surface-construct 0.8.1__tar.gz → 0.8.2__tar.gz

{surface_construct-0.8.1/surface_construct.egg-info → surface_construct-0.8.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: surface_construct
-Version: 0.8.1
+Version: 0.8.2
 Summary: Surface termination construction especially for complex model, such as oxides or carbides.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren

{surface_construct-0.8.1 → surface_construct-0.8.2}/setup.py

@@ -18,7 +18,7 @@ install_requires = [
 
 setup(
     name='surface_construct',
-    version='0.8.1',
+    version='0.8.2',
     packages=['surface_construct'],
     url='https://gitee.com/pjren/surface_construct/',
     license='GPL',

{surface_construct-0.8.1 → surface_construct-0.8.2}/surface_construct/sampling.py

@@ -1,17 +1,37 @@
 """
 TODO: 关键点采样：top 位置、hollow位，bridge 位等等。
 """
-from logging import warning
-
+import itertools
 import numpy as np
 from ase.geometry import get_distances
 from scipy.spatial import ConvexHull
 from scipy.spatial.distance import cdist
+from scipy.special import comb
 from sklearn.cluster import KMeans as Cluster
 import random
 
 from surface_construct.utils import furthest_sites
 
+MIN_HULL_ANGLE_COS = np.cos(np.pi * 30 / 180)
+
+def hull_vertices(hull):
+    hsimplices = hull.simplices
+    hvertices = hull.vertices
+    hnorms = hull.equations[:,0:-1]
+    ndim = hsimplices.shape[1]
+    vertices = []
+    # 去掉 hull 的 simplices 的角度较大的点
+    for i in hvertices:
+        p0_facets_idx = np.argwhere(hsimplices == i)[:,0]
+        p0_norms = hnorms[p0_facets_idx]
+        cosangle = lambda a,b: a.dot(b) / (np.linalg.norm(a) * np.linalg.norm(b))
+        # 求 i 凸点相邻的超平面的法向向量之间的夹角。如果存在夹角小于30度，即平面之间的夹角大于150度，则排除该点。反之，保留该点。
+        norm_angle_cos = np.absolute([cosangle(a,b) for a,b in itertools.combinations(p0_norms, 2)])
+        if np.sum(norm_angle_cos < MIN_HULL_ANGLE_COS) >= comb(ndim,2):
+            vertices.append(i)
+
+    return vertices
+
 
 def addition_samples(sg_obj, size=None, probability=None, **kwargs):
     if 'seed' in kwargs:
@@ -138,19 +158,20 @@ class InitialSampling(SamplingBase):
 
     def _samples(self, size, **kwargs):
         hull = ConvexHull(self.sg_obj.vector)
-        vertices = []
+        #vertices = []
         # 去掉 hull 的 simplices 的角度较大的点
-        for i in hull.vertices:
-            p1_idx, p2_idx = np.argwhere(hull.simplices == i)
-            p0 = hull.points[i]
-            p1 = hull.points[hull.simplices[p1_idx[0],1-p1_idx[1]]]
-            p2 = hull.points[hull.simplices[p2_idx[0],1-p2_idx[1]]]
-            a = p1 - p0
-            b = p2 - p0
-            cosangle = a.dot(b)/(np.linalg.norm(a) * np.linalg.norm(b))
-            if cosangle > np.cos(np.pi*150/180):
-                vertices.append(i)
+        #for i in hull.vertices:
+        #    p1_idx, p2_idx = np.argwhere(hull.simplices == i)
+        #    p0 = hull.points[i]
+        #    p1 = hull.points[hull.simplices[p1_idx[0],1-p1_idx[1]]]
+        #    p2 = hull.points[hull.simplices[p2_idx[0],1-p2_idx[1]]]
+        #    a = p1 - p0
+        #    b = p2 - p0
+        #    cosangle = a.dot(b)/(np.linalg.norm(a) * np.linalg.norm(b))
+        #    if cosangle > MIN_HULL_ANGLE_COS:
+        #        vertices.append(i)
         # 聚类，vector_mesh
+        vertices = hull_vertices(hull)
         n_vector_mesh = int(hull.volume / (self.sg_obj._vector_unit *
                                            self.sg_obj.interval)**self.sg_obj.vector.shape[1]) + 1
         cluster0 = Cluster(n_clusters=n_vector_mesh)
@@ -162,9 +183,11 @@ class InitialSampling(SamplingBase):
         self.sg_obj._clusters = cluster
         nvert = len(vertices)
         if nvert >= size:
-            warning("Sample number better be larger than {nvert}!")
+            print(f"Warning: Sample number better be larger than {nvert}!")
             if size == 1:
                 sample_idx = np.random.choice(vertices,1)
+            elif size==nvert:
+                sample_idx = vertices
             else:
                 sample_idx = [vertices[i] for i in
                               furthest_sites(self.sg_obj.vector[vertices], size)]

{surface_construct-0.8.1 → surface_construct-0.8.2}/surface_construct/surface_grid.py

@@ -321,7 +321,7 @@ class SurfaceGrid:
         k = d_vector / self.interval
         return np.min(k)
 
-    def grid_sample(self, probability=None, N=1, **kwargs):
+    def grid_sample(self, N=1, probability=None, **kwargs):
         """
         Warning: Obsoleted, replaced by Sampling class
         :param probability:

{surface_construct-0.8.1 → surface_construct-0.8.2}/surface_construct/utils.py

@@ -117,7 +117,7 @@ class GridGenerator:
         """
         self.atoms = atoms
         self._grid = None
-        self.atoms_num_type = set(atoms.numbers)
+        self.atoms_num_type = sorted(set(atoms.numbers))
         self.interval = interval
 
         if subtype is None:
@@ -299,6 +299,38 @@ class GridGenerator:
             print("Too much grid number, it will be very slow.")
         view(self.atoms + ase.Atoms(symbols=['X'] * len(self.grid), positions=self.grid))
 
+    def get_grid_site_type(self, site_dict=None):
+        """
+        根据第一近邻原子返回格点所对应的类型
+        :param site_dict: 格点的类型字典
+            example: {0:((atom_num, count),(atom_num, count),...), ..., 'next_idx':int}
+        :return: site label for each grid, site_dict
+        """
+
+        if site_dict is None:
+            site_dict = {'next_idx': 0}
+        _, Dga = get_distances(self.grid, self.atoms.positions, use_ase=True, cell=self.atoms.cell, pbc=self.atoms.pbc)
+        Lga = (Dga - (self.rsub+self.rads)*1.1 < 0)  # 格点与原子的连接性。如果距离小于半径之和，则为不连接
+        LTga = np.asarray([(Lga & (self.atoms.numbers==n1)).sum(-1) for n1 in self.atoms_num_type]).T  # 每个格点相连类矩阵
+        label_T_set = sorted(set(tuple(i) for i in LTga))  # 以原子类型区分，不同格点的类别集合
+        site_label = tuple(tuple((self.atoms_num_type[idx], l) for idx, l in enumerate(label)) for label in label_T_set)
+        if site_dict is None:
+            site_dict = {i:v for i,v in enumerate(site_label)}
+            site_dict['next_idx'] = len(site_label)
+        else:
+            # 比较新旧字典，如果有新的，就加入到 site_dict 中
+            old_site_label = tuple(v for k,v in site_dict.items() if type(k) == int)
+            new_site = [i for i in site_label if i not in old_site_label]
+            for ns in new_site:
+                idx = site_dict['next_idx']
+                site_dict[idx] = ns
+                site_dict['next_idx'] = idx + 1
+        site_dict_reverse = {tuple(iv[1] for iv in v):i for i,v in site_dict.items() if type(i)==int}
+        grid_T_label = [site_dict_reverse[tuple(i)] for i in LTga]
+        self.grid_site_type = grid_T_label
+        self.site_type_dict = site_dict
+        return grid_T_label, site_dict
+
 
 def rattle(positions, stdev=0.001, rng=None, seed=None):
     """Rattle the grid to make the vector distribution more smooth.

{surface_construct-0.8.1 → surface_construct-0.8.2/surface_construct.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: surface_construct
-Version: 0.8.1
+Version: 0.8.2
 Summary: Surface termination construction especially for complex model, such as oxides or carbides.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren