surface-construct 0.9.2__tar.gz → 0.9.3__tar.gz

{surface_construct-0.9.2/surface_construct.egg-info → surface_construct-0.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.9.2
+Version: 0.9.3
 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-0.9.2 → surface_construct-0.9.3}/setup.py

@@ -15,7 +15,7 @@ install_requires = [
 
 setup(
     name='surface_construct',
-    version='0.9.2',
+    version='0.9.3',
     packages=find_packages(),
     url='https://gitee.com/pjren/surface_construct/',
     license='GPL',

{surface_construct-0.9.2 → surface_construct-0.9.3}/surface_construct/structures/__init__.py

@@ -27,7 +27,7 @@ class AdsGridCombiner:
         attitude = kwargs.get('attitude') # 分子姿态，分子主轴的夹角
         internal_coord = kwargs.get('internal_coord')  # 分子内坐标
         ads_atoms = self.ads_obj.atoms.copy()
-        # TODO: 先进行 rotate and 改变分子构象
+        # TODO: 先进性 rotate and 改变分子构象
         site = self.sg_obj.points[grid_idx]
         # TODO: get_z 去更新 site 的坐标
         site = self._get_z(site, ads_atoms)
@@ -46,9 +46,5 @@ class AdsGridCombiner:
         事实上调整的是沿着格点法向向量的距离 xyz = xyz0 + r×d
         :return:
         """
-        # 该方法仅仅适用于 slab 体系，不适合 cluster 体系
-        # 先找到grid 的最大值点，分子的最小值点，然后把分子的COM 移动到距离5A以上的点
-        # 根据 ads 不同的原子类型，计算每个原子需要移动的z值，取最小的值。
         xyz = xyz0
-        move_z = 0
         return xyz

{surface_construct-0.9.2 → surface_construct-0.9.3}/surface_construct/structures/adsorbate.py

@@ -25,9 +25,6 @@ class Adsorbate:
     @property
     def rads(self):
         # 分子的半径，sg_obj 构造时作为参考
-        # 思考：这是为了生成格点的半径，格点的位置是一种参考的位置，可以尽量接近真实的吸附结构。
-        # 因而使用吸附原子的半径作为半径比较好，而不是分子的质心。当然，这是对于比较平整的slab 模型而言，对于团簇而言，也是如此吗？
-        # 可以认为是的，到时候分子的质心沿着法向向量移动就可以了。
         # TODO: 计算分子半径
         return self._rads
 

{surface_construct-0.9.2 → surface_construct-0.9.3}/surface_construct/structures/surface_grid.py

@@ -260,9 +260,9 @@ class GridGenerator:
         interval = self.interval
         lenx, leny, lenz = atoms.cell.lengths()
         pos_fz = atoms.get_scaled_positions()[:,2]
-        # 后面的 x2 是保证对于三斜格子保证足够厚
+        # 后面的 *2 是保证对于三斜格子保证足够厚
         fzmax = pos_fz.max() + (np.asarray(self.rsub).max() + self.rads + interval * 2) / lenz * 2
-        fzmin = pos_fz.min()
+        fzmin = (pos_fz.max() + pos_fz.min()) / 2
         Nx, Ny = np.asarray(np.around([lenx/self.interval ,leny/self.interval]), dtype=int)
         Nz = int(np.around((fzmax-fzmin)*lenz/self.interval))
         fx_list = np.linspace(0,1,Nx, endpoint=False)
@@ -495,8 +495,18 @@ class SurfaceGrid:
         self.subtype = subtype
         gridgen = GridGenerator(self.atoms,
                                 interval=self.interval, subtype=subtype, rads=self.rads, rsub=self.rsub)
-        self.points = gridgen.grid
         self._gridgen = gridgen
+        self.points = gridgen.grid
+        remove_unconnected = kwargs.get('remove_unconnected', False)
+        if remove_unconnected:
+            self.remove_unconnected()
+
+    def remove_unconnected(self):
+        graph = self.grid_graph
+        if not nx.is_connected(graph):
+            largest_cc = max(nx.connected_components(graph), key=len)
+            self._grid_graph = graph.subgraph(largest_cc)
+            self.points = self.points[list(largest_cc)]
 
     def _get_grid_tree(self, extend=False):
         if self.subtype == 'cluster' and extend:
@@ -504,7 +514,7 @@ class SurfaceGrid:
             extend = False
         if self._grid_tree is not None:
             l_extend = len(self.points) != self._grid_tree.n
-            if l_extend != extend:  # need recalculate
+            if l_extend != extend:  # need to be recalculated
                 self._grid_tree = None
         if self._grid_tree is None:
             if extend:
@@ -524,10 +534,13 @@ class SurfaceGrid:
             cutoff = self.interval * 2
             dlist, ilist = self._get_grid_tree(extend=True).query(self.points, k=7, distance_upper_bound=cutoff)  # 最近邻的原子最多为6, 包含自身则为7
             ilist = ilist % ngrid  # 折叠格点的序号
-            pairs = [(ii[0], i, d) for ii, dd in zip(ilist, dlist) for i, d in zip(ii[1:], self.interval / dd[1:])]
+            pairs = [(ii[0], i, d) for ii, dd in zip(ilist, dlist)
+                     for i, d in zip(ii[1:], self.interval / dd[1:]) if d > 0]
             graph = nx.Graph()
             graph.add_weighted_edges_from(pairs)
             self._grid_graph = graph
+            if not nx.is_connected(graph):
+                print("Warning: the surface grids are not fully connected!")
         return self._grid_graph
 
     @property

{surface_construct-0.9.2 → surface_construct-0.9.3/surface_construct.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.9.2
+Version: 0.9.3
 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-0.9.2 → surface_construct-0.9.3}/tests/test_surface_grid.py

@@ -62,6 +62,9 @@ class TestSurfaceGrid:
         atoms = ase.io.read('atoms_files/POSCAR_In2O3_110')
         sg_obj = SurfaceGrid(atoms, interval=0.1, ads_num=6, lpca=False)
         sg_obj.gridize(subtype='slab')
+        print(f"Number of points before remove_unconnected: {len(sg_obj.points)}")
+        sg_obj.remove_unconnected()
+        print(f"Number of points after remove_unconnected: {len(sg_obj.points)}")
         sg_obj.vectorize()
         graph = sg_obj.grid_graph
         vip = sg_obj.vip_id
@@ -80,6 +83,13 @@ class TestSurfaceGrid:
         print(len(vip))
         print(list(site_dict.keys()))
 
+    def test_Fe3C_slab2(self):
+        atoms = ase.io.read('atoms_files/Fe3C_001.vasp')
+        sg_obj = SurfaceGrid(atoms, interval=0.1, ads_num=6, lpca=False)
+        sg_obj.gridize(subtype='slab')
+        atoms = sg_obj.atoms
+        print(len(sg_obj.points))
+
     def test_ZSM5(self):
         atoms = ase.io.read('atoms_files/zsm5.cif')
         gridgen = GridGenerator(atoms, interval=0.2, subtype='bulk', rsub='vdw_radii', scale=1.0)