variable atomprev equal "v_natoms" # --- Dump data into Data file --- shell cd Fe_100STGB1 reset_timestep 0 timestep 0.001 velocity all create 20 95812384 fix 2 all npt 1 1 100 xyz 0 0 100 drag 0.2 dump 1 all custom 1000 dump.${counter}_${gbernd} id type x y z c_csym...
lattice(晶格参数),region(选择一个而区域),create_box(创建一个盒子),create-atoms(创建原子)——通过这四个命令创建原子(按晶格的方式),这种方式适合没有分子拓扑信息的晶体,如金属,盐等有规则晶体信息的物质。 五.撰写data,in文件并计算 以TIP4P水分子为例。#用in文件撰写简单的小分子模拟 水分子模型参数(看...
file = name of file to write dump info to attribute1,attribute2,… = list of attributes for a particular style 举例如下: dump 1 all custom 1000 Al.xyz type x y z 其中1是用户指定的dump名字,all是关键字,意思对所有的原子施加后面的操作,custom是自定义输出,1000的意思是每1000步输出一次,输出...
可能是在生成data文件的时候缺少了相关的参数，可以查看一下相应的原子成键参数在in文件里是否存在。例如...
Reading data file ...orthogonal box = (0.0000000 0.0000000 0.0000000) to (23.220000 100....
(I assume that the the DATA file is called "system.data") topo readlammpsdata system.data full animate write psf system.psf 2) Later, to Load a trajectory in VMD: Start VMD Select menu: File->New Molecule -Browse to select the PSF file you created above, and load it. ...
num_frame = Nf # Frame numbers equals to calculation numbers fileName = "DUT49_charge_voutput_all.lammpstrj" #Read the dump file def find_pdos(v_all, Nc, dt, omega): #Calculate the vacf from velocity data "The oringal code was written in Matlab by Fan Zheyong" ...
(I assume that the the DATA file is called "system.data") topo readlammpsdata system.data full animate write psf system.psf 2) Later, to Load a trajectory in VMD: Start VMD Select menu: File->New Molecule -Browse to select the PSF file you created above, and load it. ...
fix fxmsd gSPCE ave/time 1000 1 1000 c_msd[1] c_msd[2] c_msd[3] c_msd[4] file msd.txt#输出msd run600000#模拟时长可自行调整,此处为0.6纳秒 4. 将data文件,in文件放置在同一文件夹下,运行模拟。 此处为1000个水分子,耗时较长。推荐使用并行计算。当然你也可以自行调整水分子的数目以及模拟时...
dump 1 all xyz 100 config_${vz}.dat dump 2 all custom 100 etotal_${vz}.dat v_et velocity all create 400.0 273237 units box run 1000 clear next vz jump example.input example.dat文件为: LAMMPS data file 6 atoms 3 atoms types