surface-construct 0.5.13__tar.gz → 0.5.14__tar.gz

{surface_construct-0.5.13/surface_construct.egg-info → surface_construct-0.5.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: surface_construct
-Version: 0.5.13
+Version: 0.5.14
 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-0.5.13 → surface_construct-0.5.14}/setup.py

@@ -17,7 +17,7 @@ install_requires = [
 
 setup(
     name='surface_construct',
-    version='0.5.13',
+    version='0.5.14',
     packages=['surface_construct'],
     url='https://gitee.com/pjren/surface_construct/',
     license='GPL',

{surface_construct-0.5.13 → surface_construct-0.5.14}/surface_construct/surface_grid.py

@@ -165,22 +165,31 @@ class SurfaceGrid:
                 result[dim, int((sign+1)/2)] = v
         return np.concatenate(result)  # [xmin, xmax, ymin, ymax, zmin, zmax]
 
-    def gridize(self, surface_index=None):
+    def gridize(self, surface_index=None, gridxy=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。
+        * gridxy: [X, Y] 2D meshgrid
+        * surface_index: 表面原子的序号
         :return:
         """
-        nx, ny = self.grid_nx, self.grid_ny
-
-        fx_list = np.linspace(0, 1, nx, endpoint=False)  # endpoint=false指的是不包括右侧端点
-        fy_list = np.linspace(0, 1, ny, endpoint=False)
-        # 格点生成
-        fgrid_x, fgrid_y = np.meshgrid(fx_list, fy_list)
-        fxyz = np.zeros((nx * ny, 3))
-        fxyz[:, 0] = fgrid_x.reshape(nx * ny)
-        fxyz[:, 1] = fgrid_y.reshape(nx * ny)
-        xyz = self.atoms.cell.cartesian_positions(fxyz)
+        if gridxy is None:
+            nx, ny = self.grid_nx, self.grid_ny
+
+            fx_list = np.linspace(0, 1, nx, endpoint=False)  # endpoint=false指的是不包括右侧端点
+            fy_list = np.linspace(0, 1, ny, endpoint=False)
+            # 格点生成
+            fgrid_x, fgrid_y = np.meshgrid(fx_list, fy_list)
+            fxyz = np.zeros((nx * ny, 3))
+            fxyz[:, 0] = fgrid_x.reshape(nx * ny)
+            fxyz[:, 1] = fgrid_y.reshape(nx * ny)
+            xyz = self.atoms.cell.cartesian_positions(fxyz)
+        else:
+            Xgrid, Ygrid = gridxy
+            x = Xgrid.reshape(-1)
+            y = Ygrid.reshape(-1)
+            z = np.zeros(x.shape)
+            xyz = np.asarray([x, y, z]).T
 
         xmin, xmax, ymin, ymax, zmin, zmax = self.structure_boundary()
         condition = (xyz[:, 0] > xmin) * (xyz[:, 0] < xmax) * (xyz[:, 1] > ymin) * (xyz[:, 1] < ymax)

{surface_construct-0.5.13 → surface_construct-0.5.14/surface_construct.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: surface_construct
-Version: 0.5.13
+Version: 0.5.14
 Summary: Surface termination construction especially for complex model, such as oxides or carbides.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren