自动位点吸附与API

HTMACat/api.py

@@ -0,0 +1,56 @@
+import os
+import yaml
+import tempfile
+from pathlib import Path
+from HTMACat.model.Construct_adsorption_yaml import Construct_adsorption_yaml
+from rich import print
+
+
+def construct_adsorption(
+    config_yaml: str = None,
+    StrucInfo=None,
+    Species=None,
+    Model=None,
+    workdir="./"
+):
+    """
+    构建吸附构型。
+    支持两种调用方式：
+      1. construct_adsorption(config_yaml="config.yaml")
+      2. construct_adsorption(StrucInfo=dict, Model=dict, [Species=dict])
+    """
+
+    print("[HTMACat] Construct adsorption configuration ...")
+    workdir = Path(workdir).resolve()
+    workdir.mkdir(parents=True, exist_ok=True)
+    os.chdir(workdir)
+
+    # ============= 模式1：直接读取 config.yaml 文件 =============
+    if config_yaml and os.path.exists(config_yaml):
+        Construct_adsorption_yaml(config_yaml)
+        print("✅ Adsorption configuration generated successfully!")
+        return
+
+    # ============= 模式2：使用 Python 字典输入 =============
+    if StrucInfo and Model:
+        config_data = {"StrucInfo": StrucInfo, "Model": Model}
+        if Species:
+            config_data["Species"] = Species
+
+        # 临时 YAML 文件（不会污染用户目录）
+        with tempfile.NamedTemporaryFile("w", delete=False, suffix=".yaml") as tmp:
+            yaml.dump(config_data, tmp)
+            tmp_path = tmp.name
+
+        # 调用原有逻辑
+        Construct_adsorption_yaml(tmp_path)
+
+        # 清理临时文件
+        os.remove(tmp_path)
+        print("✅ Adsorption configuration generated successfully!")
+        return
+
+    # ============= 参数错误 =============
+    raise ValueError("❌ You must provide either config_yaml path or StrucInfo+Model dicts.")
+
+

HTMACat/catkit/gen/adsorption.py

@@ -619,7 +619,43 @@ def _single_adsorption(
                 adsorption_vector, flag = utils.solve_normal_vector_linearsvc(atoms.get_positions(), bond)
                 ### print('adsorption_vector:\n', adsorption_vector)
                 atoms.rotate(adsorption_vector, [0, 0, 1])
+                if site_coord is not None:
+                    # ========== 模拟 asphericity / hetero 的处理 ==========
+                    site_coord = np.array(site_coord, dtype=float)
+                    final_positions = slab.get_positions()
+                    max_z = np.max(final_positions[:, 2])
+
+                    z_coordinates = atoms.get_positions()[:, 2]
+                    min_z = np.min(z_coordinates)
+
+                    base_position = [0.0, 0.0, 0.0]
+                    # 用输入 site_coord 的 z 来定义分子高度
+                    effective_distance = site_coord[2]
+                    base_position[2] = round(max_z - min_z + effective_distance, 2)
+
+                    # 用输入的 site_coord 作为 xy 坐标
+                    base_position[0] = round(site_coord[0], 1)
+                    base_position[1] = round(site_coord[1], 1)
+
+                    # 平移分子
+                    atoms.translate(base_position)
+
+                    # 再做一次 xy 校正，确保 bond 原子落在 site_coord
+                    vec_tmp = site_coord - atoms.get_positions()[bond]
+                    atoms.translate([vec_tmp[0], vec_tmp[1], 0])
+                    n = len(slab)
+                    slab += atoms
+                    for metal_index in self.index[u]:
+                        slab.graph.add_edge(metal_index, bond + n)
+                    return slab
+
+                # 如果没传 site_coord，就保持 utils.trilaterate 的默认逻辑
             elif direction_mode == 'asphericity':
+                # 如果没有提供 site_coord，就使用默认位置：base_position 的 xy，加上传入的 z_bias
+                if site_coord is None:
+                    site_coord = [base_position[0], base_position[1], z_bias]
+                else:
+                    site_coord = np.array(site_coord, dtype=float)
                 # 根据分子的形状调整朝向，使其“平躺”在表面上
                 masses = atoms.get_masses()
                 positions = atoms.get_positions()
@@ -655,11 +691,7 @@ def _single_adsorption(
                     final_positions = slab.get_positions()
                     max_z = np.max(final_positions[:, 2])
 
