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### 3. Commands

This section describes how a LAMMPS input script is formatted and what commands are used to define a LAMMPS simulation.

3.1 LAMMPS input script
3.2 Parsing rules
3.3 Input script structure
3.4 Commands listed by category
3.5 Commands listed alphabetically

#### 3.1 LAMMPS input script

LAMMPS executes by reading commands from a input script (text file), one line at a time. When the input script ends, LAMMPS exits. Each command causes LAMMPS to take some action. It may set an internal variable, read in a file, or run a simulation. Most commands have default settings, which means you only need to use the command if you wish to change the default.

In many cases, the ordering of commands in an input script is not important. However the following rules apply:

(1) LAMMPS does not read your entire input script and then perform a simulation with all the settings. Rather, the input script is read one line at a time and each command takes effect when it is read. Thus this sequence of commands:

    timestep 0.5
    run      100
    run      100

does something different than this sequence:

    run      100
    timestep 0.5
    run      100

In the first case, the specified timestep (0.5 fmsec) is used for two simulations of 100 timesteps each. In the 2nd case, the default timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5 fmsec timestep is used for the 2nd one.

(2) Some commands are only valid when they follow other commands. For example you cannot set the temperature of a group of atoms until atoms have been defined and a group command is used to define which atoms belong to the group.

(3) Sometimes command B will use values that can be set by command A. This means command A must precede command B in the input script if it is to have the desired effect. For example, the read_data command initializes the system by setting up the simulation box and assigning atoms to processors. If default values are not desired, the processors and boundary commands need to be used before read_data to tell LAMMPS how to map processors to the simulation box.

Many input script errors are detected by LAMMPS and an ERROR or WARNING message is printed. This section gives more information on what errors mean. The documentation for each command lists restrictions on how the command can be used.

#### 3.2 Parsing rules

Each non-blank line in the input script is treated as a command. LAMMPS commands are case sensitive. Command names are lower-case, as are specified command arguments. Upper case letters may be used in file names or user-chosen ID strings.

Here is how each line in the input script is parsed by LAMMPS:

(1) If the last printable character on the line is a "&" character (with no surrounding quotes), the command is assumed to continue on the next line. The next line is concatenated to the previous line by removing the "&" character and newline. This allows long commands to be continued across two or more lines.

(2) All characters from the first "#" character onward are treated as comment and discarded. See an exception in (6). Note that a comment after a trailing "&" character will prevent the command from continuing on the next line. Also note that for multi-line commands a single leading "#" will comment out the entire command.

(3) The line is searched repeatedly for $ characters, which indicate variables that are replaced with a text string. See an exception in (6). If the $ is followed by curly brackets, then the variable name is the text inside the curly brackets. If no curly brackets follow the $, then the variable name is the single character immediately following the $. Thus ${myTemp} and $x refer to variable names "myTemp" and "x". See the variable command for details of how strings are assigned to variables and how they are substituted for in input script commands.

(4) The line is broken into "words" separated by whitespace (tabs, spaces). Note that words can thus contain letters, digits, underscores, or punctuation characters.

(5) The first word is the command name. All successive words in the line are arguments.

(6) If you want text with spaces to be treated as a single argument, it can be enclosed in double quotes. The quotes are removed when the single argument is stored in its final form. See the dump modify format or if commands for examples. A "#" or "$" character that is between double quotes will not be treated as a comment indicator in (2) or substituted for as a variable in (3).

#### 3.3 Input script structure

This section describes the structure of a typical LAMMPS input script. The "examples" directory in the LAMMPS distribution contains many sample input scripts; the corresponding problems are discussed in this section, and animated on the LAMMPS WWW Site.

A LAMMPS input script typically has 4 parts:

1. Initialization
2. Atom definition
3. Settings
4. Run a simulation

The last 2 parts can be repeated as many times as desired. I.e. run a simulation, change some settings, run some more, etc. Each of the 4 parts is now described in more detail. Remember that almost all the commands need only be used if a non-default value is desired.

(1) Initialization

Set parameters that need to be defined before atoms are created or read-in from a file.

The relevant commands are units, dimension, newton, processors, boundary, atom_style, atom_modify.

