surface-construct 0.12.2__tar.gz → 0.12.4__tar.gz

{surface_construct-0.12.2/surface_construct.egg-info → surface_construct-0.12.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.12.2
+Version: 0.12.4
 Summary: Surface construction and surface reaction sampling tools.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren

{surface_construct-0.12.2 → surface_construct-0.12.4}/setup.py

@@ -15,7 +15,7 @@ install_requires = [
 
 setup(
     name='surface_construct',
-    version='0.12.2',
+    version='0.12.4',
     packages=find_packages(),
     url='https://gitee.com/pjren/surface_construct/',
     license='GPL',

{surface_construct-0.12.2 → surface_construct-0.12.4}/surface_construct/structures/adsorbate.py

@@ -139,9 +139,10 @@ class Adsorbate:
                                   for ids in self.dock_point_indices for i in ids])
             return self._rads
 
+        atoms = self.atoms.copy()
         if not self.is_regulated:
-            self.regulate()
-        positions = self.atoms.positions
+            atoms_regulate(atoms)
+        positions = atoms.positions
         dim_length = np.array([
             max(positions[:,0]) - min(positions[:,0]),
             max(positions[:,1]) - min(positions[:,1]),
@@ -150,8 +151,8 @@ class Adsorbate:
         shortest_dim = np.argmin(dim_length)
         idx0 =np.argmin(positions[:,shortest_dim])
         idx1 =np.argmax(positions[:,shortest_dim])
-        num0 = self.atoms.numbers[idx0]
-        num1 = self.atoms.numbers[idx1]
+        num0 = atoms.numbers[idx0]
+        num1 = atoms.numbers[idx1]
         self._rads = (dim_length[shortest_dim] + radii[num0] + radii[num1]) / 2
         return self._rads
 

{surface_construct-0.12.2 → surface_construct-0.12.4}/surface_construct/structures/surface_grid.py

@@ -1158,7 +1158,7 @@ def combine_sg_vector(*sg_lst):
                 idx_down = idx_up + sg.vlen
                 old_idx_up, old_idx_down = old_idx*sg.vlen, (old_idx+1)*sg.vlen
                 vector[:, idx_up:idx_down] = sg._raw_vector[:, old_idx_up:old_idx_down]
-                vectors_lst.append(vector)
+            vectors_lst.append(vector)
 
     vector_combine = np.concatenate(vectors_lst, axis=0)
 

{surface_construct-0.12.2 → surface_construct-0.12.4/surface_construct.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.12.2
+Version: 0.12.4
 Summary: Surface construction and surface reaction sampling tools.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren

{surface_construct-0.12.2 → surface_construct-0.12.4}/tests/test_surface_grid.py

@@ -144,4 +144,5 @@ class TestSurfaceGrid:
         assert sg_obj2.vector.shape[1] == 30
 
         comb_vector = combine_sg_vector(sg_obj1, sg_obj2)
-        assert comb_vector.shape[1] == 75
+        assert comb_vector.shape[1] == 75
+        assert comb_vector.shape[0] == sg_obj1.vector.shape[0] + sg_obj2.vector.shape[0]

{surface_construct-0.12.2 → surface_construct-0.12.4}/tests/test_task.py

@@ -85,6 +85,33 @@ class TestTask:
         task_obj.run()
         print('Done')
 
+    def test_H2O_CuO_Cu(self):
+        """
+        Water on CuO/Cu surface
+        :return:
+        """
+        shutil.copyfile('../atoms_files/CuCHO_lasp.in', 'lasp.in')
+        shutil.copyfile('../atoms_files/CuCHO.pot', 'CuCHO.pot')
+        atoms = ase.io.read('../atoms_files/CuOx-Cu100-CONTCAR')
+        atoms.calc = Lasp()
+        ads_atoms = ase.Atoms('H2O',[[0.,0.,-1.],[0.,0.86,0.5],[0.,0.,0.]])
+        ads_obj = Adsorbate(ads_atoms,rtype='vdw_radii')
+        sg_obj = SurfaceGrid(atoms,rsub='vdw_radii',rads=ads_obj.rads)
+        ads_grid_comb = AdsGridCombiner(sg_obj, ads_obj)
+        sampler =[
+            {
+                'surface': "KeyPointSGSampler",  # 表面采样方法
+            },  # 第一步采样
+            {
+                'size': 3,  # 采样大小
+                'surface': ("MaxDiversitySGSampler", "MinEnergySGSampler", "MaxSigmaSGSampler"),  # 表面采样方法
+                'weight': (0.4, 0.3, 0.3),  # 表面采样方法的权重
+            }  # 第二步采样
+        ]
+        task_obj = SurfaceSiteSampleTask(combiner=ads_grid_comb, sampler=sampler, optimizer=LBFGS)
+        task_obj.run()
+        print('Done')
+
     def test_C4H9_Ru(self):
         adsatoms = ase.io.read('../atoms_files/C4H9.xyz')
         adsatoms.append(Atom('X', adsatoms.positions[0]))  # Add dock point with same pos with atoms[0]