structuretoolkit 0.0.41__tar.gz → 0.0.43__tar.gz

structuretoolkit-0.0.43/.gitignore

@@ -0,0 +1,217 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#   Usually these files are written by a python script from a template
+#   before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+# Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+# uv.lock
+
+# poetry
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+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+# poetry.lock
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# Redis
+*.rdb
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+
+# RabbitMQ
+mnesia/
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+#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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+#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
+# .idea/
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#   you could uncomment the following to ignore the entire vscode folder
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+
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+
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+
+# Streamlit
+.streamlit/secrets.toml

{structuretoolkit-0.0.41 → structuretoolkit-0.0.43}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: structuretoolkit
-Version: 0.0.41
+Version: 0.0.43
 Summary: build, analyse and visualise atomistic structures for materials science
 Project-URL: Homepage, https://github.com/pyiron/structuretoolkit
 Project-URL: Documentation, https://github.com/pyiron/structuretoolkit
@@ -41,35 +41,37 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: <3.15,>=3.10
-Requires-Dist: ase<=3.28.0,>=3.20.1
+Requires-Dist: ase<=3.28.0,>=3.24.0
 Requires-Dist: numpy<=2.4.3,>=1.23.5
-Requires-Dist: scipy<=1.17.0,>=1.15.0
+Requires-Dist: scipy<=1.17.1,>=1.15.0
 Provides-Extra: clusters
 Requires-Dist: scikit-learn==1.8.0; extra == 'clusters'
 Provides-Extra: dscribe
 Requires-Dist: dscribe==2.1.2; extra == 'dscribe'
 Provides-Extra: grainboundary
 Requires-Dist: aimsgb<=1.1.1,>=1.0.2; extra == 'grainboundary'
-Requires-Dist: pymatgen<=2026.3.23,>=2022.2.1; extra == 'grainboundary'
+Requires-Dist: pymatgen==2026.3.23; extra == 'grainboundary'
 Provides-Extra: matplotlib
-Requires-Dist: matplotlib==3.10.8; extra == 'matplotlib'
+Requires-Dist: matplotlib==3.10.9; extra == 'matplotlib'
+Provides-Extra: mp-api
+Requires-Dist: mp-api==0.45.15; extra == 'mp-api'
+Requires-Dist: pymatgen==2026.3.23; extra == 'mp-api'
 Provides-Extra: nglview
 Requires-Dist: nglview<=4.0.1,>=2.7.7; extra == 'nglview'
 Provides-Extra: phonopy
-Requires-Dist: phonopy<=3.2.1,>=2.16.2; extra == 'phonopy'
+Requires-Dist: phonopy<=3.5.1,>=2.21.2; extra == 'phonopy'
 Requires-Dist: spglib==2.7.0; extra == 'phonopy'
 Provides-Extra: plotly
-Requires-Dist: plotly<=6.6.0,>=4.14.3; extra == 'plotly'
+Requires-Dist: plotly<=6.6.0,>=6.0.0; extra == 'plotly'
 Provides-Extra: pyscal
 Requires-Dist: pyscal3<=3.3.2,>=3.2.5; extra == 'pyscal'
 Provides-Extra: surface
-Requires-Dist: pymatgen<=2026.3.23,>=2022.2.1; extra == 'surface'
+Requires-Dist: pymatgen==2026.3.23; extra == 'surface'
 Requires-Dist: spglib==2.7.0; extra == 'surface'
 Provides-Extra: symmetry
 Requires-Dist: spglib==2.7.0; extra == 'symmetry'

{structuretoolkit-0.0.41 → structuretoolkit-0.0.43}/pyproject.toml

@@ -18,15 +18,14 @@ classifiers = [
     "License :: OSI Approved :: BSD License",
     "Intended Audience :: Science/Research",
     "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "ase>=3.20.1,<=3.28.0",
+    "ase>=3.24.0,<=3.28.0",
     "numpy>=1.23.5,<=2.4.3",
-    "scipy>=1.15.0,<=1.17.0",
+    "scipy>=1.15.0,<=1.17.1",
 ]
 dynamic = ["version"]
 
