两侧同时换到之前的修订记录前一修订版后一修订版 | 前一修订版 |
adf:collapse [2016/10/26 23:35] – [2,设置撞击参数] liu.jun | adf:collapse [2021/05/25 14:26] (当前版本) – [3,运行任务] liu.jun |
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======如何模拟撞击====== | ======如何模拟撞击====== |
| 注意,本教程是针对版本低于2019的软件。对2019版以上,可以参考:[[adf:molgunofareaxms]] |
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| ======模型====== |
本例以两个铁片层的撞击。事实上,模拟团簇对表面的撞击,设置方式也是一摸一样的。 | 本例以两个铁片层的撞击。事实上,模拟团簇对表面的撞击,设置方式也是一摸一样的。 |
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======1,建模====== | 我们以两层铁原子为例,点击View > Axes显示坐标系(选中原子edit - set origin设置原点,选中两个原子edit - align - With X-axes设置x轴方向),并设置一般的分子动力学参数: |
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在[[http://rruff.geo.arizona.edu/AMS/amcsd.php|美国矿物学家晶体结构数据库]]可以下载Fe晶体: | |
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[[http://pan.baidu.com/s/1qXSa3rY|Fe体心立方晶体]] | |
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ADFinput > File > Import Coordinates: | |
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之后点击右下角的四个圆点图标,将默认的3*3*3周期显示切换成只显示一个周期: | |
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{{ :adf:gcmc01.png?700 |}} | |
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创建5*5*5的超包: | |
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{{ :adf:gcmc02.png?700 |}} | |
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{{ :adf:Collapse01.png?150 |}} | |
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切换到ReaxFF模块: | |
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点击View > Axises显示坐标系: | |
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{{ :adf:Collapse02.png?700 |}} | {{ :adf:Collapse02.png?700 |}} |
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之后删掉中间的原子层,保留两层(垂直于Z轴),并将Cell的C方向拉长到54.25埃: | |
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{{ :adf:Collapse03.png?700 |}} | |
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并设置模拟参数如下: | |
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{{ :adf:Collapse04.png?700 |}} | |
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详细的模拟参数,参考:[[adf:simplestexample|]] | |
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=====2,设置撞击参数===== | =====2,设置撞击参数===== |
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在任意一个eor字段后面,增加如下内容: | 在任意一个eor字段后面,增加如下内容: |
cat > vels <<eor | <code bash> |
Lattice parameters: | cat > vels <<eor |
| Lattice parameters: |
14.25000000 14.25000000 54.25000000 | 14.25000000 14.25000000 54.25000000 |
90.00000000 90.00000000 90.00000000 | 90.00000000 90.00000000 90.00000000 |
50 Atom coordinates (Angstrom): | 50 Atom coordinates (Angstrom): |
1.4250000000000000+00 -1.4250000000000000+00 7.1250000000000000+00 Fe | 1.4250000000000000+00 -1.4250000000000000+00 7.1250000000000000+00 Fe |
-4.2750000000000000+00 -4.2750000000000000+00 7.1250000000000000+00 Fe | -4.2750000000000000+00 -4.2750000000000000+00 7.1250000000000000+00 Fe |
1.4250000000000000+00 -4.2750000000000000+00 7.1250000000000000+00 Fe | 1.4250000000000000+00 -4.2750000000000000+00 7.1250000000000000+00 Fe |
-1.4250000000000000+00 1.4250000000000000+00 7.1250000000000000+00 Fe | -1.4250000000000000+00 1.4250000000000000+00 7.1250000000000000+00 Fe |
