Merge pull request #78 from zhzhang7549/dev

修改了部分bug

HTMACat/Extract_info.py

@@ -518,7 +518,7 @@ def get_atom_neigh(poscar, atom):
 
 
 # 8. TO get atoms binding with surface among adatoms
-def get_binding_adatom(poscar):
+def get_binding_adatom(poscar, layer=4):
     """Determine the adsorbed atoms and the surface atoms to which they bind.
 
     Parameters
@@ -559,7 +559,9 @@ def get_binding_adatom(poscar):
         struct = read(poscar, format="vasp")
     else:
         struct = poscar
-    layer = len(get_unique_coordinates(poscar, axis=2, tag=True, tol=0.01))-1
+    # layer = len(get_unique_coordinates(poscar, axis=2, tag=True, tol=0.01))-1
+    # print(f"layer {layer}")
+    # print(get_unique_coordinates(poscar, axis=2, tag=True, tol=0.01))
     (
         adatoms,
         adatoms_symb,
@@ -568,8 +570,8 @@ def get_binding_adatom(poscar):
         subsurfatoms,
         subsurfatoms_symb,
     ) = distinguish_atom_binding(poscar, tol=0.05, base_layer=layer)    # Changed by RxChen, 2023/06/02
-    # print(adatoms_symb,surfatoms_symb)
-    # print(struct.symbols)
+    # print(f"adatoms {adatoms_symb},surfatoms {surfatoms_symb}")
+    # print(f"struct.symbols {struct.symbols}")
     cutOff = natural_cutoffs(struct, mult=1.0)
     # print(cutOff)
     nl = NeighborList(cutOff, self_interaction=False, bothways=True)

HTMACat/model/Ads.py

@@ -77,7 +77,7 @@ def construct(self):
             else:
                 ele = ''.join(self.get_sites()[1:]) ### wzj 20230518
                 slabs_ads = self.Construct_single_adsorption(ele=ele)
-        elif self.get_sites()[0] == '2':
+        elif self.get_sites()[0] == '2': ## 使用2时有bug
             slabs_ads = self.Construct_double_adsorption()
         else:
             raise ValueError('Supports only "1" "2" adsorption sites for ads!')
@@ -92,6 +92,7 @@ def remove_same(self, slabs_ads):
         p1 = self.substrate.property["p1"]
         p1_symb = self.substrate.property["p1_symb"]
         slabs_ads_near = []
+        layer = self.substrate.get_layers()
         for slb in slabs_ads:
             (
                 bind_adatoms,
@@ -100,14 +101,9 @@ def remove_same(self, slabs_ads):
                 adspecie,
                 bind_surfatoms,
                 bind_surfatoms_symb,
-            ) = get_binding_adatom(slb)
-            if self.get_sites() == "1" and (set(p1_symb) & set(bind_surfatoms_symb[0])):
-                slabs_ads_near += [slb]
-            elif (
-                self.get_sites() == "2"
-                and (set(p1_symb) & set(bind_surfatoms_symb[0]))
-                or (set(p1_symb) & set(bind_surfatoms_symb[0]))
-            ):
+            ) = get_binding_adatom(slb,layer)
+            # print(self.get_sites(), set(p1_symb), bind_surfatoms_symb,set(bind_surfatoms_symb[0]))
+            if (set(p1_symb) & set(bind_surfatoms_symb[0])):
                 slabs_ads_near += [slb]
         return slabs_ads_near
 
@@ -245,7 +241,7 @@ def from_input(cls, init_list, substrates, species_dict=None):
     @classmethod
     def get_settings(cls,settings_dict={}):
         default_settings = {'conform_rand':1,
-                            'direction':'bond_atom',
+                            'direction':'default',
                             'rotation':'vnn',
                             'z_bias':float(0),
                             }
@@ -290,6 +286,7 @@ def remove_same(self, slabs_ads):
         p1 = self.substrate.property["p1"]
         p1_symb = self.substrate.property["p1_symb"]
         slabs_ads_near = []
+        layer = self.substrate.get_layers()
         for slb in slabs_ads:
             (
                 bind_adatoms,
@@ -298,7 +295,7 @@ def remove_same(self, slabs_ads):
                 adspecie,
                 bind_surfatoms,
                 bind_surfatoms_symb,
-            ) = get_binding_adatom(slb)
+            ) = get_binding_adatom(slb,layer)
             bind_surfatoms_symb_all = sum(bind_surfatoms_symb, [])
             if set(p1_symb) & set(bind_surfatoms_symb_all):
                 slabs_ads_near += [slb]

HTMACat/model/Species.py

@@ -28,7 +28,7 @@ def out_print(self):
         return self.alias_name
 
     def out_file_name(self):
-        return self.get_formular()
+        return self.alias_name
 
     @abstractmethod
     def get_molecule(self, randomSeed=0) -> Gratoms:
@@ -80,7 +80,10 @@ def set_filetype(self, typename):
         self.filetype = typename
 
     def out_file_name(self):
-        return self.alias_name
+        if "." in self.form:
+            return self.form.split(".")[0]
+        else:
+            return self.form
 
     @property
     def atoms(self) -> Atoms:
@@ -115,10 +118,13 @@ def __init__(self, form, formtype="sml", alias_name=None):
         super().__init__(form, formtype, alias_name)
 
     def out_file_name(self):
-        ads1 = self.get_formular()
-        mole = Chem.AddHs(Chem.MolFromSmiles(ads1))
-        ads1 = rdMolDescriptors.CalcMolFormula(mole)
-        return ads1
+        if self.alias_name == self.form:
+            ads1 = self.get_formular()
+            mole = Chem.AddHs(Chem.MolFromSmiles(ads1))
+            ads1 = rdMolDescriptors.CalcMolFormula(mole)
+            return ads1
+        else:
+            return self.alias_name.split("(")[0]
 
     def get_molecule(self, randomSeed=0) -> Gratoms:
         ### Changed by ZhaojieWang, 20230829 (<>改进：需能处理离子键可连接的SMILES)

HTMACat/model/Substrate.py

@@ -106,7 +106,7 @@ def __init__(self, in_bulk=Bulk(), facet="100", layers=4, layers_relax=2):
         self.bulk = in_bulk
         self.file = None
         self.facet = facet
-        self.property = {}
+        self.property = {} #掺杂元素序号以及元素符号p1,p1_symb
         self.layers = layers
         self.layers_relax = layers_relax
         if "p1" not in self.property or "p1_symb" not in self.property: