updated V0.11.4

ReleaseNotes.rst

@@ -1,12 +1,13 @@
 Release Notes
 --------------
 
-Mdapy 0.11.4 (Under development)
+Mdapy 0.11.4 (Nov 13, 2024)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 🏆 Highlights
 ---------------
 - Add feature to Minimizer class for optimizing the box.
+- Add many options for calculating SteinhardtBondOrientation, including the Voronoi neighbor, weighted by Voronoi face area and average version.
 
 🐞 Bug fixes
 -----------------

mdapy/minimizer.py

@@ -236,17 +236,17 @@ def compute(self):
     nep = NEP(r"D:\Study\Gra-Al\potential_test\validating\graphene\itre_45\nep.txt")
 
     element_name, lattice_constant, lattice_type, potential = (
-        "Al",
-        4.1,
-        "FCC",
+        "C",
+        1.42,
+        "GRA",
         nep,
     )
-    x, y, z = 5, 5, 5
+    x, y, z = 5, 5, 1
     fmax = 1e-5
     max_itre = 200
     lat = LatticeMaker(lattice_constant, lattice_type, x, y, z)
     lat.compute()
-
+    lat.box[2, 2] += 20
     # pe_atom, _, _ = potential.compute(
     #     lat.pos, lat.box, [element_name], lat.type_list, [1, 1, 1]
     # )
@@ -279,11 +279,11 @@ def compute(self):
         lat.type_list,
         fmax=fmax,
         max_itre=max_itre,
-        volume_change=True,
+        volume_change=False,
         hydrostatic_strain=True,
     )
     mini.compute()
-    print(mini.box / 5)
+    print(mini.box)
 
     # e, f, v = potential.compute(mini.pos, mini.box, [element_name], lat.type_list)
     # vol = np.inner(mini.box[0], np.cross(mini.box[1], mini.box[2]))

mdapy/steinhardt_bond_orientation.py

@@ -247,6 +247,10 @@ class SteinhardtBondOrientation:
         wlflag (bool, optional): whether calculate the third-order invariants :math:`W_{\ell}`. Defaults to False.
         wlhatflag (bool, optional): whether calculate the normalized third-order invariants :math:`\hat{W}_{\ell}`. If :math:`wlflag` is False, this parameter has no effect. Defaults to False.
         max_neigh (int, optional): a given maximum neighbor number per atoms. Defaults to 60.
+        use_weight (bool, optional): whether use weight. Defaults to False.
+        weight (np.ndarray, optional): a given weight to calculate the qlm. Such as a voronoi face area array. Defaults to None.
+        voronoi (bool, optional): indicate that whether the neighbor is Voronoi neighbor. Defaults to False.
+        average (bool, optional): whether average the qlm within the neighbor atoms. Defaults to False.
 
     Outputs:
         - **qnarray** (np.ndarray) - (math:`N_p, len(qlist)*(1+wlflag+wlhatflag)`) consider the :math:`qlist=[4, 6]` and :math:`wlflag` and :math:`wlhatflag` is True, the columns of :math:`qnarray` are [:math:`Q_4, Q_6, W_4, W_6, \hat{W}_4, \hat{W}_6`].

mdapy/system.py

@@ -1221,6 +1221,9 @@ def cal_steinhardt_bond_orientation(
             rc (float, optional): cutoff distance to find neighbors. Defaults to 0.0.
             wlflag (bool, optional): whether calculate the third-order invariants :math:`W_{\ell}`. Defaults to False.
             wlhatflag (bool, optional): whether calculate the normalized third-order invariants :math:`\hat{W}_{\ell}`. If :math:`wlflag` is False, this parameter has no effect. Defaults to False.
+            use_voronoi (bool, optional): whether use Voronoi neighbor. Defaults to False.
+            use_weight (bool, optional): whether use Voronoi face area to weight the qlm. Defaults to False.
+            average (bool, optional): whether avcerage the qlm with the neighbor atoms. Defaults to False.
             solidliquid (bool, optional): whether identify the solid/liquid phase. Defaults to False.
             max_neigh (int, optional): a given maximum neighbor number per atoms. Defaults to 60.
             threshold (float, optional): threshold value to determine the solid bond. Defaults to 0.7.