4.2750000000000000+00 4.2750000000000000+00 7.1250000000000000+00 Fe | 4.2750000000000000+00 4.2750000000000000+00 7.1250000000000000+00 Fe |
7.1250000000000000+00 -1.4250000000000000+00 7.1250000000000000+00 Fe | 7.1250000000000000+00 -1.4250000000000000+00 7.1250000000000000+00 Fe |
7.1250000000000000+00 -4.2750000000000000+00 7.1250000000000000+00 Fe | 7.1250000000000000+00 -4.2750000000000000+00 7.1250000000000000+00 Fe |
-1.4250000000000000+00 7.1250000000000000+00 7.1250000000000000+00 Fe | -1.4250000000000000+00 7.1250000000000000+00 7.1250000000000000+00 Fe |
-1.4250000000000000+00 -4.2750000000000000+00 7.1250000000000000+00 Fe | -1.4250000000000000+00 -4.2750000000000000+00 7.1250000000000000+00 Fe |
4.2750000000000000+00 7.1250000000000000+00 7.1250000000000000+00 Fe | 4.2750000000000000+00 7.1250000000000000+00 7.1250000000000000+00 Fe |
1.4250000000000000+00 7.1250000000000000+00 7.1250000000000000+00 Fe | 1.4250000000000000+00 7.1250000000000000+00 7.1250000000000000+00 Fe |
7.1250000000000000+00 7.1250000000000000+00 7.1250000000000000+00 Fe | 7.1250000000000000+00 7.1250000000000000+00 7.1250000000000000+00 Fe |
1.4250000000000000+00 1.4250000000000000+00 7.1250000000000000+00 Fe | 1.4250000000000000+00 1.4250000000000000+00 7.1250000000000000+00 Fe |
4.2750000000000000+00 -4.2750000000000000+00 7.1250000000000000+00 Fe | 4.2750000000000000+00 -4.2750000000000000+00 7.1250000000000000+00 Fe |
7.1250000000000000+00 4.2750000000000000+00 7.1250000000000000+00 Fe | 7.1250000000000000+00 4.2750000000000000+00 7.1250000000000000+00 Fe |
4.2750000000000000+00 1.4250000000000000+00 7.1250000000000000+00 Fe | 4.2750000000000000+00 1.4250000000000000+00 7.1250000000000000+00 Fe |
4.2750000000000000+00 -1.4250000000000000+00 7.1250000000000000+00 Fe | 4.2750000000000000+00 -1.4250000000000000+00 7.1250000000000000+00 Fe |
-1.4250000000000000+00 4.2750000000000000+00 7.1250000000000000+00 Fe | -1.4250000000000000+00 4.2750000000000000+00 7.1250000000000000+00 Fe |
-4.2750000000000000+00 1.4250000000000000+00 7.1250000000000000+00 Fe | -4.2750000000000000+00 1.4250000000000000+00 7.1250000000000000+00 Fe |
-1.4250000000000000+00 -1.4250000000000000+00 7.1250000000000000+00 Fe | -1.4250000000000000+00 -1.4250000000000000+00 7.1250000000000000+00 Fe |
-4.2750000000000000+00 -1.4250000000000000+00 7.1250000000000000+00 Fe | -4.2750000000000000+00 -1.4250000000000000+00 7.1250000000000000+00 Fe |
-4.2750000000000000+00 4.2750000000000000+00 7.1250000000000000+00 Fe | -4.2750000000000000+00 4.2750000000000000+00 7.1250000000000000+00 Fe |
1.4250000000000000+00 4.2750000000000000+00 7.1250000000000000+00 Fe | 1.4250000000000000+00 4.2750000000000000+00 7.1250000000000000+00 Fe |
-4.2750000000000000+00 7.1250000000000000+00 7.1250000000000000+00 Fe | -4.2750000000000000+00 7.1250000000000000+00 7.1250000000000000+00 Fe |
7.1250000000000000+00 1.4250000000000000+00 7.1250000000000000+00 Fe | 7.1250000000000000+00 1.4250000000000000+00 7.1250000000000000+00 Fe |