-
-                    if abs(site_coord[2]) < 1e-6:  # 如果为 0 或非常接近 0
-                        effective_distance = 2
-                    else:
-                        effective_distance = site_coord[2]
+                    effective_distance = site_coord[2]
 
                     base_position[2] = round(max_z - min_z + effective_distance, 2)
 
@@ -724,16 +756,44 @@ def _single_adsorption(
 
         # zjwang 20240815
         if direction_mode == 'hetero':
+            if site_coord is None:
+                site_coord = [base_position[0], base_position[1], z_bias]
+            else:
+                site_coord = np.array(site_coord, dtype=float)
+            final_positions = slab.get_positions()
             max_z = np.max(slab.get_positions()[:,2]) #获取slabz轴最大值
             n = len(slab)
             slabs_list = []
             score_configurations = [] # 各个吸附构型(slab)的“分数”
-            for ia,a in enumerate(atoms_list):
+            for ia, a_orig in enumerate(atoms_list):
                 slabs_list.append(copy.deepcopy(slab))
-                dealt_positions = a.get_positions()
-                min_z = np.min(dealt_positions[:,2]) #得到分子z轴最小值
-                base_position[2] = max_z - min_z + 2 # 吸附物种最低原子处于slab以上2.2A，随后再尝试降低
+                a = copy.deepcopy(a_orig)  # 确保每次处理原始未改动的 adsorbate
+                z_coordinates = a.get_positions()[:, 2]
+                min_z = np.min(z_coordinates)
+                # Step 1: Z 方向平移
+                effective_distance = site_coord[2]
+                base_position = [0.0, 0.0, 0.0]
+                base_position[2] = round(max_z - min_z + effective_distance, 2)
+
+               # 计算 slab 中心坐标
+                slab_positions = slab.get_positions()
+                center_x, center_y = utils.center_slab(slab_positions)
+                # 使用输入的 site_coord 作为 xy 坐标
+                base_position[0] = round(site_coord[0], 1)
+                base_position[1] = round(site_coord[1], 1)
+
+                # 打印检查
+                print(f"min_z (adsorbate): {min_z}, max_z (slab): {max_z}, new base_position: {base_position}")
+
+                # 平移吸附分子
                 a.translate(base_position)
+
+                # 将分子平移到指定的 site_coord 位置
+                xy_translation = site_coord[:2] - a.get_positions()[bond][:2]
+                a.translate([xy_translation[0], xy_translation[1], 0])  # 只移动 x-y，不改变 z
+                print('Final base_position:', base_position)
+
+                # 组合 slab 和吸附物 
                 slabs_list[-1] += a
                 # Add graph connections
                 for metal_index in self.index[u]:
@@ -772,7 +832,7 @@ def _single_adsorption(
                 for i,idx in enumerate(np.argsort(score_configurations)[::-1]):
                     f.write(str(i).ljust(4)+':    '+str(idx).ljust(8)+str(score_configurations[idx])+'\n')
             return slabs_list
-        
+
         #lbx
         if base_position[2] == 0.0:
             #z_coordinates = rotated_positions[:, 2]

HTMACat/command.py

@@ -38,20 +38,24 @@ def main_command():
 @htmat.command(context_settings=CONTEXT_SETTINGS)
 def ads(
     in_dir: str = typer.Option("./", "-i", "--inputdir", help="relative directory of input file"),
-    out_dir: str = typer.Option(
-        "./", "-o", "--outputdir", help="relative directory of output file"
-    ),
 ):
     """Construct adsorption configuration."""
-    print("Construct adsorption configuration ... ...")
-    wordir = Path(in_dir).resolve()
-    outdir = Path(out_dir).resolve()
-    StrucInfo = "config.yaml"
-    if not outdir == wordir:
-        outdir.mkdir(parents=True, exist_ok=True)
-        shutil.copy(wordir / StrucInfo, outdir)
-        os.chdir(outdir)
-    Construct_adsorption_yaml(StrucInfo)
+    import os
+    from HTMACat.api import construct_adsorption
+    from rich import print
+
+    print("[bold green]Construct adsorption configuration via API...[/bold green]")
+
+    # 找到配置文件路径
+    config_path = os.path.join(in_dir, "config.yaml")
+    if not os.path.exists(config_path):
+        print(f"[red]Error:[/red] config.yaml not found in {in_dir}")
+        raise typer.Exit(code=1)
+
+    # 直接传入路径，不需要读取内容
+    construct_adsorption(config_yaml=config_path)
+
+    print("[bold green]✅ Adsorption configuration generated successfully![/bold green]")
 
