dump 1 all custom 10 tip4.lammpstrj id type x y z #将信息写入tip4.lammpstrj,此后可用vmd打开视图 dump_modify 1 sort id #dielectric 80.0 fix 1 all shake 0.0001 2 0 b 1 a 1 #设置偏差控制精度提示,步数,步数,键和角 fix 2 all nve #系综,后面可跟定义的参数 fix 3 all temp/rescale 1...
h h h 一 h 1 h 2 h h 二 h 1 h 2 h h 四一 h h h VMD:amolecularvisualizationprogramfordisplaying,animating,andanalyzing large
需要kspace安装包才支持dump1 all custom 10 tip4.lammpstrj id type x y z#将信息写入tip4.lammpstrj,此后可用vmd打开视图dump_modify 1sort id#dielectric 80.0fix1 all shake 0.0001 2 0 b 1 a 1#设置偏差控制精度提示,步数,步数,键和角fix 2 all nve#系综,后面可跟定义的参数fix 3 all temp/...
% sort the atoms according to their types for i = 2: length(atoms{1})flag = 0;for j = ...
dump_modify 1 sort id compute 3 all msd fix msd all ave/time 1 5 1000 c_3 file dump mode vector run 1000000 === control.file 如下 === simulation_name CHO_example ! output files will carry this name + their specific ext tabulate_long_range 1000 ! denotes the granularity of long ...
make LAMMPS python module compatible with mpi4py version 4.x.x avoid issues with write_dump re-using and existing dump ID when a previous command crashed improve error handling when parsing the MEAM user parameter file: catch value tokenizer exceptions record line numbers and report filename and...
The 10 deleted atoms were chosen randomly from the central part of the CNT.} \label{fig:CNT-underformed-deleted} \end{figure} \paragraph{The molecular dynamics} Let us give an initial temperature to the atoms of \textit{carbon\_mid}: {\normalsize \begin{verbatim} reset_atoms id sort ...
dump 1 all custom 1000 traj.lammpstrj id mol type q x y z#输出格式 dump_modify 1 sort id#按原子id排序 fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0#npt系综 run50000 unfix fxnpt#解除npt fix fxnvt all nvt temp 300.0 300.0 100.0#nvt系综nose-hoover热浴 thermo...
kspace_style pppm/tip4p 1.0e-5 #计算长程库仑项,需要kspace安装包才支持 dump 1 all custom 10 tip4.lammpstrj id type x y z #将信息写入tip4.lammpstrj,此后可用vmd打开视图 dump_modify 1 sort id #dielectric 80.0 fix 1 all shake 0.0001 2 0 b 1 a 1 #设置偏差控制精度提示,步数,步数,键和...
input文件首先检索到fix命令,开始对fix类的调用,随后fix.cpp接收字符串**arg作为参数,读取前三个,给fix赋予独一无二的id,确定fix操作的原子组为all,最后识别出fix类型为nvt系综。随后fix_nvt.cpp被调用,接受到字符串后读取属于自己的三个参数,分别为temp 100 100 0.1。