surface-construct 0.12.1__tar.gz → 0.12.2__tar.gz

{surface_construct-0.12.1/surface_construct.egg-info → surface_construct-0.12.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.12.1
+Version: 0.12.2
 Summary: Surface construction and surface reaction sampling tools.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren

{surface_construct-0.12.1 → surface_construct-0.12.2}/setup.py

@@ -15,7 +15,7 @@ install_requires = [
 
 setup(
     name='surface_construct',
-    version='0.12.1',
+    version='0.12.2',
     packages=find_packages(),
     url='https://gitee.com/pjren/surface_construct/',
     license='GPL',

{surface_construct-0.12.1 → surface_construct-0.12.2}/surface_construct/structures/surface_grid.py

@@ -1143,45 +1143,23 @@ def combine_sg_vector(*sg_lst):
     elif len(sg_lst) == 1:
         return sg_lst[0]._raw_vector
 
-    species_num_lst = sorted(set([s[0] for sg in sg_lst for s in sg.species]))
-    species_default_dct = {num: 0 for num in species_num_lst}
-    species_lsts = []
-    vlen_max = species_default_dct.copy()
+    species_lst = sorted({s[0] for sg in sg_lst for s in sg.species})
+    vlen = max([sg.vlen for sg in sg_lst])
+    vectors_lst = []
     for sg in sg_lst:
-        species_dct = species_default_dct.copy()
-        species_dct.update({num: min(sg.vlen, cnt) for num, cnt in sg.species})
-        # 对 species_dcts 中的元素进行排序
-        species_lst = sorted(species_dct.items(), key=lambda x: x[0])
-        species_lsts.append(species_lst)
-        vlen_max = {num: max(vlen_max[num], vlen) for num, vlen in species_dct.items()}  # 更新向量最大值
-    # 对 vlen_max 进行排序
-
-    new_vector_lst = []
-    for sg, species_lst in zip(sg_lst, species_lsts):
-        # 提取 raw_vector, 对不足的 vector 进行补齐
-        raw_vector = sg._raw_vector
-        nvector = len(raw_vector)  # 总行数
-        pointer = 0  # 列指针
-        new_vector = []
-        for num, cnt in species_lst:
-            new_vlen = vlen_max[num]
-            new_v = np.zeros([nvector, new_vlen])
-            new_v += 1.0 * raw_vector.min()  # 超过截断的使用最小值的三分之二，从而减小不同表面之间的结构差异
-            # 判断长度是不是 0
-            if cnt == 0:
-                new_vector.append(new_v)
-                continue
-            # 取出对应的 vector 列
-            old_v = raw_vector[:, pointer:pointer+cnt]
-            # 判断是不是要补齐
-            if cnt == new_vlen:
-                new_vector.append(old_v)
-            else:
-                new_v[:, :cnt] = old_v
-                new_vector.append(new_v)
-            pointer += cnt
-        new_vector = np.concatenate(new_vector, axis=1)
-        new_vector_lst.append(new_vector)
-    vector_combine = np.concatenate(new_vector_lst, axis=0)
+        sp0 = [s[0] for s in sg.species]  # 所有的物种
+        if species_lst == sp0 and sg.vlen==vlen:  #如果元素相同，vlen相同，直接合并
+            vectors_lst.append(sg._raw_vector)
+        else:  # 如果元素或者vlen不同，都要重新定义 vector
+            vector = np.zeros((len(sg.vector), vlen*len(species_lst)))
+            for old_idx, atomnum in enumerate(sp0):
+                new_idx = species_lst.index(atomnum)
+                idx_up = new_idx*vlen
+                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)
+
+    vector_combine = np.concatenate(vectors_lst, axis=0)
 
     return vector_combine

{surface_construct-0.12.1 → surface_construct-0.12.2/surface_construct.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.12.1
+Version: 0.12.2
 Summary: Surface construction and surface reaction sampling tools.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren

{surface_construct-0.12.1 → surface_construct-0.12.2}/tests/test_surface_grid.py

@@ -6,6 +6,8 @@ import ase
 from surface_construct import GridGenerator
 from ase.cluster.cubic import FaceCenteredCubic
 from surface_construct import SurfaceGrid
+from surface_construct.structures.surface_grid import combine_sg_vector
+
 
 class TestSurfaceGrid:
     def test_Cu_cluster(self):
@@ -126,4 +128,20 @@ class TestSurfaceGrid:
         sg_obj.gridize(subtype='slab')
         sg_obj.vectorize()
         assert sg_obj.vector.shape==(6582, 40)
-        pass
+
+    def test_sg_combiner(self):
+        atoms1 = ase.io.read('atoms_files/C4H4O_Cu.vasp')
+        sg_obj1 = SurfaceGrid(atoms1, interval=0.2, ads_num=6, lpca=False)
+        sg_obj1.gridize(subtype='slab')
+        sg_obj1.vectorize()
+        assert sg_obj1.vector.shape[1] == 40
+
+        atoms2 = ase.io.read('atoms_files/Fe28C12_115_12_POSCAR')
+        sg_obj2 = SurfaceGrid(atoms2, interval=0.2, ads_num=6, lpca=False, vlen=15)
+        sg_obj2.gridize(subtype='slab')
+        sg_obj2.vectorize()
+
+        assert sg_obj2.vector.shape[1] == 30
+
+        comb_vector = combine_sg_vector(sg_obj1, sg_obj2)
+        assert comb_vector.shape[1] == 75