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adf:collapse

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:Molecule Gun:模拟分子的入射、撞击

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。

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:

2,设置撞击参数

修改*.run文件:

在任意一个eor字段后面,增加如下内容:

cat > vels <<eor
Lattice parameters:
   14.25000000    14.25000000    54.25000000
   90.00000000    90.00000000    90.00000000
       50 Atom coordinates (Angstrom):
  1.4250000000000000+00  -1.4250000000000000+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   1.4250000000000000+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  -4.2750000000000000+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
  4.2750000000000000+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
  1.4250000000000000+00   1.4250000000000000+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
  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
 -4.2750000000000000+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   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
  7.1250000000000000+00   1.4250000000000000+00   7.1250000000000000+00    Fe
 -5.7000000000000000+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   0.0000000000000000+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 
  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
 -2.8500000000000000+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
  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
  0.0000000000000000+00   0.0000000000000000+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
  0.0000000000000000+00   2.8500000000000000+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 
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
  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
  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
  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
  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
  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
  0.000000000000000D+00   0.000000000000000D+00  -0.999754312886992D+11
  0.000000000000000D+00   0.000000000000000D+00  -0.999754312886992D+11
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
  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
  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
  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
  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
  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
  0.000000000000000D+00   0.000000000000000D+00  -0.313616213868668D+27
  0.000000000000000D+00   0.000000000000000D+00  -0.313616213868668D+27
MD-temperature (K):
  0.147071142605903D+02
 
eor

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个原子的初始坐标、速度、加速度、温度。

如果运行出现问题,最好参考本例*.run文件,在上面进行修改。

3,运行任务

在ADFjobs窗口,选中该任务,之后点击Job > Run提交任务。

在SCM Logo > Movie,查看GCMC模拟的动画过程。动画观看(点击)

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:

第1帧:

逐渐接近

初步接触:

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。

adf/collapse.txt · 最后更改: 2020/05/18 16:02 由 liu.jun

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