 
 @htmat.command(context_settings=CONTEXT_SETTINGS)

HTMACat/model/Ads.py

@@ -25,7 +25,7 @@ def __init__(self, species: list, sites: list, settings={}, spec_ads_stable=None
                 "NH2": [2],
                 "NH": [2, 4],
                 "N": [2, 4],
-                "O": [2, 4],
+                "O": [1,2, 3],
                 "OH": [2, 4],
                 "NO": [2, 4],
                 "H2O": [1],
@@ -136,15 +136,30 @@ def dist_of_nearest_diff_neigh_site(self, slab, site_coords):
         imagesites_distances = [np.sqrt(np.sum(np.square(v[:2]-coord_images[0][:2]))) for v in coord_images]
         d = np.min(imagesites_distances[1:])
         return d
-
+
+    def adjust_fractional_coordinates(self, atoms):
+        cell = atoms.get_cell()
+        fractional_coords = atoms.get_scaled_positions()
+
+        # 调整x坐标范围
+        fractional_coords[:, 0] += 0.5
+        fractional_coords[:, 0] %= 1.0  # 将x坐标重新映射到0到1之间
+        # 调整y坐标范围
+        fractional_coords[:, 1] += 0.5
+        fractional_coords[:, 1] %= 1.0  # 将y坐标重新映射到0到1之间
+
+        # 将调整后的分数坐标应用回结构
+        atoms.set_scaled_positions(fractional_coords)
+
     def Construct_single_adsorption(self, ele=None):
         _direction_mode = self.settings['direction']
         _rotation_mode = self.settings['rotation']
-        print('>>>>>>>>> ', self.settings['rotation'])
         _z_bias = float(self.settings['z_bias'])
         # generate surface adsorption configuration
         slab_ad = []
         slabs = self.substrate.construct()
+        # 判断是否提供了自定义位点坐标
+        has_custom_site_coords = 'site_coords' in self.settings.keys()
         for i, slab in enumerate(slabs):
             if 'site_coords' in self.settings.keys():
                 coordinates = np.array(self.settings['site_coords'], dtype=np.float64)
@@ -173,7 +188,7 @@ def Construct_single_adsorption(self, ele=None):
                 for j, coord in enumerate(coordinates):
                     vec_to_neigh_imgsite = self.vec_to_nearest_neighbor_site(slab=slab, site_coords=[coord])
                     site_ = j
-                    coord_ = None
+                    coord_ = coord if has_custom_site_coords else None
                     if 'site_coords' in self.settings.keys():
                         coord_ = coord
                     # confirm z coord (height of the adsorbate)
@@ -185,18 +200,22 @@ def Construct_single_adsorption(self, ele=None):
                                                                direction_mode=_direction_mode,
                                                                site_coord = coord_,
                                                                z_bias=_z_bias)
-                        if type(tmp) == list:
+                        if isinstance(tmp, list):
                             for ii, t in enumerate(tmp):
+                                if not has_custom_site_coords:
+                                    self.adjust_fractional_coordinates(t)
                                 slab_ad += [t]
                         else:
-                            slab_ad += [tmp]
+                            if not has_custom_site_coords:
+                                self.adjust_fractional_coordinates(tmp)
+                            slab_ad.append(tmp)
                         #if len(bond_atom_ids) > 1:
                         #    slab_ad += [builder._single_adsorption(ads_use, bond=bond_id, site_index=j, direction_mode='decision_boundary', direction_args=bond_atom_ids)]
             else:
                 for j, coord in enumerate(coordinates):
                     vec_to_neigh_imgsite = self.vec_to_nearest_neighbor_site(slab=slab, site_coords=[coord])
                     site_ = j
-                    coord_ = None
+                    coord_ = coord if has_custom_site_coords else None
                     if 'site_coords' in self.settings.keys():
                         coord_ = coord
                     tmp = builder._single_adsorption(ads_use, bond=0, site_index=site_,
@@ -205,11 +224,17 @@ def Construct_single_adsorption(self, ele=None):
                                                            direction_mode=_direction_mode,
                                                            site_coord = coord_,
                                                            z_bias=_z_bias)
-                    if type(tmp) == list:
+                    if isinstance(tmp, list):
                         for ii, t in enumerate(tmp):
-                            slab_ad += [t]
+                            if not has_custom_site_coords:
+                            # 调整分数坐标范围
+                                self.adjust_fractional_coordinates(t)
+                            slab_ad.append(t)
                     else:
-                        slab_ad += [tmp]
+                        if not has_custom_site_coords:
+                        # 调整分数坐标范围
+                            self.adjust_fractional_coordinates(tmp)
+                        slab_ad.append(tmp)
         return slab_ad
 
