python examples

.github/workflows/ci-python.yaml

@@ -19,6 +19,29 @@ permissions:
   packages: write  # for uraimo/run-on-arch-action to cache docker images
 
 jobs:
+  examples:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: Swatinem/rust-cache@v2
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          args: --release --out dist --manifest-path moyopy/Cargo.toml
+          sccache: 'true'
+          manylinux: auto
+      - name: examples
+        shell: bash
+        run: |
+          set -e
+          pip install moyopy[dev] --find-links dist --force-reinstall
+          pip install -r moyopy/examples/requirements.txt
+          python moyopy/examples/basic.py
+          python moyopy/examples/pymatgen_structure.py
+
   linux:
     runs-on: ubuntu-latest
     strategy:

bench/mp/analysis.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -255,7 +255,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
@@ -280,7 +280,7 @@
     "ax.set_aspect('equal')\n",
     "ax.set_title(\"mp_computed_structure_entries\")\n",
     "ax.grid()\n",
-    "fig.savefig('mp.png', bbox_inches=\"tight\", pad_inches=0.0, dpi=500)"
+    "fig.savefig('mp.png', bbox_inches=\"tight\", pad_inches=0.0, dpi=200)"
    ]
   },
   {

moyopy/README.md

@@ -5,3 +5,7 @@
 [![image](https://img.shields.io/pypi/pyversions/moyopy.svg)](https://pypi.python.org/pypi/moyopy)
 
 Python interface of Moyo
+
+## Examples
+
+See [example directory](examples)

moyopy/examples/basic.py

@@ -0,0 +1,31 @@
+from __future__ import annotations
+
+from math import sqrt
+
+import moyopy
+
+if __name__ == "__main__":
+    # https://next-gen.materialsproject.org/materials/mp-560588
+    a = 3.81
+    c = 6.24
+    basis = [
+        [a, 0.0, 0.0],
+        [-a / 2.0, a * sqrt(3.0) / 2.0, 0.0],
+        [0.0, 0.0, c],
+    ]
+    z1_2b = 0.00014
+    z2_2b = 0.37486
+    positions = [
+        # 2b
+        [1 / 3, 2 / 3, z1_2b],
+        [2 / 3, 1 / 3, z1_2b + 0.5],
+        # 2b
+        [1 / 3, 2 / 3, z2_2b],
+        [2 / 3, 1 / 3, z2_2b + 0.5],
+    ]
+    numbers = [0, 0, 1, 1]
+    cell = moyopy.Cell(basis, positions, numbers)
+
+    dataset = moyopy.MoyoDataset(cell, symprec=1e-5, angle_tolerance=None, setting=None)
+    assert dataset.number == 186
+    assert dataset.hall_number == 480

moyopy/examples/pymatgen_structure.py

@@ -0,0 +1,131 @@
+from __future__ import annotations
+
+import numpy as np
+from pymatgen.core import Element, Structure
+
+import moyopy
+
+
+class MoyoAdapter:
+    @staticmethod
+    def get_structure(cell: moyopy.Cell) -> Structure:
+        species = [Element.from_Z(number) for number in cell.numbers]
+        return Structure(lattice=cell.basis, species=species, coords=cell.positions)
+
+    @staticmethod
+    def get_moyo_cell(structure: Structure) -> moyopy.Cell:
+        basis = structure.lattice.matrix
+        positions = structure.frac_coords
+        numbers = [site.specie.Z for site in structure]
+
+        return moyopy.Cell(
+            basis=basis.tolist(),
+            positions=positions.tolist(),
+            numbers=numbers,
+        )
+
+
+class MoyoSpacegroupAnalyzer:
+    def __init__(
+        self,
+        structure: Structure,
+        symprec: float = 1e-5,
+        angle_tolerance: float | None = None,
+        setting: moyopy.Setting | None = None,
+    ):
+        self._cell = MoyoAdapter.get_moyo_cell(structure)
+        self._dataset = moyopy.MoyoDataset(
+            cell=self._cell,
+            symprec=symprec,
+            angle_tolerance=angle_tolerance,
+            setting=setting,
+        )
+
+    @property
+    def number(self) -> int:
+        return self._dataset.number
+
+    @property
+    def hall_number(self) -> int:
+        return self._dataset.hall_number
+
+    @property
+    def rotations(self) -> np.ndarray:
+        return np.array(self._dataset.operations.rotations)
+
+    @property
+    def translations(self) -> np.ndarray:
+        return np.array(self._dataset.operations.translations)
+
+    @property
+    def orbits(self) -> list[int]:
+        return self._dataset.orbits
+
+    @property
+    def wyckoffs(self) -> list[str]:
+        return self._dataset.wyckoffs
+
+    @property
+    def site_symmetry_symbols(self) -> list[str]:
+        return self._dataset.site_symmetry_symbols
+
+    @property
+    def std_structure(self) -> Structure:
+        return MoyoAdapter.get_structure(self._dataset.std_cell)
+
+    @property
+    def std_linear(self) -> np.ndarray:
+        return np.array(self._dataset.std_linear)
+
+    @property
+    def std_origin_shift(self) -> np.ndarray:
+        return np.array(self._dataset.std_origin_shift)
+
+    @property
+    def std_rotation_matrix(self) -> np.ndarray:
+        return np.array(self._dataset.std_rotation_matrix)
+
+    @property
+    def prim_std_structure(self) -> Structure:
+        return MoyoAdapter.get_structure(self._dataset.prim_std_cell)
+
+    @property
+    def prim_std_linear(self) -> np.ndarray:
+        return np.array(self._dataset.prim_std_linear)
+
+    @property
+    def prim_std_origin_shift(self) -> np.ndarray:
+        return np.array(self._dataset.prim_std_origin_shift)
+
+    @property
+    def mapping_std_prim(self) -> list[int]:
+        return self._dataset.mapping_std_prim
+
+    @property
+    def symprec(self) -> float:
+        return self._dataset.symprec
+
+    @property
+    def angle_tolerance(self) -> float | None:
+        return self._dataset.angle_tolerance
+
+
+if __name__ == "__main__":
+    a = 4.0
+    structure = Structure(
+        lattice=np.eye(3) * a,
+        species=["Al"] * 4,
+        coords=np.array(
+            [
+                [0.0, 0.0, 0.0],
+                [0.0, 0.5, 0.5],
+                [0.5, 0.0, 0.5],
+                [0.5, 0.5, 0.0],
+            ]
+        ),
+    )
+    msa = MoyoSpacegroupAnalyzer(structure)
+    assert msa.number == 225
+    assert msa.rotations.shape == (48 * 4, 3, 3)
+    assert msa.orbits == [0, 0, 0, 0]
+    assert msa.prim_std_structure.num_sites == 1

moyopy/examples/requirements.txt

@@ -0,0 +1 @@
+pymatgen