From f45cb8f8ac0aea9e6cfadc73df32f9b98b2c60a6 Mon Sep 17 00:00:00 2001
From: lan496 <kshinohara0508@gmail.com>
Date: Sun, 10 Mar 2024 14:36:42 +0900
Subject: [PATCH] Fix array major

---
 justfile                                  |  3 +++
 moyo/tests/test_moyo_dataset.rs           |  2 +-
 moyo_py/python/moyo/_moyo.pyi             |  2 +-
 moyo_py/python/tests/conftest.py          | 12 +++++++++---
 moyo_py/python/tests/test_moyo_dataset.py |  3 ++-
 moyo_py/src/base.rs                       |  9 +++++++--
 moyo_py/src/lib.rs                        |  2 +-
 7 files changed, 24 insertions(+), 9 deletions(-)

diff --git a/justfile b/justfile
index aa6590d..410d06c 100644
--- a/justfile
+++ b/justfile
@@ -4,6 +4,9 @@ set positional-arguments
 default:
     just --list
 
+build-python:
+    maturin develop --release --manifest-path moyo_py/Cargo.toml
+
 install-python:
     maturin develop --release --manifest-path moyo_py/Cargo.toml
     pip install -e "moyo_py[dev]"
diff --git a/moyo/tests/test_moyo_dataset.rs b/moyo/tests/test_moyo_dataset.rs
index 6e74666..c0c854c 100644
--- a/moyo/tests/test_moyo_dataset.rs
+++ b/moyo/tests/test_moyo_dataset.rs
@@ -254,7 +254,7 @@ fn test_with_wurtzite() {
     let numbers = vec![0, 0, 1, 1];
     let cell = Cell::new(lattice, positions, numbers);
 
-    let symprec = 1e-2;
+    let symprec = 1e-4;
     let angle_tolerance = AngleTolerance::Default;
     let setting = Setting::Standard;
 
diff --git a/moyo_py/python/moyo/_moyo.pyi b/moyo_py/python/moyo/_moyo.pyi
index 71f4046..d2f55a8 100644
--- a/moyo_py/python/moyo/_moyo.pyi
+++ b/moyo_py/python/moyo/_moyo.pyi
@@ -40,7 +40,7 @@ class MoyoDataset:
     def __init__(
         self,
         structure: Structure,
-        symprec: float = 1e-5,
+        symprec: float = 1e-4,
         angle_tolerance: float | None = None,
         setting: Setting | None = None,
     ): ...
diff --git a/moyo_py/python/tests/conftest.py b/moyo_py/python/tests/conftest.py
index 69c9e3c..9c176d5 100644
--- a/moyo_py/python/tests/conftest.py
+++ b/moyo_py/python/tests/conftest.py
@@ -15,11 +15,17 @@ def wurtzite() -> moyo.Structure:
         [-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 = [
-        [1 / 3, 2 / 3, 0.00014],
-        [1 / 3, 2 / 3, 0.37486],
+        # 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, 1]
+    numbers = [0, 0, 1, 1]
 
     structure = moyo.Structure(basis, positions, numbers)
     return structure
diff --git a/moyo_py/python/tests/test_moyo_dataset.py b/moyo_py/python/tests/test_moyo_dataset.py
index 6c4f02e..0d1eadc 100644
--- a/moyo_py/python/tests/test_moyo_dataset.py
+++ b/moyo_py/python/tests/test_moyo_dataset.py
@@ -2,4 +2,5 @@
 
 
 def test_moyo_dataset(wurtzite: moyo.Structure):
-    _dataset = moyo.MoyoDataset(wurtzite)
+    dataset = moyo.MoyoDataset(wurtzite)
+    assert dataset.number == 186
diff --git a/moyo_py/src/base.rs b/moyo_py/src/base.rs
index 6a84d5b..cd9a9d6 100644
--- a/moyo_py/src/base.rs
+++ b/moyo_py/src/base.rs
@@ -1,4 +1,4 @@
-use nalgebra::{OMatrix, Vector3};
+use nalgebra::{OMatrix, RowVector3, Vector3};
 use pyo3::exceptions::PyValueError;
 use pyo3::prelude::*;
 
@@ -24,7 +24,12 @@ impl PyStructure {
             ));
         }
 
-        let lattice = Lattice::new(OMatrix::from(basis));
+        // let lattice = Lattice::new(OMatrix::from(basis));
+        let lattice = Lattice::new(OMatrix::from_rows(&[
+            RowVector3::from(basis[0]),
+            RowVector3::from(basis[1]),
+            RowVector3::from(basis[2]),
+        ]));
         let positions = positions
             .iter()
             .map(|x| Vector3::new(x[0], x[1], x[2]))
diff --git a/moyo_py/src/lib.rs b/moyo_py/src/lib.rs
index a7a900d..349e416 100644
--- a/moyo_py/src/lib.rs
+++ b/moyo_py/src/lib.rs
@@ -19,7 +19,7 @@ pub struct PyMoyoDataset(MoyoDataset);
 #[pymethods]
 impl PyMoyoDataset {
     #[new]
-    #[pyo3(signature = (structure, *, symprec=1e-5, angle_tolerance=None, setting=None))]
+    #[pyo3(signature = (structure, *, symprec=1e-4, angle_tolerance=None, setting=None))]
     pub fn new(
         structure: &PyStructure,
         symprec: f64,