From e7ed5d2c96cf45fd32ba553cab1d891b015044a9 Mon Sep 17 00:00:00 2001
From: Minye Zhang <minyez.physchem@gmail.com>
Date: Sun, 15 Dec 2024 11:29:22 +0100
Subject: [PATCH] add MX2 factory method

---
 mushroom/core/cell.py           | 26 ++++++++++++++++++++++++++
 mushroom/core/test/test_cell.py |  1 +
 2 files changed, 27 insertions(+)

diff --git a/mushroom/core/cell.py b/mushroom/core/cell.py
index c2fa966..37958bd 100644
--- a/mushroom/core/cell.py
+++ b/mushroom/core/cell.py
@@ -1862,6 +1862,32 @@ def marcasite(cls, atom1: str = "Fe", atom2: str = "S",
             kwargs.update({"comment": "Marcasite {}{}2".format(atom1, atom2)})
         return cls(latt, atms, posi, **kwargs)
 
+    @classmethod
+    def MX2(cls, atom1: str = "Mo", atom2: str = "S",
+            a: float = 3.22, c: float = 12.36, d: float = 2.31, kind: str = "2H",
+            **kwargs):
+        '''Generate a standardized  lattice (space group 58).
+
+        Args:
+            atom1 (str): symbol of the M atom
+            atom2 (str): symbol of the X atom
+            a, c (float): the lattice constants of the cell.
+            d (float): bond length of M-X
+            kwargs: keyword argument for ``Cell`` except ``coord_sys``
+        '''
+        if kind == "2H":
+            d_frac = np.sqrt(d ** 2 - a ** 2 / 3.0e0) / c
+            ha = 0.5e0 * a
+            latt = [[a, 0.0, 0.0], [-ha, ha * SQRT3, 0], [0.0, 0.0, c]]
+            atms = [str(atom1),] * 1 + [str(atom2),] * 2
+            posi = [[0.0, 0.0, 0.5],
+                    [1 / 3, 2 / 3, 0.5 - d_frac],
+                    [1 / 3, 2 / 3, 0.5 + d_frac],]
+        else:
+            raise NotImplementedError("kind {}".format(kind))
+        _logger.debug("creating MX2: latt %r, posi %r, atms %r", latt, posi, atms)
+        return cls(latt, atms, posi, **kwargs)
+
 
 def latt_equal(cell1: Cell, cell2: Cell) -> bool:
     """compare the lattice vectors of two cell"""
diff --git a/mushroom/core/test/test_cell.py b/mushroom/core/test/test_cell.py
index 7f24f47..2e9e2a7 100644
--- a/mushroom/core/test/test_cell.py
+++ b/mushroom/core/test/test_cell.py
@@ -191,6 +191,7 @@ def test_typical_systems(self):
         Cell.wurtzite("Zn", "O")
         Cell.pyrite()
         Cell.marcasite()
+        Cell.MX2()
 
 
 class cell_reader(ut.TestCase):