect_list) @@ -2183,6 +2592,10 @@ def test_write_vasp_files_from_list(self): V_Cd_POSCAR.comment, "-50.0% N(Distort)=2 ~[0.0,0.0,0.0]", ) # default + self.assertEqual( + len(V_Cd_POSCAR.site_symbols), len(set(V_Cd_POSCAR.site_symbols)) + ) # no duplicates + self.assertNotEqual(V_Cd_POSCAR.structure, self.V_Cd_minus0pt5_struc_rattled) # old default rattling @@ -2193,6 +2606,9 @@ def test_write_vasp_files_from_list(self): Int_Cd_2_POSCAR.comment, "-60.0% N(Distort)=2 ~[0.8,0.2,0.8]", ) + self.assertEqual( + len(Int_Cd_2_POSCAR.site_symbols), len(set(Int_Cd_2_POSCAR.site_symbols)) + ) # no duplicates self.assertEqual( # Int_Cd_2_minus0pt6_struc_rattled is with new default `stdev` & `seed` Int_Cd_2_POSCAR.structure, @@ -3018,6 +3434,9 @@ def test_from_structures(self): V_Cd_POSCAR.comment, "-50.0% N(Distort)=2 ~[0.0,0.0,0.0]", ) # default + self.assertEqual( + len(V_Cd_POSCAR.site_symbols), len(set(V_Cd_POSCAR.site_symbols)) + ) # no duplicates self.assertNotEqual(V_Cd_POSCAR.structure, self.V_Cd_minus0pt5_struc_rattled) # old default rattling @@ -3065,6 +3484,9 @@ def test_from_structures(self): Int_Cd_2_Bond_Distortion_folder = "Cd_i_C3v_0/Bond_Distortion_-60.0%" self.assertTrue(os.path.exists(Int_Cd_2_Bond_Distortion_folder)) Int_Cd_2_POSCAR = Poscar.from_file(Int_Cd_2_Bond_Distortion_folder + "/POSCAR") + self.assertEqual( + len(Int_Cd_2_POSCAR.site_symbols), len(set(Int_Cd_2_POSCAR.site_symbols)) + ) # no duplicates self.assertEqual( Int_Cd_2_POSCAR.comment, "-60.0% N(Distort)=2 ~[0.8,0.2,0.8]", diff --git a/tests/test_plotting.py b/tests/test_plotting.py index fbd8f365..78061381 100644 --- a/tests/test_plotting.py +++ b/tests/test_plotting.py @@ -683,6 +683,11 @@ def test_plot_with_multiple_imported_distortions_from_same_charge_state(self): "-20.0%_from_+2": -623.59064927, "-30.0%_from_0": -623.49069487, "-30.0%_from_+2": -623.64233181, + "-30.0%_from_+5": -624.65113207, + "0.0%_from_+4": -624.65313207, + "-15.0%_from_+7": -624.06113207, + "30.0%_from_+5": -624.65513207, + "25.0%_from_+7": -624.06513207, "10.0%_from_+2": -624.66110949, "20.0%_from_+2": -624.65991904, "30.0%_from_+2": -624.66113207, @@ -954,6 +959,24 @@ def test_plot_defect_unrecognised_name(self): ) return fig + @pytest.mark.mpl_image_compare( + baseline_dir=f"{_DATA_DIR}/remote_baseline_plots", + filename="Te_i_Td_Te2.83_+2.png", + style=f"{_file_path}/../shakenbreak/shakenbreak.mplstyle", + savefig_kwargs={"transparent": True, "bbox_inches": "tight"}, + ) + def test_plot_defect_doped_v2(self): + """Test plot_defect() function using doped v2 naming""" + return plotting.plot_defect( + output_path=self.VASP_CDTE_DATA_DIR, + defect_species="Te_i_Td_Te2.83_+2", + energies_dict=self.V_Cd_energies_dict, + num_nearest_neighbours=2, + neighbour_atom="Te", + include_site_info_in_name=False, + save_plot=False, + ) + @pytest.mark.mpl_image_compare( baseline_dir=f"{_DATA_DIR}/remote_baseline_plots", filename="vac_1_Cd_0_include_site_info_in_name.png", @@ -973,6 +996,24 @@ def test_plot_defect_include_site_info_in_name(self): save_plot=False, ) + @pytest.mark.mpl_image_compare( + baseline_dir=f"{_DATA_DIR}/remote_baseline_plots", + filename="Te_i_Td_Te2.83_+2_include_site_info_in_name.png", + style=f"{_file_path}/../shakenbreak/shakenbreak.mplstyle", + savefig_kwargs={"transparent": True, "bbox_inches": "tight"}, + ) + def