From 0d239299be8890c125b6b2c89d9053740203a9b3 Mon Sep 17 00:00:00 2001 From: zqxian <2821838490@qq.com> Date: Mon, 12 May 2025 15:02:36 +0800 Subject: [PATCH] =?UTF-8?q?=E5=9F=BA=E5=BA=95=E4=B8=AD=E5=BF=83=E3=80=81?= =?UTF-8?q?=E8=B7=9D=E7=A6=BB=E8=B0=83=E6=95=B4?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- HTMACat/catkit/gen/adsorption.py | 42 ++++++++++++++++++++------------ 1 file changed, 27 insertions(+), 15 deletions(-) diff --git a/HTMACat/catkit/gen/adsorption.py b/HTMACat/catkit/gen/adsorption.py index ff80692..b2bb17f 100644 --- a/HTMACat/catkit/gen/adsorption.py +++ b/HTMACat/catkit/gen/adsorption.py @@ -629,11 +629,13 @@ def _single_adsorption( # 自动处理三种惯性矩方向 slabs_list = [] for inertia_mode in range(1, 4): # 遍历第一、第二、第三惯性矩 + atoms_copy = atoms.copy() # ✅ 每次都从原始结构复制 + base_position = [0.0, 0.0, 0.0] adsorption_vector = principal_axes[:, inertia_mode - 1] - atoms.rotate(adsorption_vector, [0, 0, 1]) + atoms_copy.rotate(adsorption_vector, [0, 0, 1]) if enable_rotate_xoy and rotation_mode == 'vnn' and rotation_args != {}: - principle_axe = utils.solve_principle_axe_pca(atoms.get_positions()) + principle_axe = utils.solve_principle_axe_pca(atoms_copy.get_positions()) if abs(rotation_args['vec_to_neigh_imgsite'][0]) < 1e-8: target_vec = [1, 0, 0] elif abs(rotation_args['vec_to_neigh_imgsite'][1]) < 1e-8: @@ -641,14 +643,21 @@ def _single_adsorption( else: target_vec = [-1/rotation_args['vec_to_neigh_imgsite'][0], 1/rotation_args['vec_to_neigh_imgsite'][1], 0] - atoms.rotate([principle_axe[0], principle_axe[1], 0], target_vec) + atoms_copy.rotate([principle_axe[0], principle_axe[1], 0], target_vec) + # =============== ✅ 关键部分：设置 Z 高度 =============== + z_coordinates = atoms_copy.get_positions()[:, 2] + min_z = np.min(z_coordinates) - # 【关键改动】确保每次都重新计算 `base_position[2]` - z_coordinates = atoms.get_positions()[:, 2] - min_z = np.min(z_coordinates) # 得到分子 z 轴最小值 - final_positions = slab.get_positions() # slab 坐标 - max_z = np.max(final_positions[:, 2]) # 获取 slab z 轴最大值 - base_position[2] = round(0 - min_z + 2.5 + max_z, 1) + 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 = 2.5 + else: + effective_distance = site_coord[2] + + base_position[2] = round(max_z - min_z + effective_distance, 2) # 如果输入的 xy 为 [0, 0]，则将分子放在 slab 的 xy 中心 if site_coord[0] == 0 and site_coord[1] == 0: @@ -660,15 +669,15 @@ def _single_adsorption( base_position[0] = round(site_coord[0], 1) base_position[1] = round(site_coord[1], 1) - atoms.translate(base_position) # 确保所有构型都以正确的 z 轴间距平移 + atoms_copy.translate(base_position) # 确保所有构型都以正确的 z 轴间距平移 # 将分子平移到指定的 site_coord 位置 - vec_tmp = site_coord - atoms.get_positions()[bond] # 计算平移量 - atoms.translate([vec_tmp[0], vec_tmp[1], 0]) # 只平移 x-y，不改变 z + vec_tmp = site_coord - atoms_copy.get_positions()[bond] # 计算平移量 + atoms_copy.translate([vec_tmp[0], vec_tmp[1], 0]) # 只平移 x-y，不改变 z slab_with_adsorbate = slab.copy() - slab_with_adsorbate += atoms + slab_with_adsorbate += atoms_copy slabs_list.append(slab_with_adsorbate) return slabs_list # 返回三种吸附构型的列表 @@ -727,11 +736,14 @@ def _single_adsorption( 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)) + a = copy.deepcopy(a_orig) # 确保每次处理原始未改动的 adsorbate dealt_positions = a.get_positions() min_z = np.min(dealt_positions[:,2]) #得到分子z轴最小值 - base_position[2] = round(max_z - min_z + 2.5,1) # 吸附物种最低原子处于slab以上?A，随后再尝试降低 + # Step 1: Z 方向平移 + z_translation = max_z - min_z + (2.5 if site_coord[2] == 0 else site_coord[2]) + a.translate([0, 0, z_translation]) # 计算 slab 中心坐标 slab_positions = slab.get_positions() center_x, center_y = utils.center_slab(slab_positions)