surface-construct 0.5.9__tar.gz → 0.5.11__tar.gz

{surface_construct-0.5.9 → surface_construct-0.5.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: surface_construct
-Version: 0.5.9
+Version: 0.5.11
 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-0.5.9 → surface_construct-0.5.11}/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-0.5.9 → surface_construct-0.5.11}/setup.py

@@ -17,7 +17,7 @@ install_requires = [
 
 setup(
     name='surface_construct',
-    version='0.5.9',
+    version='0.5.11',
     packages=['surface_construct'],
     url='https://gitee.com/pjren/surface_construct/',
     license='GPL',

{surface_construct-0.5.9 → surface_construct-0.5.11}/surface_construct/surface_grid.py

@@ -156,7 +156,16 @@ class SurfaceGrid:
         # 格点向量化
         self.vectorize(pca=self.lpca)
 
-    def gridize(self):
+    def structure_boundary(self):
+        result = np.zeros((3, 2))  # [[xmin, xmax], [ymin, ymax], [zmin, zmax]]
+        for dim in (0, 1, 2):
+            for func, sign in zip((np.argmin, np.argmax), (-1, 1)):
+                atom_idx = func(self.atoms.positions[:, dim])
+                v = self.atoms.positions[atom_idx, dim] + sign * (self.radii[self.atoms.numbers[atom_idx]] + self.rads)
+                result[dim, int((sign+1)/2)] = v
+        return np.concatenate(result)  # [xmin, xmax, ymin, ymax, zmin, zmax]
+
+    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。
@@ -172,36 +181,35 @@ class SurfaceGrid:
         fxyz[:, 0] = fgrid_x.reshape(nx * ny)
         fxyz[:, 1] = fgrid_y.reshape(nx * ny)
         xyz = self.atoms.cell.cartesian_positions(fxyz)
-        # 设定初始 z 为 atom.z 最大值 + radii + ads radii
-        zmax = self.rads + max(self.atoms.positions[:, 2] +
-                               np.array([self.radii[self.atoms.numbers[i]]
-                                         for i in range(len(self.atoms))]))
-        # z 最小值
-        atom_idx_zmin = np.argmin(self.atoms.positions[:, 2])
-        atom_zmin = self.atoms.positions[atom_idx_zmin, 2]
-        zmin = atom_zmin - self.radii[self.atoms.numbers[atom_idx_zmin]] - self.rads
+
+        xmin, xmax, ymin, ymax, zmin, zmax = self.structure_boundary()
+        condition = (xyz[:, 0] > xmin) * (xyz[:, 0] < xmax) * (xyz[:, 1] > ymin) * (xyz[:, 1] < ymax)
+        xyz = xyz[condition]
 
         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))
 
             if z < zmin:
-                z_index = xyz[:, 2] < z
-                xyz[z_index] = zmin
-                grid_dist_array[z_index], grid_dist[z_index] = get_distances(
-                    xyz[z_index], self.atoms.positions,
-                    cell=self.atoms.cell, pbc=self.atoms.pbc)
+                z_index = xyz[:, 2] > z
+                xyz = xyz[z_index]  # exclude the points that lower than zmin
+                grid_dist_array = grid_dist_array[z_index]
+                grid_dist = grid_dist[z_index]
                 break
         self.points = xyz
         self._Dga = grid_dist
@@ -340,7 +348,7 @@ class SurfaceGrid:
         """
         nsample = 10
         rng = np.random.default_rng()
-        idx = rng.choice(range(self.grid_nx * self.grid_ny - 1), size=nsample)
+        idx = rng.choice(range(len(self.points)), size=nsample)
         d_grid = [get_distances(self.points[i], self.points[i+1], cell=self.atoms.cell, pbc=self.atoms.pbc)[1][0, 0]
                   for i in idx]
         idx_filtered = [i for i, d in zip(idx, d_grid) if d < 1.2 * self.interval]  # 去掉不相邻的格点对
@@ -541,7 +549,7 @@ class SurfaceGrid:
 
     def plot_property(self, key='energy', sample=True, figname=None, vmax=None, vmin=None):
         """
-
+        TODO: 支持 cluster 作图。保存原始 meshgrid 和 id？或者重新插值？
         :param key: 画图的内容，对应于 grid_property 中的 key
         :param sample: 是否画上 sample 点，默认是
         :param figname: 图片名字，默认 key_iter_niter.png
@@ -640,6 +648,7 @@ class SurfaceGrid:
         return line_x, line_values
 
     def plot_sigma(self, key='energy', figname=None, vmax=None, vmin=None):
+        # TODO: 支持 cluster 作图。保存原始 meshgrid 和 id？或者重新插值？
         assert key in self.grid_property_sigma
 
         X = self.points[:, 0].reshape((self.grid_ny, self.grid_nx))

{surface_construct-0.5.9 → surface_construct-0.5.11}/surface_construct.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
-Name: surface-construct
-Version: 0.5.9
+Name: surface_construct
+Version: 0.5.11
 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