test_plot_defect_include_site_info_in_name_doped_v2(self): + """Test plot_defect() function when include_site_info_in_name = True, using doped v2 naming""" + return plotting.plot_defect( + output_path=self.VASP_CDTE_DATA_DIR, + defect_species="Te_i_Td_Te2.83_+2", + energies_dict=self.V_Cd_energies_dict, + num_nearest_neighbours=2, + neighbour_atom="Te", + include_site_info_in_name=True, + save_plot=False, + ) + @pytest.mark.mpl_image_compare( baseline_dir=f"{_DATA_DIR}/remote_baseline_plots", filename="vac_1_Cd_0_plot_defect_without_title_units_meV.png", diff --git a/tutorials/ShakeNBreak_Example_Workflow.ipynb b/tutorials/ShakeNBreak_Example_Workflow.ipynb index c9d0023b..3d5a4978 100644 --- a/tutorials/ShakeNBreak_Example_Workflow.ipynb +++ b/tutorials/ShakeNBreak_Example_Workflow.ipynb @@ -4023,9 +4023,9 @@ }, "source": [ "### Further Defect Analysis\n", - "Once the ground state (and metastable) defect structures have been identified, we will want to compute their formation energies using our final fully-converged calculation parameters (i.e. plane-wave cutoff and k-point sampling). This can be done using [`doped`](https://github.com/SMTG-UCL/doped), manually (not recommended) or using the other defect codes listed on the [Code Compatibility](https://shakenbreak.readthedocs.io/en/latest/Code_Compatibility.html) page.\n", + "Once the ground state (and metastable) defect structures have been identified, we will want to compute their formation energies using our final fully-converged calculation parameters (i.e. plane-wave cutoff and k-point sampling). This can be done using [`doped`](https://github.com/SMTG-Bham/doped), manually (not recommended) or using the other defect codes listed on the [Code Compatibility](https://shakenbreak.readthedocs.io/en/latest/Code_Compatibility.html) page.\n", "\n", - "As shown in the [`doped`](https://github.com/SMTG-UCL/doped) examples and docs, you may want to further analyse the behaviour and impact on material properties of your defects using advanced defect analysis codes such as [`easyunfold`](https://smtg-ucl.github.io/easyunfold/) (to analyse the electronic structure of defects in your material), [`py-sc-fermi`](https://py-sc-fermi.readthedocs.io/en/latest/) (to analyse defect concentrations, doping and Fermi level tuning), or [`nonrad`](https://nonrad.readthedocs.io/en/latest/)/[`CarrierCapture.jl`](https://wmd-group.github.io/CarrierCapture.jl/dev/) (to analyse non-radiative electron-hole recombination at defects)." + "As shown in the [`doped`](https://github.com/SMTG-Bham/doped) examples and docs, you may want to further analyse the behaviour and impact on material properties of your defects using advanced defect analysis codes such as [`easyunfold`](https://smtg-bham.github.io/easyunfold/) (to analyse the electronic structure of defects in your material), [`py-sc-fermi`](https://py-sc-fermi.readthedocs.io/en/latest/) (to analyse defect concentrations, doping and Fermi level tuning), or [`nonrad`](https://nonrad.readthedocs.io/en/latest/)/[`CarrierCapture.jl`](https://wmd-group.github.io/CarrierCapture.jl/dev/) (to analyse non-radiative electron-hole recombination at defects)." ] }, {