@@ -39,22 +38,26 @@ Repository = "https://github.com/pyiron/structuretoolkit"
 dscribe = ["dscribe==2.1.2"]
 grainboundary = [
     "aimsgb>=1.0.2,<=1.1.1",
-    "pymatgen>=2022.2.1,<=2026.3.23",
+    "pymatgen==2026.3.23",
 ]
 pyscal = ["pyscal3>=3.2.5,<=3.3.2"]
 nglview = ["nglview>=2.7.7,<=4.0.1"]
-matplotlib = ["matplotlib==3.10.8"]
-plotly = ["plotly>=4.14.3,<=6.6.0"]
+matplotlib = ["matplotlib==3.10.9"]
+plotly = ["plotly>=6.0.0,<=6.6.0"]
 clusters = ["scikit-learn==1.8.0"]
 symmetry = ["spglib==2.7.0"]
 surface = [
     "spglib==2.7.0",
-    "pymatgen>=2022.2.1,<=2026.3.23",
+    "pymatgen==2026.3.23",
 ]
 phonopy = [
-    "phonopy>=2.16.2,<=3.2.1",
+    "phonopy>=2.21.2,<=3.5.1",
     "spglib==2.7.0",
 ]
+mp-api = [
+    "mp-api==0.45.15",
+    "pymatgen==2026.3.23",
+]
 
 [tool.ruff]
 exclude = [".ci_support", "tests", "setup.py", "_version.py"]

{structuretoolkit-0.0.41 → structuretoolkit-0.0.43}/src/structuretoolkit/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.0.41'
-__version_tuple__ = version_tuple = (0, 0, 41)
+__version__ = version = '0.0.43'
+__version_tuple__ = version_tuple = (0, 0, 43)
 
 __commit_id__ = commit_id = None

{structuretoolkit-0.0.41 → structuretoolkit-0.0.43}/src/structuretoolkit/analyse/symmetry.py

@@ -4,6 +4,7 @@
 import ast
 import dataclasses
 import string
+import warnings
 
 import numpy as np
 import spglib
@@ -400,26 +401,40 @@ class Symmetry(dict):
         >>> symmetry = Symmetry(structure)
         >>> len(symmetry.get_primitive_cell()) == len(basis)
         True
+
+        .. warning::
+            Custom arrays defined in the base structures
+            :attr:`ase.atoms.Atoms.arrays` and other state (.info, .calc, etc.) are not copied to the new structure!
         """
+        if not all(self._structure.pbc):
+            raise ValueError("Can only symmetrize periodic structures.")
         ret = spglib.standardize_cell(
             self._get_spglib_cell(use_elements=use_elements, use_magmoms=use_magmoms),
             to_primitive=not standardize,
         )
         if ret is None:
             raise SymmetryError(spglib.error.get_error_message())
-        cell, positions, indices = ret
-        positions = (cell.T @ positions.T).T
-        new_structure = self._structure.copy()
-        new_structure.cell = cell
-        new_structure = new_structure[: len(indices)]
+        cell, scaled_positions, indices = ret
         indices_dict = {
             v: k
             for k, v in structuretoolkit.common.helper.get_species_indices_dict(
                 structure=self._structure
             ).items()
         }
-        new_structure.symbols = [indices_dict[i] for i in indices]
-        new_structure.positions = positions
+        symbols = [indices_dict[i] for i in indices]
+        new_structure = type(self._structure)(
+            symbols=symbols,
+            scaled_positions=scaled_positions,
+            cell=cell,
+            pbc=[True, True, True],
+        )
+        keys = set(self._structure.arrays) - {"numbers", "positions"}
+        if len(keys) > 0:
+            warnings.warn(
+                f"Custom arrays {keys} do not carry over to new structure!",
+                stacklevel=2,
+            )
+
         return new_structure
 
     def get_ir_reciprocal_mesh(

{structuretoolkit-0.0.41 → structuretoolkit-0.0.43}/src/structuretoolkit/build/__init__.py

@@ -2,6 +2,10 @@ from structuretoolkit.build.aimsgb import get_grainboundary_info, grainboundary
 from structuretoolkit.build.compound import B2, C14, C15, C36, D03
 from structuretoolkit.build.mesh import create_mesh
 from structuretoolkit.build.sqs import sqs_structures
+from structuretoolkit.build.materialsproject import (
+    search as materialsproject_search,
+    by_id as materialsproject_by_id,
+)
 from structuretoolkit.build.surface import (
     get_high_index_surface_info,
     high_index_surface,
@@ -19,4 +23,6 @@ __all__ = [
     "sqs_structures",
     "get_high_index_surface_info",
     "high_index_surface",
+    "materialsproject_search",
+    "materialsproject_by_id",
 ]

structuretoolkit-0.0.43/src/structuretoolkit/build/geometry.py

@@ -0,0 +1,141 @@
+"""Utilities that operate purely geometric aspects of structures."""
+
+import numpy as np
+from ase.atoms import Atoms
+
+from structuretoolkit.analyse import get_neighbors
+
+
+def repulse(
+    structure: Atoms,
+    min_dist: float = 1.5,
+    step_size: float = 0.2,
+    axis: int | None = None,
+    iterations: int = 100,
+    inplace: bool = False,
+) -> Atoms:
+    """Iteratively displace atoms apart until all interatomic distances exceed a minimum threshold.
+
+    For each pair of atoms closer than ``min_dist``, the atom is displaced away from its nearest
+    neighbour by up to ``step_size`` along the direction of the interatomic vector.  The loop
+    repeats until all nearest-neighbour distances satisfy the minimum criterion or the iteration
+    limit is reached.
+
+    Args:
+        structure (:class:`ase.Atoms`):
+            Structure to modify.
+        min_dist (float):
+            Minimum interatomic distance (in Å) to enforce between every pair of atoms.
+            Defaults to 1.5.
+        step_size (float):
+            Maximum displacement (in Å) applied to a single atom per iteration.
+            Smaller values give smoother convergence but require more iterations.
+            Defaults to 0.2.
+        axis (int or None):
+            Cartesian axis index (0, 1, or 2) along which displacements are restricted.
+            When *None* (default) displacements are applied in all three directions.
+        iterations (int):
+            Maximum number of displacement steps before raising a :class:`RuntimeError`.
+            Defaults to 100.
+        inplace (bool):
+            If *True*, the positions of ``structure`` are modified directly.
+            If *False* (default), a copy is made and the original is left unchanged.
+
+    Returns:
+        :class:`ase.Atoms`: The structure with adjusted atomic positions.  This is the
+        same object as ``structure`` when ``inplace=True``, or a new copy otherwise.
+
+    Raises:
+        RuntimeError: If the minimum distance criterion is not satisfied within
+            ``iterations`` steps.
+    """
+    if not inplace:
+        structure = structure.copy()
+    if axis is None:
+        axis = slice(None)
+    for _ in range(iterations):
+        neigh = get_neighbors(structure, num_neighbors=1)
+        dd = neigh.distances[:, 0]
+        if dd.min() >= min_dist:
+            break
+
+        I = dd < min_dist
+
+        dd_I = dd[I]
+        vv = neigh.vecs[I, 0, :].copy()
+        # Avoid division by zero for coincident atoms (distance == 0).
+        # Assign opposite fallback directions based on atom-index ordering so
+        # the two coincident atoms separate rather than move together.
+        atom_indices = np.where(I)[0]
+        zero_mask = dd_I == 0
+        if np.any(zero_mask):
+            neighbor_indices = neigh.indices[atom_indices[zero_mask], 0]
+            sign = np.where(atom_indices[zero_mask] < neighbor_indices, 1.0, -1.0)
+            vv[zero_mask] = sign[:, None] * np.array([1.0, 0.0, 0.0])
+        safe_dd = np.where(dd_I > 0, dd_I, 1.0)
+        vv /= safe_dd[:, None]
+
+        disp = np.clip(min_dist - dd[I], 0, step_size)
+
+        displacement = disp[:, None] * vv  # (N_close, 3)
+        structure.positions[I, axis] -= displacement[:, axis]
+
+    else:
+        raise RuntimeError(f"repulse did not converge within {iterations} iterations")
+
+    return structure
+
+
+def merge(
+    structure: "ase.Atoms", cutoff: float = 1.8, iterations: int = 10
+) -> "ase.Atoms":
+    """Merge pairs of atoms that are closer than ``cutoff`` by collapsing each
+    pair to their midpoint and deleting one of the two atoms.
+
+    The operation is applied repeatedly (up to ``iterations`` times) to handle
+    cases where a merge creates new close contacts.
+
+    .. note::
+        The structure is modified **in place**.  Pass a copy if you need the
+        original to remain unchanged.
+
+    Args:
+        structure (:class:`ase.Atoms`):
+            Structure to modify.
+        cutoff (float):
+            Distance threshold in Ångström below which two atoms are
+            considered clashing and will be merged.  Defaults to ``1.8``.
+        iterations (int):
+            Maximum number of recursive merge passes.  Defaults to ``10``.
+
+    Returns:
+        :class:`ase.Atoms`: The modified structure with clashing atom pairs
+        replaced by single atoms at their midpoints.
+    """
+    neigh = get_neighbors(structure, 1)
+    clashing = np.argwhere(neigh.distances[:, 0] < cutoff).ravel()
+    if len(clashing) == 0:
+        return structure
+
+    moving = []
+    deleting = []
+
+    for c in clashing:
+        if c in deleting:
+            continue
+
+        moving.append(c)
+        deleting.append(neigh.indices[c, 0])
+
+    structure.positions[moving] += neigh.vecs[moving, 0] / 2
+    del structure[deleting]
+
+    if iterations > 0:
+        return merge(structure, cutoff=cutoff, iterations=iterations - 1)
+    return structure
+
+
+__all__ = [
+    "merge",
+    "repulse",
+]

