玩烂了的三层结构
金属：fixed atoms------thermostat atoms------newtonian atoms
聚合物：fixed atoms------thermal quench------free layer
其中thermostat atoms和thermal quench需要控温，一般300K，金属我见的NVT比较多，聚合物是Langevin控温，newtonian atoms和free layer一般都是nve。fix固定的命令其实有很多中，我就列举一下我用过的：
#-----------------------A层固定
velocity A set 0.0 0.0 0.0
fix 10 A nve/noforce
#-----------------------A层固定
velocity A setforce 0.0 0.0 0.0
velocity A set 0.0 0.0 0.0 #没有这个貌似也OK
nve/nofore和setforce 0 0 0 的区别在于前者是受力的，如果没有速度清0，在noforce的命令下，group还是会有位置更新的。这个命令的特点是，可以dump出该层的原子受力。
热浴方面：
注意NVT是Nose-Hoover强耦合热浴，NH是强耦合热与，速度分布满足BZ分布，但当体系初始态远离平衡时，温度振荡厉害，不容易进入平衡态。Berendsen是弱耦合热与，没有上述缺点，但是速度不能严格按照BZ分布建议在NH热与下进行数据采样，Berendsen热与下进行系统弛豫其他还是，DPD，langevin热浴，是随机热浴，rescale只能说是一种温度控制方法。转自热浴区别
要注意采样的时候不要用nve/limit !!!，这个命令害了我很多个模型，注意热浴系综的选择，不是温度到了压力到了就ok了！
在这里我还有个问题，我有时在使用temp/rescale或者Berendsen的时候会报错，提示我:
Computed temperature for fix temp/rescale cannot be 0.0
反正我是没解决，貌似是个很普遍的问题？？
部分论文截图
图表 1: Geometry of the model (left), temperature evolution of the interface (middle), boundary conditions (right). [1]
图表 2: Schematic views of the tribopair system set-up shown in 3D (a) and 2D (b). The initial information is shown in (a), and different layers are introduced in (b) [2]
图表 3: Molecular dynamics model [3]
图表 4: MD simulation model used for Al and Cu ultrasonic welding: (a) Initial configuration of sample; (b) Equilibrated configuration after relaxation under zero pressure at 300 K [4]
图表 5: model [5]
图表 6: Illustration of the set-up model and configuration of the atoms in the slider (red) and substrate (others). [6]
图表 7: Front cross-section view of the DLC/PFPE/DLC model [7]
图表 8: Basic elements of the MD model for SiO2 [8]
图表 9: Representative NEMD system with molecular structure of the studied fluids shown. Visualized with VMD. [9]
图表 10: 3-Dimensional MD model of sliding friction for amorphous polyethylene [10]
References
[1] Mostafavi S, Markert B. Molecular dynamics simulation of ultrasonic metal welding of aluminum alloys. Proc. Appl. Math. Mech. 2019;19(1). https://doi.org/10.1002/pamm.201900304 .
[2] Chen K, Wang L, Chen Y, Wang Q. Molecular dynamics simulation of microstructure evolution and heat dissipation of nanoscale friction. International Journal of Heat and Mass Transfer 2017;109:293–301. https://doi.org/10.1016/j.ijheatmasstransfer.2017.01.105 .
[3] Tong R-t, Han B, Quan Z-f, Liu G. Molecular dynamics simulation of friction and heat properties of Nano-texture GOLD film in space environment. Surface and Coatings Technology 2019;358:775–84. https://doi.org/10.1016/j.surfcoat.2018.11.084 .
[4] Yang J, Zhang J, Qiao J. Molecular Dynamics Simulations of Atomic Diffusion during the Al-Cu Ultrasonic Welding Process. Materials (Basel) 2019;12(14). https://doi.org/10.3390/ma12142306 .
[5] Dong Y, Li Q, Martini A. Molecular dynamics simulation of atomic friction: A review and guide. Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films 2013;31(3):30801. https://doi.org/10.1116/1.4794357 .
[6] Uehara T. Molecular Dynamics Simulation of Stick-Slip Friction on a Metal Surface. AMM 2013;459:26–33. https://doi.org/10.4028/www.scientific.net/AMM.459.26 .
[7] Dai L, Sorkin V, Sha ZD, Pei QX, Branicio PS, Zhang YW. Molecular dynamics simulations on the frictional behavior of a perfluoropolyether film sandwiched between diamond-like-carbon coatings. Langmuir 2014;30(6):1573–9. https://doi.org/10.1021/la404680v .
[8] Dmitriev A, Nikonov A, Österle W. MD Sliding Simulations of Amorphous Tribofilms Consisting of either SiO2 or Carbon. Lubricants 2016;4(3):24. https://doi.org/10.3390/lubricants4030024 .
[9] Ewen JP, Gao H, Müser MH, Dini D. Shear heating, flow, and friction of confined molecular fluids at high pressure. Phys Chem Chem Phys 2019;21(10):5813–23. https://doi.org/10.1039/c8cp07436d .
[10] Zhan S, Xu H, Duan H, Pan L, Jia D, Tu J et al. Molecular dynamics simulation of microscopic friction mechanisms of amorphous polyethylene. Soft Matter 2019;15(43):8827–39. https://doi.org/10.1039/c9sm01533g .
