surface-construct 0.5.9__tar.gz → 0.5.10__tar.gz

{surface_construct-0.5.9 → surface_construct-0.5.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: surface_construct
-Version: 0.5.9
+Version: 0.5.10
 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-0.5.9 → surface_construct-0.5.10}/setup.py

@@ -17,7 +17,7 @@ install_requires = [
 
 setup(
     name='surface_construct',
-    version='0.5.9',
+    version='0.5.10',
     packages=['surface_construct'],
     url='https://gitee.com/pjren/surface_construct/',
     license='GPL',

{surface_construct-0.5.9 → surface_construct-0.5.10}/surface_construct/surface_grid.py

@@ -156,6 +156,15 @@ class SurfaceGrid:
         # 格点向量化
         self.vectorize(pca=self.lpca)
 
+    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):
         """
         格点化。
@@ -172,14 +181,10 @@ 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
@@ -197,11 +202,10 @@ class SurfaceGrid:
             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 +344,7 @@ 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 +545,7 @@ 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 +644,7 @@ 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-0.5.10}/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: 0.5.10
 Summary: Surface termination construction especially for complex model, such as oxides or carbides.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren