lammp中文手册(3)

dump custom args id = atom ID

mol = molecule ID type = atom type

x,y,z = unscaled atom coordinates xs,ys,zs = scaled atom coordinates

xu,yu,zu = unwrapped atom coordinates ix,iy,iz = box image that the atom is in vx,vy,vz = atom velocities fx,fy,fz = forces on atoms q = atom charge

mux,muy,muz = orientation of dipolar atom radius = radius of extended spherical particle

omegax,omegay,omegaz = angular velocity of extended particle

angmomx,angmomy,angmomz = angular momentum of extended particle quatw,quati,quatj,quatk = quaternion components for aspherical particles tqx,tqy,tqz = torque on extended particles

c_ID = per?atom scalar value calculated by a compute with ID

c_ID[N] = Nth component of per?atom vector calculated by a compute with ID f_ID = per?atom scalar value calculated by a fix with ID

f_ID[N] = Nth component of per?atom vector calculated by a fix with ID v_name = per?atom value calculated by an atom?style variable with name

dump_modify dump?ID format/scale/image/flush/unwrap/every/precision/region/thresh values

dump_modify 1 format \dump_modify myDump image yes scale no flush yes

dump_modify 1 region mySphere thresh x <0.0 thresh epair >= 3.2 dump_modify xtcdump precision 10000 定义如何输出dump文件。

default：scale=yes; image=no; flush=yes; unwrap=no; thresh=none format string：输出格式。

scale yes/no：是否输出归一化坐标。

image yes/no：是否输出原子穿越边界次数。 flush yes/no：是否实时输出。 every N：重新设定输出间隔

region Rid：只输出区域内原子。

thresh attribute operation value：设置条件，只输出符合条件。 attribute=dump custom args operation= “ ” “>=” “==” “!=”

unwrap yes/no：dcd/xtc，输出未穿过边界的坐标。 precision N：xtc，定义输出精度。10-1000000

undump dump?ID

关闭之前定义的dump。关闭和dump关联的文件。

thermo_style one/multi/custom(args) thermo_style multi

thermo_style custom step temp pe etotal press vol v_abc default = thermo_style one

custom args：定制要输出什么信息

one=\otal press“

multi=\ 可能会产生一些compute，可通过compute_modify修改。 compute thermo_temp all temp

compute thermo_press all pressure thermo_temp compute thermo_pe all pe

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该命令应在创建晶胞后使用。

thermo_style custom args step = timestep atoms = # of atoms

cpu = elapsed CPU time temp = temperature press = pressure

pe = total potential energy ke = kinetic energy

etotal = total energy (pe + ke)

enthalpy = enthalpy (etotal + press*vol) evdwl = VanderWaal pairwise energy ecoul = Coulombic pairwise energy

epair = pairwise energy (evdwl + ecoul + elong + etail) ebond = bond energy eangle = angle energy edihed = dihedral energy eimp = improper energy

emol = molecular energy (ebond + eangle + edihed + eimp) elong = long?range kspace energy

etail = VanderWaal energy long?range tail correction vol = volume

lx,ly,lz = box lengths in x,y,z

xlo,xhi,ylo,yhi,zlo,zhi = box boundaries

xy,xz,yz = box tilt for triclinic (non?orthogonal) simulation boxes pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor c_ID = global scalar value calculated by a compute with ID

c_ID[N] = Nth component of global vector calculated by a compute with ID f_ID = global scalar value calculated by a fix with ID

f_ID[N] = Nth component of global vector calculated by a fix with ID v_name = global value calculated by an equal?style variable with name

thermo_modify lost/norm/flush/line/format/temp/press value

thermo_modify lost ignore flush yes

thermo_modify temp myTemp format 3 .8g thermo_modify line multi format float %g 定制热力学信息如何输出。

default：lost=error； norm=no(real)；flush=no。 lost error/warn/ignore：发现原子丢失如何处理。 norm yes/no：是/否输出原子平均。 flush yes/no：是/否实时输出。

line one/multi：输出一行；一行限制为3变量。 format M string：定义输出格式。 temp compute-id：如何计算温度。 press compute-id：如何计算压力。

注意temp和press的顺序。因为press已经定义了自己的温度计算方法，如果temp在press前，将覆盖其定义，如果temp在press后则不受影响。

thermo N

default = thermo 0

每隔N步输出热力学信息到屏幕上。 N=0表示只在开始和结束输出。

print string

print \

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print \输出字符串，以双引号括起。 可以使用变量。

restart N root

restart 0

restart 1000 poly.restart restart 1000 restart.*.equil restart 10000 poly.%.1 poly.%.2

default = restart 0：不输出重启文件。

root = filename to which timestep # is appended

restart N file1 file2：file1,file2 = two full filenames, 在两个文件之间交替书写。 两个广义字符：*：表示以当前的时间步替换; %：以CPU id替换

第一步不会产生重启文件。run：最后一步不会产生重启文件，除非刚好是N倍数。minimize：最后一步会产生重启文件。

write_restart file

write_restart restart.equil write_restart poly.%.*

把当前模拟状态输出到一个续算文件中。 两个广义字符：

*：表示以当前的时间步替换 %：以CPU id替换

restart2data可以转为文本文件。

echo none/screen/log/both

定义输入文件是否输出到屏幕和log。 命令行选项会替换这个命令。

log filename

打开一个新的log文件，之后的信息将输出到新log文件中。 文件名可以是变量。

系统默认的log文件是log.lammps

5. FIX

fix ID group?ID style args

在计算过程中，对组中原子做特定的计算。fix不同于compute，compute是一次性计算，fix是在这个计算过程中，每一个时间步长都会计算的值。如果有多个fix，按顺序执行，不同的顺序可能产生不同的结果。 fix-ID可以是文本数字和下划线。

fix可以通过unfix命令来删除。如果多次指定同一ID的fix，将会删除之前的fix。和unfix的效果一样。 fix计算两类量，一类是全局量，一类是每个原子的量。全局量有一些和原子数成正比(extensive)，有一些是无关的。 ? addforce ? add a force to each atom

? aveforce ? add an averaged force to each atom

? ave/atom ? compute per?atom time?averaged quantities

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? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?

