lammps模拟实例详解

# Big colloid particles and small LJ particles

units lj

This command sets the style of units used for a simulation. It determines the units of all quantities specified in the input script and data file, as well as quantities output to the screen, log file, and dump files. Typically, this command is used at the very beginning of an input script.这个指令设定模拟的格式，它决定了在输入脚本文件和数据文件以及在屏幕上显示的输出物，日志文件和垃圾文件中所有的单元格式。典型的是，它经常用于输入脚本的开头

For style lj, all quantities are unitless. Without loss of generality, LAMMPS sets the fundamental quantities mass, sigma, epsilon, and the Boltzmann constant = 1. The masses, distances, energies you specify are multiples of these fundamental values. The formulas relating the reduced or unitless quantity (with an asterisk) to the same quantity with units is also given. Thus you can use the mass & sigma & epsilon values for a specific material and convert the results from a unitless LJ simulation into physical quantities.

对于lj格式，所有数量都是无量纲的。不失一般性的，lammps设定了基本量质量sigma epsilon 和波尔兹曼常数=1。你定义的质量，距离，能量是这些基本值的倍数。公式把衰减量或者是无量纲量（用*）和单元给出的相同的量关联起来。因此你可以用mass，sigma，epsilon值表示一个具体材料并且改变一个无量纲lj模拟的物理量的结果。

mass = mass or m

distance = sigma, where x* = x / sigma

time = tau, where tau = t* = t (epsilon / m / sigma^2)^1/2

energy = epsilon, where E* = E / epsilon

velocity = sigma/tau, where v* = v tau / sigma

force = epsilon/sigma, where f* = f sigma / epsilon

torque = epsilon, where t* = t / epsilon

temperature = reduced LJ temperature, where T* = T Kb / epsilon

pressure = reduced LJ pressure, where P* = P sigma^3 / epsilon

dynamic viscosity = reduced LJ viscosity, where eta* = eta sigma^3 / epsilon / tau

charge = reduced LJ charge, where q* = q / (4 pi perm0 sigma epsilon)^1/2

dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2

electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon density = mass/volume, where rho* = rho sigma^dim

atom_style atomic 原子类型atomic（原子的)

Define what style of atoms to use in a simulation. This determines what attributes are associated with the atoms. This command must be used before a simulation is setup via a read_data, read_restart, or create_box command.

定义在模拟中用到的原子类型，这个决定了与原子有关的属性，这个命令必须用在模拟被设定之前通过read_data, read_restart, or create_box

Atomic only the default values coarse-grain liquids, solids, metals

Atomic 附加属性是只是默认值用于粗粒液体，固体和金属的模拟

dimension 2 二维

lattice sq 0.01 建造一个sq类型的二维晶格，lj折合密度rho*=0.01

Lattice Define a lattice for use by other commands. In LAMMPS, a lattice is simply a set of points in space, determined by a unit cell with basis atoms, that is replicated infinitely in all dimensions. The arguments of the lattice command can be used to define a wide variety of crystallographic lattices.

Lattice 指令定义了一个其他指令可以使用的晶格，在lammps中，一个晶格是一个空间中简单的点集，被基本原子构成的所有维度中无限复制的晶胞在所决定。Lattice指令额参数可以被用来定义各种各样的晶格。

A lattice is used by LAMMPS in two ways. First, the create_atoms command creates atoms on the lattice points inside the simulation box. Note that the create_atoms command allows different atom types to be assigned to different basis atoms of the lattice. Second, the lattice spacing in the x,y,z dimensions implied by the lattice, can be used by other commands as distance units (e.g. create_box, region and velocity), which are often convenient to use when the underlying problem geometry is atoms on a lattice.一个lattice 明令在lammps中有两种实用方式，首先，create_atoms command 在模拟盒子内部的格点上创建原子。注意，e create_atoms command允许不同的原子类型去分配到晶格中不同的基本原子。第二，晶格间距在x，y，z轴分量隐含在晶格中，可以被其他命令应用作为距离单元。这个距离单元当潜在问题的几何构型是在晶格中的原子的时候经常被方便的使用。

A lattice consists of a unit cell, a set of basis atoms within that cell, and a set of transformation parameters (scale, origin, orient) that map the unit cell into the simulation box. The vectors a1,a2,a3 are the edge vectors of the unit cell. This is the nomenclature for "primitive" vectors in solid-state crystallography, but in LAMMPS the unit cell they determine does not have to be a "primitive cell" of minimum volume.一个晶格由晶胞，晶胞内部的基本原子构成的集合，一个将晶胞绘制入模拟盒子的基本参数构成的集合构成。矢量a1，a2，a3是晶胞的棱矢量，在固态物理学里面用术语primitive矢量来表示。但是在lammps中不一定要用最小体积的原胞来定义晶胞

Lattice应用：

lattice style scale keyword values

style = none or sc or bcc or fcc or hcp or diamond or sq or sq2 or hex or custom scale = scale factor between lattice and simulation box

for style none:

scale is not specified (nor any optional arguments)

for all other styles:

scale = reduced density rho* (for LJ units)

scale = lattice constant in distance units (for non-LJ units)

Lattices of style sq and sq2 are 2d lattices that define a square unit cell with edge length = 1.0. This means a1 = 1 0 0 and a2 = 0 1 0. A sq lattice has 1 basis atom at the lower-left corner of the square. A sq2 lattice has 2 basis atoms, one at the corner and one at the center of the square.

sq and sq2格式的晶格是一个2维晶格这个晶格定义了一个棱长为1.0的直角晶胞的2维