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"增加了对example中adsorb例子的说明，增添了split的例子，改变了split功能中最终吸附高度并设置为2.0埃" #75

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Dec 19, 2023
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"增加了对example中adsorb例子的说明，增添了split的例子，改变了split功能中最终吸附高度并设置为2.0埃" #75

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4 changes: 2 additions & 2 deletions HTMACat/Split.py
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Original file line number Diff line number Diff line change
Expand Up @@ -270,8 +270,8 @@ def separate_rows(molecule_coords, selected_rows):
z_2 = (ase_atoms2.positions+cartesian_coordinates[first_atom])[:, 2]
min_z1 = np.min(z_1)
min_z2 = np.min(z_2)
dez1 = max_z - min_z1 + 2.4 #2埃处
dez2 = max_z - min_z2 + 2.4
dez1 = max_z - min_z1 + 2.0 #2埃处
dez2 = max_z - min_z2 + 2.0
dez1 = np.array([dez1]).reshape(1,-1)
dez2 = np.array([dez2]).reshape(1,-1)
ase_atoms1.positions[:, 2] = ase_atoms1.positions[:, 2] + dez1
Expand Down
17 changes: 17 additions & 0 deletions example/adsorb/说明.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
StrucInfo:
file: CONTCAR
Model:
ads:
- [f: '1.xyz', 1Si, settings: {site_coords: [[5.9, 8.1, 0.0]], direction: 'asphericity'}]
yaml文件内容如上

cmd打开
输入htmat ads
生成吸附结构的CONTCAR

说明：
StrucInfo:
file: CONTCAR(基底文件名)
Model:
ads:
- [f: '1.xyz'(分子为xyz文件，此处为分子文件名), 1Si(1为模式1，Si为指定的中心原子), settings: {site_coords: [[5.9, 8.1, 0.0(0.0为指定自动吸附模式，xyz值自动生成，使得分子最低点离基底表面3.4埃)]], direction: 'asphericity'(旋转模式，使用该参数使得分子按最大惯性矩旋转，尽可能平铺于基底表面)}]
138 changes: 138 additions & 0 deletions example/split/CONTCAR
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Original file line number Diff line number Diff line change
@@ -0,0 +1,138 @@
C Cu H N Si
1.0000000000000000
15.3430999999999997 0.0000000000000000 0.0000000000000000
-7.6715499999999999 13.2875143730000005 0.0000000000000000
0.0000000000000000 0.0000000000000000 24.4292000000000016
C Cu H N Si
4 108 14 2 1
Selective dynamics
Direct
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0.6666272435457896 0.7049725792199155 0.3503183165202467 T T T
0.9999996197482027 0.0000003802517973 0.1743671852479537 T T T
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0.2777799999999999 0.2222200000000001 0.0906499999999966 F F F
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0.1111099999999965 0.2222200000000001 0.0906499999999966 F F F
0.9999994466296892 0.1667388947370076 0.1743905713477971 T T T
0.8888900000000035 0.1111099999999965 0.0000000000000000 T T T
0.9444400000000003 0.0555599999999998 0.0906499999999966 F F F
0.8332611052629924 0.0000005533703108 0.1743905713477971 T T T
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0.7777799999999999 0.0555599999999998 0.0906499999999966 F F F
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0.2777799999999999 0.3888900000000035 0.0906499999999966 F F F
0.2222200000000001 0.4444400000000002 0.0000000000000000 T T T
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0.7777799999999999 0.2222200000000001 0.0906499999999966 F F F
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0.9444400000000003 0.2222200000000001 0.0906499999999966 F F F
0.7222200000000001 0.2777799999999999 0.0000000000000000 T T T
0.0000015232286207 0.3332626691621671 0.1743898652643083 T T T
0.1111099999999965 0.3888900000000035 0.0906499999999966 F F F
0.0555599999999998 0.4444400000000002 0.0000000000000000 T T T
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0.8888900000000035 0.2777799999999999 0.0000000000000000 T T T
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0.3794549592864795 0.2986801999845580 0.3657007577004434 T T T
0.3113072376000763 0.3182294349042600 0.4188831354787296 T T T
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0.3584534265668490 0.4934974364554195 0.4431965945623975 T T T
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0.6460993763337208 0.6528984421866241 0.4589599549513602 T T T
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8 changes: 8 additions & 0 deletions example/split/说明.txt
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运行cmd
使用命令htmat split CONTCAR(文件名) Si(中心原子)
即可得到分子解离吸附后的CONTACR文件以及一些过渡文件
说明：
CONTCAR初始文件应该是包含分子和基底的情况
Si为指定的中心原子，即断键的位置
处理后的分子最低点距离表面2埃，基团与主体部分沿着成键矢量分离3.8埃
旋转后的基团和主体部分各自成键矢量指向-z轴