Merge pull request #71 from spglib/moyopy-msg

Python interface for MSG

justfile

@@ -10,7 +10,7 @@ build-python:
 install-python:
     python -m pip install uv maturin
     maturin develop --release --manifest-path moyopy/Cargo.toml
-    python -m uv pip install -e "moyopy[dev]"
+    python -m pip install -e "moyopy[dev]"
     pre-commit install
 
 test-python:

moyo/src/base/lattice.rs

@@ -1,4 +1,4 @@
-use nalgebra::base::{Matrix3, Vector3};
+use nalgebra::base::{Matrix3, OMatrix, RowVector3, Vector3};
 use serde::{Deserialize, Serialize};
 
 use crate::math::{
@@ -22,6 +22,14 @@ impl Lattice {
         }
     }
 
+    pub fn from_basis(basis: [[f64; 3]; 3]) -> Self {
+        Self::new(OMatrix::from_rows(&[
+            RowVector3::from(basis[0]),
+            RowVector3::from(basis[1]),
+            RowVector3::from(basis[2]),
+        ]))
+    }
+
     /// Return Minkowski reduced lattice and transformation matrix to it
     pub fn minkowski_reduce(&self) -> Result<(Self, Matrix3<i32>), MoyoError> {
         let (reduced_basis, trans_mat) = minkowski_reduce(&self.basis);

moyo/src/base/magnetic_cell.rs

@@ -30,7 +30,7 @@ pub trait MagneticMoment: Sized + Clone {
     }
 }
 
-#[derive(Debug, Clone)]
+#[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Collinear(pub f64);
 
 impl MagneticMoment for Collinear {
@@ -66,7 +66,7 @@ impl MagneticMoment for Collinear {
     }
 }
 
-#[derive(Debug, Clone)]
+#[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct NonCollinear(pub Vector3<f64>);
 
 impl MagneticMoment for NonCollinear {

moyo/src/data.rs

@@ -20,7 +20,8 @@ pub use hall_symbol::{HallSymbol, MagneticHallSymbol};
 pub use hall_symbol_database::{hall_symbol_entry, HallNumber, HallSymbolEntry, Number};
 pub use magnetic_hall_symbol_database::{magnetic_hall_symbol_entry, MagneticHallSymbolEntry};
 pub use magnetic_space_group::{
-    get_magnetic_space_group_type, ConstructType, UNINumber, NUM_MAGNETIC_SPACE_GROUP_TYPES,
+    get_magnetic_space_group_type, ConstructType, MagneticSpaceGroupType, UNINumber,
+    NUM_MAGNETIC_SPACE_GROUP_TYPES,
 };
 pub use setting::Setting;
 

moyo/src/data/magnetic_space_group.rs

@@ -19,12 +19,17 @@ pub enum ConstructType {
 
 #[derive(Debug, Clone)]
 pub struct MagneticSpaceGroupType {
+    /// Serial number of UNI (and BNS) symbols
     pub uni_number: UNINumber,
+    /// Serial number in Litvin's [Magnetic group tables](https://www.iucr.org/publ/978-0-9553602-2-0)
     pub litvin_number: i32,
+    /// BNS number e.g. '151.32'
     pub bns_number: &'static str,
+    /// OG number e.g. '153.4.1270'
     pub og_number: &'static str,
     /// ITA number for reference space group in BNS setting
     pub number: Number,
+    /// Construct type of magnetic space group
     pub construct_type: ConstructType,
 }
 

moyo/src/lib.rs

@@ -18,10 +18,15 @@ moyo = "*"
 The basic usage of **moyo** is to create a [`moyo::base::Cell`](Cell) representing a crystal structure, and then create a [`moyo::MoyoDataset`](MoyoDataset) from the [`moyo::base::Cell`](Cell).
 The [`moyo::MoyoDataset`](MoyoDataset) contains symmetry information of the input crystal structure: for example, the space group number, symmetry operations, and standardized cell.
 
+Magnetic symmetry is also supported in **moyo**.
+Magnetic moments are represented by a struct implementing the [`moyo::base::MagneticMoment`](MagneticMoment) trait: for example, [`moyo::base::Collinear`](Collinear) or [`moyo::base::NonCollinear`](NonCollinear).
+Magnetic cell is represented by a [`moyo::base::MagneticCell`](MagneticCell) struct.
+The [`moyo::MoyoMagneticDataset`](MoyoMagneticDataset) contains magnetic symmetry information of the input magnetic cell: for example, the magnetic space-group type, magnetic symmetry operations, and standardized magnetic cell.
+
 ```
 use nalgebra::{matrix, vector, Matrix3, Vector3};
-use moyo::MoyoDataset;
-use moyo::base::{Cell, AngleTolerance, Lattice};
+use moyo::{MoyoDataset, MoyoMagneticDataset};
+use moyo::base::{Cell, MagneticCell, AngleTolerance, Lattice, NonCollinear, RotationMagneticMomentAction};
 use moyo::data::Setting;
 
 let lattice = Lattice::new(matrix![
@@ -39,15 +44,29 @@ let positions = vec![
     Vector3::new(x_4f + 0.5, -x_4f + 0.5, 0.5), // O(4f)
 ];
 let numbers = vec![0, 0, 1, 1, 1, 1];
-let cell = Cell::new(lattice, positions, numbers);
+let cell = Cell::new(lattice.clone(), positions.clone(), numbers.clone());
 
-let symprec = 1e-5;
+let symprec = 1e-4;
 let angle_tolerance = AngleTolerance::Default;
 let setting = Setting::Standard;
 
 let dataset = MoyoDataset::new(&cell, symprec, angle_tolerance, setting).unwrap();
-
 assert_eq!(dataset.number, 136);  // P4_2/mnm
+
+let magnetic_moments = vec![
+    NonCollinear(vector![0.0, 0.0, 0.7]),
+    NonCollinear(vector![0.0, 0.0, -0.7]),
+    NonCollinear(vector![0.0, 0.0, 0.0]),
+    NonCollinear(vector![0.0, 0.0, 0.0]),
+    NonCollinear(vector![0.0, 0.0, 0.0]),
+    NonCollinear(vector![0.0, 0.0, 0.0]),
+];
+let magnetic_cell = MagneticCell::new(lattice, positions, numbers, magnetic_moments);
+
+let action = RotationMagneticMomentAction::Axial;
+
+let magnetic_dataset = MoyoMagneticDataset::new(&magnetic_cell, symprec, angle_tolerance, None, action).unwrap();
+assert_eq!(magnetic_dataset.uni_number, 1159);  // BNS 136.499
 ```
 
 ## Features
@@ -57,6 +76,7 @@ assert_eq!(dataset.number, 136);  // P4_2/mnm
 - Space-group type identification
 - Wyckoff position assignment
 - Crystal structure symmetrization
+- Magnetic space group support
 
 */
 #[allow(unused_imports)]
@@ -90,7 +110,7 @@ use nalgebra::Matrix3;
 /// A dataset containing symmetry information of the input crystal structure.
 pub struct MoyoDataset {
     // ------------------------------------------------------------------------
-    // Space-group type
+    // Identification
     // ------------------------------------------------------------------------
     /// Space group number.
     pub number: Number,

moyo/src/symmetrize/magnetic_standardize.rs

@@ -114,7 +114,7 @@ impl<M: MagneticMoment> StandardizedMagneticCell<M> {
             action,
         );
         let prim_std_mag_cell =
-            MagneticCell::from_cell(ref_std_cell.cell.clone(), prim_std_magnetic_moments);
+            MagneticCell::from_cell(ref_std_cell.prim_cell.clone(), prim_std_magnetic_moments);
 
         // To (conventional) standardized magnetic cell
         let refined_prim_mag_cell = ref_std_cell

moyopy/examples/basic.py

@@ -23,7 +23,7 @@
 numbers = [0, 0, 1, 1]
 cell = moyopy.Cell(basis, positions, numbers)
 
-dataset = moyopy.MoyoDataset(cell, symprec=1e-5, angle_tolerance=None, setting=None)
+dataset = moyopy.MoyoDataset(cell, symprec=1e-4, angle_tolerance=None, setting=None)
 assert dataset.number == 186
 assert dataset.hall_number == 480
 

moyopy/examples/pymatgen_structure.py

@@ -11,7 +11,7 @@ class MoyoSpacegroupAnalyzer:
     def __init__(
         self,
         structure: Structure,
-        symprec: float = 1e-5,
+        symprec: float = 1e-4,
         angle_tolerance: float | None = None,
         setting: moyopy.Setting | None = None,
     ):

moyopy/python/moyopy/_base.pyi

@@ -11,6 +11,52 @@ class Cell:
     def positions(self) -> list[list[float]]: ...
     @property
     def numbers(self) -> list[int]: ...
+    @property
+    def num_atoms(self) -> int: ...
+    def serialize_json(self) -> str: ...
+    @classmethod
+    def deserialize_json(cls, json_str: str) -> Cell: ...
+
+class CollinearMagneticCell:
+    def __init__(
+        self,
+        basis: list[list[float]],
+        positions: list[list[float]],
+        numbers: list[int],
+        magnetic_moments: list[float],
+    ): ...
+    @property
+    def basis(self) -> list[list[float]]: ...
+    @property
+    def positions(self) -> list[list[float]]: ...
+    @property
+    def numbers(self) -> list[int]: ...
+    @property
+    def magnetic_moments(self) -> list[float]: ...
+    @property
+    def num_atoms(self) -> int: ...
+    def serialize_json(self) -> str: ...
+    @classmethod
+    def deserialize_json(cls, json_str: str) -> Cell: ...
+
+class NonCollinearMagneticCell:
+    def __init__(
+        self,
+        basis: list[list[float]],
+        positions: list[list[float]],
+        numbers: list[int],
+        magnetic_moments: list[list[float]],
+    ): ...
+    @property
+    def basis(self) -> list[list[float]]: ...
+    @property
+    def positions(self) -> list[list[float]]: ...
+    @property
+    def numbers(self) -> list[int]: ...
+    @property
+    def magnetic_moments(self) -> list[list[float]]: ...
+    @property
+    def num_atoms(self) -> int: ...
     def serialize_json(self) -> str: ...
     @classmethod
     def deserialize_json(cls, json_str: str) -> Cell: ...
@@ -23,3 +69,14 @@ class Operations:
     @property
     def num_operations(self) -> int: ...
     def __len__(self) -> int: ...
+
+class MagneticOperations:
+    @property
+    def rotations(self) -> list[list[list[float]]]: ...
+    @property
+    def translations(self) -> list[list[float]]: ...
+    @property
+    def time_reversals(self) -> list[bool]: ...
+    @property
+    def num_operations(self) -> int: ...
+    def __len__(self) -> int: ...

moyopy/python/moyopy/_data.pyi

@@ -104,4 +104,26 @@ class SpaceGroupType:
         for string values.
         """
 
+class MagneticSpaceGroupType:
+    """Magnetic space-group type information."""
+    def __init__(self, uni_number: int): ...
+    @property
+    def uni_number(self) -> int:
+        """Serial number of UNI (and BNS) symbols."""
+    @property
+    def litvin_number(self) -> int:
+        """Serial number in Litvin's `Magnetic group tables <https://www.iucr.org/publ/978-0-9553602-2-0>`_."""
+    @property
+    def bns_number(self) -> str:
+        """BNS number e.g. '151.32'"""
+    @property
+    def og_number(self) -> str:
+        """OG number e.g. '153.4.1270'"""
+    @property
+    def number(self) -> int:
+        """ITA number for reference space group in BNS setting."""
+    @property
+    def construct_type(self) -> int:
+        """Construct type of magnetic space group from 1 to 4."""
+
 def operations_from_number(number: int, setting: Setting) -> Operations: ...