structuretoolkit-0.0.43/src/structuretoolkit/build/materialsproject.py

@@ -0,0 +1,138 @@
+from typing import Any, Iterable
+from collections.abc import Generator
+from ase.atoms import Atoms
+from structuretoolkit.common.pymatgen import pymatgen_to_ase
+
+
+def search(
+    chemsys: str | list[str], fields: Iterable[str] = (), api_key=None, **kwargs
+) -> Generator[dict[str, Any], None, None]:
+    """
+    Search the database for all structures matching the given query.
+
+    Note that `chemsys` takes distinct values for unaries, binaries and so!  A query with `chemsys=["Fe", "O"]` will
+    return iron and oxygen structures but not iron oxide.  Similarly `chemsys=["Fe-O"]` will
+    not return unary structures.
+
+    All keyword arguments for filtering from the original API are supported.  See the
+    `original docs <https://docs.materialsproject.org/downloading-data/using-the-api>`_ for them.
+
+    Search for all iron structures:
+
+    >>> irons = structuretoolkit.build.materialsproject.search("Fe")
+    >>> len(list(irons))
+    10
+
+    Search for all structures with Al, Li that are on the T=0 convex hull:
+
+    >>> alli = structuretoolkit.build.materialsproject.search(['Al', 'Li', 'Al-Li'], is_stable=True)
+    >>> len(list(alli))
+    6
+
+    Usage is only possible with an API key obtained from the Materials Project.  To do this, create an account with
+    them, login and access `this webpage <https://next-gen.materialsproject.org/api#api-key>`.
+
+    Once you have a key, either pass it as the `api_key` parameter or export an
+    environment variable, called `MP_API_KEY`, in your shell setup.
+
+    Args:
+        chemsys (str, list of str): confine search to given elements; either an element symbol or multiple element
+            symbols separated by dashes; if a list of strings is given return structures matching either of them
+        fields (iterable of str): pass as `fields` to :meth:`mp_api.MPRester.summary.search` to request additional
+            database entries beyond the structure
+        api_key (str, optional): if your API key is not exported in the environment flag MP_API_KEY, pass it here
+        **kwargs: passed verbatim to :meth:`mp_api.MPRester.summary.search` to further filter the results
+
+    Returns:
+        list of dict: one dictionary for each search results with at least keys
+            'material_id': database key of the hit
+            'structure': ASE atoms object
+            plus any requested via `fields`.
+    """
+    from mp_api.client import MPRester
+
+    rest_kwargs = {
+        "use_document_model": False,  # returns results as dictionaries
+        "include_user_agent": True,  # send some additional software version info to MP
+    }
+    if api_key is not None:
+        rest_kwargs["api_key"] = api_key
+    with MPRester(**rest_kwargs) as mpr:
+        results = mpr.summary.search(
+            chemsys=chemsys,
+            **kwargs,
+            fields=list(fields) + ["structure", "material_id"],
+        )
+    for r in results:
+        if "structure" in r:
+            r["structure"] = pymatgen_to_ase(r["structure"])
+        yield r
+
+
+def by_id(
+    material_id: str | int,
+    final: bool = True,
+    conventional_unit_cell: bool = False,
+    api_key=None,
+) -> Atoms | list[Atoms]:
+    """
+    Retrieve a structure by material id.
+
+    This is how you would ask for the iron ground state:
+
+    >>> structuretoolkit.build.materialsproject.by_id('mp-13')
+    Fe: [0. 0. 0.]
+    tags:
+        spin: [(0: 2.214)]
+    pbc: [ True  True  True]
+    cell:
+    Cell([[2.318956, 0.000185, -0.819712], [-1.159251, 2.008215, -0.819524], [2.5e-05, 0.000273, 2.459206]])
+
+    Usage is only possible with an API key obtained from the Materials Project.  To do this, create an account with
+    them, login and access `this webpage <https://next-gen.materialsproject.org/api#api-key>`.
+
+    Once you have a key, either pass it as the `api_key` parameter or export an
+    environment variable, called `MP_API_KEY`, in your shell setup.
+
+    Args:
+        material_id (str): the id assigned to a structure by the materials project
+        api_key (str, optional): if your API key is not exported in the environment flag MP_API_KEY, pass it here
+        final (bool, optional): if set to False, returns the list of initial structures,
+        else returns the final structure. (Default is True)
+        conventional_unit_cell (bool, optional): if set to True, returns the standard conventional unit cell.
+        (Default is False)
+
+    Returns:
+        :class:`~.Atoms`: requested final structure if final is True
+        list of :class:~.Atoms`:  a list of initial (pre-relaxation) structures if final is False
+
+    Raises:
+        ValueError: material id does not exist
+    """
+    from mp_api.client import MPRester
+
+    rest_kwargs = {
+        "include_user_agent": True,  # send some additional software version info to MP
+    }
+    if api_key is not None:
+        rest_kwargs["api_key"] = api_key
+    with MPRester(**rest_kwargs) as mpr:
+        if final:
+            return pymatgen_to_ase(
+                mpr.get_structure_by_material_id(
+                    material_id=material_id,
+                    final=final,
+                    conventional_unit_cell=conventional_unit_cell,
+                )
+            )
+        else:
+            return [
+                pymatgen_to_ase(mpr_structure)
+                for mpr_structure in (
+                    mpr.get_structure_by_material_id(
+                        material_id=material_id,
+                        final=final,
+                        conventional_unit_cell=conventional_unit_cell,
+                    )
+                )
+            ]