这是本文档旧的修订版!
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。下载本例计算输入输出文件(点击)
在美国矿物学家晶体结构数据库可以下载Fe晶体:
ADFinput > File > Import Coordinates:
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:
创建5*5*5的超包:
切换到ReaxFF模块:
点击View > Axises显示坐标系:
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:
并设置模拟参数如下:
详细的模拟参数,参考:案例:398K下H2与F2摩尔比1:1的反应(ReaxFF基本参数范例详解)
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。