?

? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?

ave/spatial ? output per?atom quantities by layer ave/time ? output time?averaged compute quantities bond/break ? break bonds on the fly bond/create ? create bonds on the fly bond/swap ? Monte Carlo bond swapping

box/relax ? relax box size during energy minimization com ? compute a center?of?mass

coord/original ? store original coords of each atom deform ? change the simulation box size/shape deposit ? add new atoms above a surface

drag ? drag atoms towards a defined coordinate

dt/reset ? reset the timestep based on velocity, forces efield ? impose electric field on system

enforce2d ? zero out z?dimension velocity and force evaporate ? remove atoms from simulation periodically freeze ? freeze atoms in a granular simulation

gravity ? add gravity to atoms in a granular simulation gyration ? compute radius of gyration

heat ? add/subtract momentum?conserving heat indent ? impose force due to an indenter langevin ? Langevin temperature control lineforce ? constrain atoms to move in a line

msd ? compute mean?squared displacement (i.e. diffusion coefficient) momentum ? zero the linear and/or angular momentum of a group of atoms nph ? constant NPH time integration via Nose/Hoover npt ? constant NPT time integration via Nose/Hoover npt/asphere ? NPT for aspherical particles npt/sphere ? NPT for spherical particles nve ? constant NVE time integration

nve/asphere ? NVT for aspherical particles nve/limit ? NVE with limited step length nve/noforce ? NVE without forces (v only) nve/sphere ? NVT for spherical particles

nvt ? constant NVT time integration via Nose/Hoover nvt/asphere ? NVT for aspherical particles

nvt/sllod ? NVT for NEMD with SLLOD equations nvt/sphere ? NVT for spherical particles

orient/fcc ? add grain boundary migration force planeforce ? constrain atoms to move in a plane

poems ? constrain clusters of atoms to move as coupled rigid bodies pour ? pour new atoms into a granular simulation domain press/berendsen ? pressure control by Berendsen barostat print ? print text and variables during a simulation rdf ? compute radial distribution functions

reax/bonds ? write out ReaxFF bond information

recenter ? constrain the center?of?mass position of a group of atoms rigid ? constrain one or more clusters of atoms to move as a rigid body setforce ? set the force on each atom

shake ? SHAKE constraints on bonds and/or angles spring ? apply harmonic spring force to group of atoms spring/rg ? spring on radius of gyration of group of atoms spring/self ? spring from each atom to its origin

temp/berendsen ? temperature control by Berendsen thermostat temp/rescale ? temperature control by velocity rescaling

thermal/conductivity ? Muller?Plathe kinetic energy exchange for thermal conductivity calculation tmd ? guide a group of atoms to a new configuration

ttm ? two?temperature model for electronic/atomic coupling

viscosity ? Muller?Plathe momentum exchange for viscosity calculation

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? ? ? ? ?

viscous ? viscous damping for granular simulations wall/gran ? frictional wall(s) for granular simulations wall/lj126 ? Lennard?Jones 12?6 wall wall/lj93 ? Lennard?Jones 9?3 wall wall/reflect ? reflecting wall(s)

? wiggle ? oscillate walls and frozen atoms

系综相关

fix ID group?ID nph p?style args keyword value ...

fix ID group?ID npt Tstart Tstop Tdamp p?style args keyword value ... fix ID group?ID nve

fix ID group?ID nve/limit xmax fix ID group?ID nve

fix ID group?ID nvt Tstart Tstop Tdamp keyword value ...

fix ID group?ID press/berendsen p?style args keyword value ... fix ID group?ID temp/berendsen Tstart Tstop Tdamp

fix ID group?ID temp/rescale N Tstart Tstop window fraction keyword values ...

fix ID group?ID langevin Tstart Tstop damp seed keyword values ... fix 3 boundary langevin 1.0 1.0 1000.0 699483 fix 1 all langevin 1.0 1.1 100.0 48279 scale 3 1.5 对组内原子运用Langevin恒温方法。

fix_modify fix?ID keyword value ... keyword = temp or press or energy

temp value = compute ID that calculates a temperature press value = compute ID that calculates a pressure

energy value = yes or no. For fixes that calculate a contribution to the potential energy of the system, the energy keyword will include that contribution in thermodynamic output of potential energy.

力和速度的控制

fix ID group?ID addforce fx fy fz fix kick flow addforce 1.0 0.0 0.0

给组内原子增加特定的力，fx,fy,fz为三个方向的力的大小。比如原子重力。

fix ID group?ID aveforce fx fy fz

fix pressdown topwall aveforce 0.0 ?1.0 0.0 fix 2 bottomwall aveforce NULL ?1.0 0.0

设置改组原子的力为fd_averaged+fd，即为各方向的平均值+外力，所以组内每个原子的力都一样。NULL表示这个方向的力不改变，0.0表示设置改方向的力为平均值。

fix ID group?ID efield ex ey ez

给电荷原子增加一个外加电场。F=qE

fix ID group?ID enforce2d fix 5 all enforce2d

设置Z方向的力和速度为0，用于2D模拟。

fix ID group?ID heat N efflux fix 3 qin heat 1 1.0 fix 4 qout heat 1 ?1.0

给组内原子增加一个非平动能。

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