     def Construct_double_adsorption(self):
@@ -244,7 +269,7 @@ def get_settings(cls,settings_dict={}):
         default_settings = {'conform_rand':1,
                             'direction':'default',
                             'rotation':'vnn',
-                            'z_bias':float(0),
+                            'z_bias':float(2.0),
                             }
         for key,value in settings_dict.items():
             default_settings[key] = value
@@ -263,13 +288,10 @@ def construct(self):
         if ([self.get_sites()[0][0], self.get_sites()[1][0]] == ['1','1']):
             ele = [''.join(self.get_sites()[0][1:]),''.join(self.get_sites()[1][1:])]
             slabs_ads = self.Construct_coadsorption_11(ele=ele)
-            print('a')
         elif ([self.get_sites()[0][0], self.get_sites()[1][0]] == ['1','2']):
             slabs_ads = self.Construct_coadsorption_12()
-            print('b')
         elif ([self.get_sites()[0][0], self.get_sites()[1][0]] == ['2','2']):
             slabs_ads = self.Construct_coadsorption_22()
-            print('c')
         else:
             raise ValueError("Supports only '1' or '2' adsorption sites for coads!")### end
         if self.substrate.is_dope():
@@ -312,9 +334,8 @@ def Construct_coadsorption_11(self, ele=['','']):
             _direction_mode = 'bond_atom'
         if 'rotation' in self.settings.keys():
             _rotation_mode = self.settings['rotation']
-            print(">>> self.settings['rotation'] =", self.settings['rotation'])
         else:
-            _rotation_mode = 'xzq'
+            _rotation_mode = 'vnn'
         if 'site_locate_ads1' in self.settings.keys():
             _site_locate_ads1 = self.settings['site_locate_ads1']
         else:
@@ -457,17 +478,21 @@ def Construct_coadsorption_11(self, ele=['','']):
                 bind_surfatoms,
                 bind_surfatoms_symb,
             ) = get_binding_adatom(adslab)
+            print(f"Adsorption  {j+1}: {adspecie, bind_type_symb}")
             adspecie_tmp, bind_type_symb_tmp = [], []
             for k, spe in enumerate(adspecie):
                 if spe in ads_type.keys():
                     adspecie_tmp += [spe]
                     bind_type_symb_tmp += [bind_type_symb[k]]
+            print(f"Adsorption configuration1 {j+1}: {adspecie_tmp, bind_type_symb_tmp}")
             if len(adspecie_tmp) < 2:
                 # print('Can not identify the config!')
                 slab_ad_final += [adslab]
             elif typ.get(bind_type_symb_tmp[0]) in ads_type.get(adspecie_tmp[0]) and \
                  typ.get(bind_type_symb_tmp[1]) in ads_type.get(adspecie_tmp[1]):
                 slab_ad_final += [adslab]
+        print(len(slab_ad_final))
+        print(slab_ad_final)
         return slab_ad_final
 
     def Construct_coadsorption_12(self):

example/adsorb/config.yaml

@@ -1,5 +1,23 @@
 StrucInfo:
-  file: CONTCAR
+  element: Pt
+  lattice_type: fcc
+  lattice_constant: 4.16
+  facet:
+  - '100'
+  dope:
+    Cu:
+    - '0'
 Model:
   ads:
-    - [f: '1.xyz', 1Si, settings: {site_coords: [[5.9, 8.1, 0.0]], direction: 'asphericity'}]
+  - - 's: ''O'''
+    - 1O
+    - settings:
+        site_coords:
+        - - 1
+          - 1
+          - 2
+        direction: asphericity
+  - - 's: ''O'''
+    - 1O
+    - settings:
+        direction: asphericity