Skip to content

Dev #85

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
zqxian merged 2 commits into from
Apr 30, 2025
Merged

Dev #85

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
8f5ee57
基底中心
zqxian Apr 28, 2025
a047717
基地中心
zqxian Apr 30, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
31 changes: 21 additions & 10 deletions HTMACat/catkit/gen/adsorption.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -650,16 +650,22 @@ def _single_adsorption(
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)

# 计算 slab 中心坐标，确保吸附分子位于 slab 的正中心
center_x, center_y = utils.center_slab(final_positions)
base_position[0] = round(center_x, 1)
base_position[1] = round(center_y, 1)
# 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:
center_x, center_y = utils.center_slab(final_positions) # 计算 slab 的 xy 中心
base_position[0] = round(center_x, 1) # 将分子放置在 xy 中心
base_position[1] = round(center_y, 1)
else:
# 否则，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)

atoms.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]
atoms.translate([vec_tmp[0], vec_tmp[1], 0])
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


slab_with_adsorbate = slab.copy()
slab_with_adsorbate += atoms
Expand Down Expand Up @@ -729,20 +735,25 @@ def _single_adsorption(
# 计算 slab 中心坐标
slab_positions = slab.get_positions()
center_x, center_y = utils.center_slab(slab_positions)
base_position[0] = round(center_x, 1)
base_position[1] = round(center_y, 1)
# 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:
base_position[0] = round(center_x, 1)
base_position[1] = round(center_y, 1)
else:
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
Expand Down
Loading