-5.7000000000000000+00 5.7000000000000000+00 -5.7000000000000000+00 Fe | -5.7000000000000000+00 5.7000000000000000+00 -5.7000000000000000+00 Fe |
0.0000000000000000+00 5.7000000000000000+00 -5.7000000000000000+00 Fe | 0.0000000000000000+00 5.7000000000000000+00 -5.7000000000000000+00 Fe |
2.8500000000000000+00 2.8500000000000000+00 -5.7000000000000000+00 Fe | 2.8500000000000000+00 2.8500000000000000+00 -5.7000000000000000+00 Fe |
-2.8500000000000000+00 0.0000000000000000+00 -5.7000000000000000+00 Fe | -2.8500000000000000+00 0.0000000000000000+00 -5.7000000000000000+00 Fe |
-2.8500000000000000+00 2.8500000000000000+00 -5.7000000000000000+00 Fe | -2.8500000000000000+00 2.8500000000000000+00 -5.7000000000000000+00 Fe |
0.0000000000000000+00 -5.7000000000000000+00 -5.7000000000000000+00 Fe | 0.0000000000000000+00 -5.7000000000000000+00 -5.7000000000000000+00 Fe |
2.8500000000000000+00 -2.8500000000000000+00 -5.7000000000000000+00 Fe | 2.8500000000000000+00 -2.8500000000000000+00 -5.7000000000000000+00 Fe |
-5.7000000000000000+00 -2.8500000000000000+00 -5.7000000000000000+00 Fe | -5.7000000000000000+00 -2.8500000000000000+00 -5.7000000000000000+00 Fe |
-5.7000000000000000+00 2.8500000000000000+00 -5.7000000000000000+00 Fe | -5.7000000000000000+00 2.8500000000000000+00 -5.7000000000000000+00 Fe |
5.7000000000000000+00 2.8500000000000000+00 -5.7000000000000000+00 Fe | 5.7000000000000000+00 2.8500000000000000+00 -5.7000000000000000+00 Fe |
-2.8500000000000000+00 -2.8500000000000000+00 -5.7000000000000000+00 Fe | -2.8500000000000000+00 -2.8500000000000000+00 -5.7000000000000000+00 Fe |
0.0000000000000000+00 -2.8500000000000000+00 -5.7000000000000000+00 Fe | 0.0000000000000000+00 -2.8500000000000000+00 -5.7000000000000000+00 Fe |
2.8500000000000000+00 5.7000000000000000+00 -5.7000000000000000+00 Fe | 2.8500000000000000+00 5.7000000000000000+00 -5.7000000000000000+00 Fe |
-2.8500000000000000+00 5.7000000000000000+00 -5.7000000000000000+00 Fe | -2.8500000000000000+00 5.7000000000000000+00 -5.7000000000000000+00 Fe |
5.7000000000000000+00 -2.8500000000000000+00 -5.7000000000000000+00 Fe | 5.7000000000000000+00 -2.8500000000000000+00 -5.7000000000000000+00 Fe |
2.8500000000000000+00 -5.7000000000000000+00 -5.7000000000000000+00 Fe | 2.8500000000000000+00 -5.7000000000000000+00 -5.7000000000000000+00 Fe |
-2.8500000000000000+00 -5.7000000000000000+00 -5.7000000000000000+00 Fe | -2.8500000000000000+00 -5.7000000000000000+00 -5.7000000000000000+00 Fe |
0.0000000000000000+00 0.0000000000000000+00 -5.7000000000000000+00 Fe | 0.0000000000000000+00 0.0000000000000000+00 -5.7000000000000000+00 Fe |
5.7000000000000000+00 -5.7000000000000000+00 -5.7000000000000000+00 Fe | 5.7000000000000000+00 -5.7000000000000000+00 -5.7000000000000000+00 Fe |
5.7000000000000000+00 0.0000000000000000+00 -5.7000000000000000+00 Fe | 5.7000000000000000+00 0.0000000000000000+00 -5.7000000000000000+00 Fe |
-5.7000000000000000+00 0.0000000000000000+00 -5.7000000000000000+00 Fe | -5.7000000000000000+00 0.0000000000000000+00 -5.7000000000000000+00 Fe |
0.0000000000000000+00 2.8500000000000000+00 -5.7000000000000000+00 Fe | 0.0000000000000000+00 2.8500000000000000+00 -5.7000000000000000+00 Fe |
2.8500000000000000+00 0.0000000000000000+00 -5.7000000000000000+00 Fe | 2.8500000000000000+00 0.0000000000000000+00 -5.7000000000000000+00 Fe |
-5.7000000000000000+00 -5.7000000000000000+00 -5.7000000000000000+00 Fe | -5.7000000000000000+00 -5.7000000000000000+00 -5.7000000000000000+00 Fe |
5.7000000000000000+00 5.7000000000000000+00 -5.7000000000000000+00 Fe | 5.7000000000000000+00 5.7000000000000000+00 -5.7000000000000000+00 Fe |
Atom velocities (Angstrom/s): | Atom velocities (Angstrom/s): |
0.000000000000000D+00 0.000000000000000D+00 0.999754312886992D+11 | 0.000000000000000D+00 0.000000000000000D+00 0.999754312886992D+11 |
0.000000000000000D+00 0.000000000000000D+00 0.999754312886992D+11 | 0.000000000000000D+00 0.000000000000000D+00 0.999754312886992D+11 |
0.000000000000000D+00 0.000000000000000D+00 -0.999754312886992D+11 | 0.000000000000000D+00 0.000000000000000D+00 -0.999754312886992D+11 |
0.000000000000000D+00 0.000000000000000D+00 -0.999754312886992D+11 | 0.000000000000000D+00 0.000000000000000D+00 -0.999754312886992D+11 |
Atom accelerations (Angstrom/s**2): | Atom accelerations (Angstrom/s**2): |
0.000000000000000D+00 0.000000000000000D+00 0.313616213868668D+27 | 0.000000000000000D+00 0.000000000000000D+00 0.313616213868668D+27 |
0.000000000000000D+00 0.000000000000000D+00 0.313616213868668D+27 | 0.000000000000000D+00 0.000000000000000D+00 0.313616213868668D+27 |
0.000000000000000D+00 0.000000000000000D+00 -0.313616213868668D+27 | 0.000000000000000D+00 0.000000000000000D+00 -0.313616213868668D+27 |
0.000000000000000D+00 0.000000000000000D+00 -0.313616213868668D+27 | 0.000000000000000D+00 0.000000000000000D+00 -0.313616213868668D+27 |
MD-temperature (K): | MD-temperature (K): |
0.298000000000000D+03 | 0.147071142605903D+02 |
eor | |
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这段内容,对数字的格式要求非常严格,也就是数字的位数,必须和上述一致。上述四组数字,分别描述ADFinput中50个原子的坐标、速度、加速度、温度。 | eor |
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| </code> |
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| 这段内容,对数字的格式要求非常严格,也就是数字的位数,必须和上述一致。上述四组数字,分别描述ADFinput中50个原子的<color blue>初始</color>坐标、速度、加速度、温度。 |
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如果运行出现问题,最好参考本例*.run文件,在上面进行修改。 | 如果运行出现问题,最好参考本例*.run文件,在上面进行修改。 |
在ADFjobs窗口,选中该任务,之后点击Job > Run提交任务。 | 在ADFjobs窗口,选中该任务,之后点击Job > Run提交任务。 |
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在SCM Logo > Movie,查看GCMC模拟的动画过程。动画观看(点击) | 在SCM Logo > Movie,查看动画过程。上述设置的速度相反、加速度也相反,因此必然会撞击在一起: |
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上述设置的速度相反、加速度也相反,因此必然会撞击在一起: | |
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第1帧: | 第1帧: |
{{ :adf:Collapse07.png?400 |}} | {{ :adf:Collapse07.png?400 |}} |
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撞击: | 撞在一起后,互相速度抵消,在该位置进行平衡的热振动,并发生不规则的形变。 |
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{{ :adf:Collapse08.png?400 |}} | {{ :adf:Collapse08.png?400 |}} |
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撞在一起后,互相速度抵消,在该位置进行平衡的热振动,并发生不规则的形变。 | |
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{{ :adf:Collapse09.png?400 |}} | |