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Merged
zqxian merged 2 commits into from
May 12, 2025
Merged

Dev #86

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0d23929
基底中心、距离调整
zqxian May 12, 2025
4743d3e
Merge branch 'dev' of github.com:zqxian/HTMACat-kit into dev
zqxian May 12, 2025
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42 changes: 27 additions & 15 deletions HTMACat/catkit/gen/adsorption.py
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Original file line number Diff line number Diff line change
Expand Up @@ -629,26 +629,35 @@ 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:
target_vec = [0, 1, 0]
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)

# xzq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:
Expand All @@ -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
Expand Down Expand Up @@ -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)
Expand Down
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