5.3. Input script structure¶
This page describes the structure of a typical LAMMPS input script. The examples directory in the LAMMPS distribution contains many sample input scripts; it is discussed on the Examples doc page.
A LAMMPS input script typically has 4 parts:
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 commands need only be used if a non-default value is desired.
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.
5.3.2. System definition¶
There are 3 ways to define the simulation cell and reserve space for force field info and fill it with atoms in LAMMPS. Read them in from (1) a data file or (2) a restart file via the read_data or read_restart commands, respectively. These files can also contain molecular topology information. Or (3) create a simulation cell and fill it with atoms on a lattice (with no molecular topology), using these commands: lattice, region, create_box, create_atoms or read_dump.
The entire set of atoms can be duplicated to make a larger simulation using the replicate command.
5.3.3. Simulation settings¶
Once atoms and molecular topology are defined, a variety of settings can be specified: force field coefficients, simulation parameters, output options, and more.
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.
5.3.4. 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.