If force-field parameters appear in the files that will be read, these commands tell LAMMPS what kinds of force fields are being used: pair_style, bond_style, angle_style, dihedral_style, improper_style.

(2) Atom definition

There are 3 ways to define atoms in LAMMPS. Read them in from a data or restart file via the read_data or read_restart commands. These files can contain molecular topology information. Or create atoms on a lattice (with no molecular topology), using these commands: lattice, region, create_box, create_atoms. The entire set of atoms can be duplicated to make a larger simulation using the replicate command.

(3) Settings

Once atoms and molecular topology are defined, a variety of settings can be specified: force field coefficients, simulation parameters, output options, etc.

Force field coefficients are set by these commands (they can also be set in the read-in files): pair_coeff, bond_coeff, angle_coeff, dihedral_coeff, improper_coeff, kspace_style, dielectric, special_bonds.

Various simulation parameters are set by these commands: neighbor, neigh_modify, group, timestep, reset_timestep, run_style, min_style, min_modify.

Fixes impose a variety of boundary conditions, time integration, and diagnostic options. The fix command comes in many flavors.

Various computations can be specified for execution during a simulation using the compute, compute_modify, and variable commands.

Output options are set by the thermo, dump, and restart commands.

(4) Run a simulation

A molecular dynamics simulation is run using the run command. Energy minimization (molecular statics) is performed using the minimize command. A parallel tempering (replica-exchange) simulation can be run using the temper command.

#### 3.4 Commands listed by category

This section lists all LAMMPS commands, grouped by category. The next section lists the same commands alphabetically. Note that some style options for some commands are part of specific LAMMPS packages, which means they cannot be used unless the package was included when LAMMPS was built. Not all packages are included in a default LAMMPS build. These dependencies are listed as Restrictions in the command's documentation.

Initialization:

atom_modify, atom_style, boundary, dimension, newton, processors, units

Atom definition:

create_atoms, create_box, lattice, read_data, read_restart, region, replicate

Force fields:

angle_coeff, angle_style, bond_coeff, bond_style, dielectric, dihedral_coeff, dihedral_style, improper_coeff, improper_style, kspace_modify, kspace_style, pair_coeff, pair_modify, pair_style, pair_write, special_bonds

Settings:

communicate, dipole, group, mass, min_modify, min_style, neigh_modify, neighbor, reset_timestep, run_style, set, shape, timestep, velocity

Fixes:

fix, fix_modify, unfix

Computes:

compute, compute_modify, uncompute

Output:

dump, dump_modify, restart, thermo, thermo_modify, thermo_style, undump, write_restart

Actions:

delete_atoms, delete_bonds, displace_atoms, displace_box, minimize, prd, run, temper

Miscellaneous:

clear, echo, if, include, jump, label, log, next, print, shell, variable

#### 3.5 Individual commands

This section lists all LAMMPS commands alphabetically, with a separate listing below of styles within certain commands. The previous section lists the same commands, grouped by category. Note that some style options for some commands are part of specific LAMMPS packages, which means they cannot be used unless the package was included when LAMMPS was built. Not all packages are included in a default LAMMPS build. These dependencies are listed as Restrictions in the command's documentation.

angle_coeff | angle_style | atom_modify | atom_style | bond_coeff | bond_style
boundary | change_box | clear | communicate | compute | compute_modify
create_atoms | create_box | delete_atoms | delete_bonds | dielectric | dihedral_coeff
dihedral_style | dimension | dipole | displace_atoms | displace_box | dump
dump_modify | echo | fix | fix_modify | group | if
improper_coeff | improper_style | include | jump | kspace_modify | kspace_style
label | lattice | log | mass | minimize | min_modify
min_style | neigh_modify | neighbor | newton | next | pair_coeff
pair_modify | pair_style | pair_write | prd | print | processors
read_data | read_restart | region | replicate | reset_timestep | restart
run | run_style | set | shape | shell | special_bonds
temper | thermo | thermo_modify | thermo_style | timestep | uncompute
undump | unfix | units | variable | velocity | write_restart

#### Fix styles

See the fix command for one-line descriptions of each style or click on the style itself for a full description:

addforce | aveforce | ave/atom | ave/histo | ave/spatial | ave/time | bond/break | bond/create
bond/swap | box/relax | deform | deposit | drag | dt/reset | efield | enforce2d
evaporate | freeze | gravity | heat | indent | langevin | lineforce | momentum
move | nph | npt | npt/asphere | npt/sphere | nve | nve/asphere | nve/limit
nve/noforce | nve/sphere | nvt | nvt/asphere | nvt/sllod | nvt/sphere | orient/fcc | planeforce
poems | pour | press/berendsen | print | reax/bonds | recenter | rigid | setforce
shake | spring | spring/rg | spring/self | store/coord | store/force | temp/berendsen | temp/rescale
thermal/conductivity | tmd | ttm | viscosity | viscous | wall/colloid | wall/gran | wall/harmonic
wall/lj126 | wall/lj93 | wall/reflect | wall/region

These are fix styles contributed by users, which can be used if LAMMPS is built with the appropriate package.

atc | imd | smd

#### Compute styles

See the compute command for one-line descriptions of each style or click on the style itself for a full description:

angle/local | bond/local | centro/atom | cna/atom | com | com/molecule
coord/atom | damage/atom | dihedral/local | displace/atom | erotate/asphere | erotate/sphere
event/displace | group/group | gyration | gyration/molecule | heat/flux | improper/local
ke | ke/atom | msd | msd/molecule | pair/local | pe
pe/atom | pressure | property/atom | property/local | property/molecule | rdf
reduce | reduce/region | stress/atom | temp | temp/asphere | temp/com
temp/deform | temp/partial | temp/profile | temp/ramp | temp/region | temp/sphere

These are compute styles contributed by users, which can be used if LAMMPS is built with the appropriate package.

ackland/atom

#### Pair_style potentials

See the pair_style command for an overview of pair potentials. Click on the style itself for a full description:

none | hybrid | hybrid/overlay | airebo
born/coul/long | buck | buck/coul/cut | buck/coul/long
colloid | coul/cut | coul/debye | coul/long
dipole/cut | dpd | dsmc | eam
eam/opt | eam/alloy | eam/alloy/opt | eam/fs
eam/fs/opt | gayberne | gayberne/gpu | gran/hertz/history
gran/hooke | gran/hooke/history | lj/charmm/coul/charmm | lj/charmm/coul/charmm/implicit
lj/charmm/coul/long | lj/charmm/coul/long/opt | lj/class2 | lj/class2/coul/cut
lj/class2/coul/long | lj/cut | lj/cut/gpu | lj/cut/opt
lj/cut/coul/cut | lj/cut/coul/debye | lj/cut/coul/long | lj/cut/coul/long/tip4p
lj/expand | lj/gromacs | lj/gromacs/coul/gromacs | lj/smooth
lj96/cut | lubricate | meam | morse
morse/opt | peri/pmb | reax | resquared
soft | sw | table | tersoff
tersoff/zbl | yukawa | yukawa/colloid

These are pair styles contributed by users, which can be used if LAMMPS is built with the appropriate package.

buck/coul | cg/cmm | cg/cmm/coul/cut | cg/cmm/coul/long
eam/cd | lj/coul

#### Bond_style potentials

See the bond_style command for an overview of bond potentials. Click on the style itself for a full description:

none | hybrid | class2 | fene
fene/expand | harmonic | morse | nonlinear
quartic | table

#### Angle_style potentials

See the angle_style command for an overview of angle potentials. Click on the style itself for a full description:

none | hybrid | charmm | class2
cosine | cosine/delta | cosine/squared | harmonic
table

These are angle styles contributed by users, which can be used if LAMMPS is built with the appropriate package.

cg/cmm

#### Dihedral_style potentials

See the dihedral_style command for an overview of dihedral potentials. Click on the style itself for a full description:

none | hybrid | charmm | class2
harmonic | helix | multi/harmonic | opls

#### Improper_style potentials

See the improper_style command for an overview of improper potentials. Click on the style itself for a full description:

none | hybrid | class2 | cvff
harmonic

#### Kspace solvers

See the kspace_style command for an overview of Kspace solvers. Click on the style itself for a full description:

ewald | pppm | pppm/tip4p

These are Kspace solvers contributed by users, which can be used if LAMMPS is built with the appropriate package.

ewald/n