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### 3. Commands

This section describes how a LIGGGHTS(R)-PUBLIC input script is formatted and the input script commands used to define a LIGGGHTS(R)-PUBLIC simulation.

3.1 LIGGGHTS(R)-PUBLIC input script
3.2 Parsing rules
3.3 Input script structure
3.4 An example input script

#### 3.1 LIGGGHTS(R)-PUBLIC input script

LIGGGHTS(R)-PUBLIC executes by reading commands from a input script (text file), one line at a time. When the input script ends, LIGGGHTS(R)-PUBLIC exits. Each command causes LIGGGHTS(R)-PUBLIC 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) LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC how to map processors to the simulation box.

Many input script errors are detected by LIGGGHTS(R)-PUBLIC 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. LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC:

(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".

If the $ is followed by parenthesis, then the text inside the parenthesis is treated as an "immediate" variable and evaluated as an equal-style variable. This is a way to use numeric formulas in an input script without having to assign them to variable names. For example, these 3 input script lines:

    variable X equal (xlo+xhi)/2+sqrt(v_area)
    region 1 block $X 2 INF INF EDGE EDGE
    variable X delete

can be replaced by

    region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE

so that you do not have to define (or discard) a temporary variable X.

Note that neither the curly-bracket or immediate form of variables can contain nested $ characters for other variables to substitute for. Thus you cannot do this:

    variable        a equal 2
    variable        b2 equal 4
    print           "B2 = ${b$a}"

Nor can you specify this $($x-1.0) for an immediate variable, but you could use $(v_x-1.0), since the latter is valid syntax for an equal-style variable.

See the variable command for more details of how strings are assigned to variables and evaluated, and how they can be used 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 either double or single quotes. E.g.

    print "Volume = $v"
    print 'Volume = $v'
    if "$steps > 1000" then quit

The quotes are removed when the single argument is stored internally. See the dump modify format or print or if commands for examples. A "#" or "$" character that is between quotes will not be treated as a comment indicator in (2) or substituted for as a variable in (3).

IMPORTANT NOTE: If the argument is itself a command that requires a quoted argument (e.g. using a print command as part of an if or run every command), then the double and single quotes can be nested in the usual manner. See the doc pages for those commands for examples. Only one of level of nesting is allowed, but that should be sufficient for most use cases.

#### 3.3 Input script structure

This section describes the structure of a typical LIGGGHTS(R)-PUBLIC input script. The "examples" directory in the LIGGGHTS(R)-PUBLIC distribution contains many sample input scripts; the corresponding problems are discussed in Section_example, and animated on the LIGGGHTS(R)-PUBLIC WWW Site.

A LIGGGHTS(R)-PUBLIC input script typically has 4 parts:

1. Initialization
2. Atom/particle definition and insertion
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/particles 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 LIGGGHTS(R)-PUBLIC what kinds of force fields are being used: pair_style, bond_style, fix wall/gran .

Granular walls typically require meshes to be used. See fix mesh/surface for details.

(2) Atom/particle definition and insertion

There are 3 ways to define atoms in LIGGGHTS(R)-PUBLIC. Read them in from a data or restart file via the read_data or read_restart commands. Or create atoms on a lattice using these commands: lattice, region, create_box, create_atoms.

However, the most common way to insert granular particles is to use one of the fix insert/* commands: fix insert/pack, "fix insert/stream"stream.html, fix insert/rate/region

Before these insertion commands can be used, particle distributions (fix particledistribution/discrete) are built up using particle templates. For spherical particles, such particle templates are defined using fix particletemplate/sphere.

(3) Settings

Once atoms are defined, a variety of settings can be specified: simulation parameters, output options, etc.

Material parameters and force field coefficients are set by these commands fix property/global, or pair_coeff, bond_coeff.

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

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 simulation is run using the run command.

#### 3.4 An example input script

This shows an example input script for a LIGGGHTS(R)-PUBLIC simulation.

    #Contact model example
    atom_style   granular
    atom_modify  map array
    boundary     m m m
    newton       off
    communicate	 single vel yes
    units        si
    region       reg block -0.05 0.05 -0.05 0.05 0. 0.15 units box
    create_box   1 reg
    neighbor     0.002 bin
    neigh_modify delay 0
    #Material properties required for pair style
    fix          m1 all property/global youngsModulus peratomtype 5.e6
    fix          m2 all property/global poissonsRatio peratomtype 0.45
    fix          m3 all property/global coefficientRestitution peratomtypepair 1 0.95
    fix          m4 all property/global coefficientFriction peratomtypepair 1 0.05
    pair_style   gran model hertz tangential history
    pair_coeff	 * *
    timestep     0.00001
    fix          gravi all gravity 9.81 vector 0.0 0.0 -1.0
    fix          zwalls1 all wall/gran model hertz tangential history primitive type 1 zplane 0.0
    fix          zwalls2 all wall/gran model hertz tangential history primitive type 1 zplane 0.15
    fix          cylwalls all wall/gran model hertz tangential history primitive type 1 zcylinder 0.05 0. 0.
    #region of insertion
    region       bc cylinder z 0. 0. 0.045 0.00 0.15 units box
    #particle distributions
    fix          pts1 all particletemplate/sphere 1 atom_type 1 density constant 2500 radius constant 0.0025
    fix          pdd1 all particledistribution/discrete 1.  1 pts1 1.0
    fix          ins all insert/pack seed 100001 distributiontemplate pdd1 vel constant 0. 0. -0.5 &
                 insert_every once overlapcheck yes all_in yes particles_in_region 1800 region bc
    #apply nve integration to all particles
    fix          integr all nve/sphere
    #output settings, include total thermal energy
    compute         rke all erotate/sphere
    thermo_style    custom step atoms ke c_rke vol
    thermo          1000
    thermo_modify   lost ignore norm no
    compute_modify  thermo_temp dynamic yes
    dump            dmp all custom 800 post/dump*.newModels id type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius
    #insert particles and run
    run             5000