Add mp-api interface

.ci_support/environment.yml

@@ -20,3 +20,4 @@ dependencies:
 - sqsgenerator =0.5.4
 - hatchling =1.29.0
 - hatch-vcs =0.5.0
+- mp-api =0.37.2

src/structuretoolkit/build/__init__.py

@@ -2,6 +2,10 @@
 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 @@
     "sqs_structures",
     "get_high_index_surface_info",
     "high_index_surface",
+    "materialsproject_search",
+    "materialsproject_by_id",
 ]

src/structuretoolkit/build/materialsproject.py

@@ -0,0 +1,139 @@
+from typing import Any
+from collections.abc import Generator
+from ase.atoms import Atoms
+from structuretoolkit.common.pymatgen import pymatgen_to_ase
+
+
+def search(
+    chemsys: str | list[str], api_key=None, **kwargs
+) -> Generator[dict[str, Any]]:
+    """
+    Search the database for all structures matching the given query.
+
+    Note that `chemsys` takes distint values for unaries, binaries and so!  A query with `chemsys=["Fe", "O"]` will
+    return iron structures and oxygen structures, but no iron oxide structures.  Similarily `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:
+
+    >>> pr = Project(...)
+    >>> irons = pr.create.structure.materialsproject.search("Fe")
+    >>> irons.number_of_structures
+    10
+
+    The returned :class:`~.MPQueryResults` object implements :class:`~.HasStructure` and can be accessed with the
+    material ids as a short-hand
+
+    >>> irons.get_structure(1) == irons.get_structure('mp-13')
+    True
+
+    Search for all structures with Al, Li that are on the T=0 convex hull:
+
+    >>> alli = pr.create.structure.materialsproject.search(['Al', 'Li', 'Al-Li'], is_stable=True)
+    >>> len(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 seperated by dashes; if a list of strings is given return structures matching either of them
+        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:
+        :class:`~.MPQueryResults`: resulting structures from the query
+    """
+    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=["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:
+
+    >>> pr = Project(...)
+    >>> pr.create.structure.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,
+                    )
+                )
+            ]