surface-construct 0.5.10__tar.gz → 0.5.12__tar.gz

{surface_construct-0.5.10/surface_construct.egg-info → surface_construct-0.5.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: surface_construct
-Version: 0.5.10
+Version: 0.5.12
 Summary: Surface termination construction especially for complex model, such as oxides or carbides.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren
@@ -67,6 +67,11 @@ A Method with Stratified Sampling Strategy for Comprehensive Analysis of Catalys
 
 `pip install -U surface-construct`
 
+## 发布新版本 （only for 管理员）
+
+python -m build
+twine upload --verbose dist/*
+
 ## 使用方法 Manual
 
 ### 所需文件 Required Files

{surface_construct-0.5.10 → surface_construct-0.5.12}/README.md

@@ -44,6 +44,11 @@ A Method with Stratified Sampling Strategy for Comprehensive Analysis of Catalys
 
 `pip install -U surface-construct`
 
+## 发布新版本 （only for 管理员）
+
+python -m build
+twine upload --verbose dist/*
+
 ## 使用方法 Manual
 
 ### 所需文件 Required Files

{surface_construct-0.5.10 → surface_construct-0.5.12}/setup.py

@@ -17,7 +17,7 @@ install_requires = [
 
 setup(
     name='surface_construct',
-    version='0.5.10',
+    version='0.5.12',
     packages=['surface_construct'],
     url='https://gitee.com/pjren/surface_construct/',
     license='GPL',

{surface_construct-0.5.10 → surface_construct-0.5.12}/surface_construct/surface_grid.py

@@ -165,7 +165,7 @@ class SurfaceGrid:
                 result[dim, int((sign+1)/2)] = v
         return np.concatenate(result)  # [xmin, xmax, ymin, ymax, zmin, zmax]
 
-    def gridize(self):
+    def gridize(self, surface_index=None):
         """
         格点化。
         这种方法仅仅适用于无孔的材料，表面为z方向，且方向向上。
@@ -189,15 +189,19 @@ class SurfaceGrid:
         xyz[:, 2] = zmax
         z = zmax
         nonbond_index = np.ones(len(xyz), bool)
-        grid_dist_array = np.zeros((len(xyz), len(self.atoms), 3))
-        grid_dist = np.zeros((len(xyz), len(self.atoms)))
+        atoms_pos = self.atoms.positions
+        atoms_num = self.atoms.numbers
+        if surface_index is not None:
+            atoms_pos = atoms_pos[surface_index]
+            atoms_num = atoms_num[surface_index]
+        grid_dist_array = np.zeros((len(xyz), len(atoms_pos), 3))
+        grid_dist = np.zeros((len(xyz), len(atoms_pos)))
         while np.any(nonbond_index):
             z -= self.interval / 10.0
             xyz[nonbond_index, 2] = z
             grid_dist_array[nonbond_index], grid_dist[nonbond_index] = get_distances(
-                xyz[nonbond_index], self.atoms.positions,
-                cell=self.atoms.cell, pbc=self.atoms.pbc)
-            R0 = np.asarray([self.radii[i] for i in self.atoms.numbers]) + self.rads
+                xyz[nonbond_index], atoms_pos, cell=self.atoms.cell, pbc=self.atoms.pbc)
+            R0 = np.asarray([self.radii[i] for i in atoms_num]) + self.rads
             # 判断最小距离是否小于共价半径之和
             nonbond_index = nonbond_index & (~np.any(grid_dist - R0 <= 0, axis=1))
 
@@ -208,6 +212,11 @@ class SurfaceGrid:
                 grid_dist = grid_dist[z_index]
                 break
         self.points = xyz
+
+        if surface_index is not None:  # grid_dist should contain all atoms
+            grid_dist_array, grid_dist = get_distances(
+                xyz[nonbond_index], atoms_pos, cell=self.atoms.cell, pbc=self.atoms.pbc)
+
         self._Dga = grid_dist
         self._DAga = grid_dist_array
 

{surface_construct-0.5.10 → surface_construct-0.5.12/surface_construct.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: surface_construct
-Version: 0.5.10
+Version: 0.5.12
 Summary: Surface termination construction especially for complex model, such as oxides or carbides.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren
@@ -67,6 +67,11 @@ A Method with Stratified Sampling Strategy for Comprehensive Analysis of Catalys
 
 `pip install -U surface-construct`
 
+## 发布新版本 （only for 管理员）
+
+python -m build
+twine upload --verbose dist/*
+
 ## 使用方法 Manual
 
 ### 所需文件 Required Files