96 lines
3.5 KiB
Plaintext
96 lines
3.5 KiB
Plaintext
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
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Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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Input script structure :h3
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This page describes the structure of a typical LAMMPS input script.
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The examples directory in the LAMMPS distribution contains many sample
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input scripts; it is discussed on the "Examples"_Examples.html doc
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page.
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A LAMMPS input script typically has 4 parts:
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Initialization
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Atom definition
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Settings
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Run a simulation :ol
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The last 2 parts can be repeated as many times as desired. I.e. run a
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simulation, change some settings, run some more, etc. Each of the 4
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parts is now described in more detail. Remember that almost all
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commands need only be used if a non-default value is desired.
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(1) Initialization
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Set parameters that need to be defined before atoms are created or
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read-in from a file.
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The relevant commands are "units"_units.html,
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"dimension"_dimension.html, "newton"_newton.html,
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"processors"_processors.html, "boundary"_boundary.html,
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"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
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If force-field parameters appear in the files that will be read, these
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commands tell LAMMPS what kinds of force fields are being used:
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"pair_style"_pair_style.html, "bond_style"_bond_style.html,
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"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
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"improper_style"_improper_style.html.
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(2) Atom definition
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There are 3 ways to define atoms in LAMMPS. Read them in from a data
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or restart file via the "read_data"_read_data.html or
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"read_restart"_read_restart.html commands. These files can contain
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molecular topology information. Or create atoms on a lattice (with no
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molecular topology), using these commands: "lattice"_lattice.html,
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"region"_region.html, "create_box"_create_box.html,
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"create_atoms"_create_atoms.html. The entire set of atoms can be
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duplicated to make a larger simulation using the
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"replicate"_replicate.html command.
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(3) Settings
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Once atoms and molecular topology are defined, a variety of settings
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can be specified: force field coefficients, simulation parameters,
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output options, etc.
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Force field coefficients are set by these commands (they can also be
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set in the read-in files): "pair_coeff"_pair_coeff.html,
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"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
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"dihedral_coeff"_dihedral_coeff.html,
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"improper_coeff"_improper_coeff.html,
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"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
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"special_bonds"_special_bonds.html.
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Various simulation parameters are set by these commands:
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"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
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"group"_group.html, "timestep"_timestep.html,
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"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
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"min_style"_min_style.html, "min_modify"_min_modify.html.
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Fixes impose a variety of boundary conditions, time integration, and
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diagnostic options. The "fix"_fix.html command comes in many flavors.
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Various computations can be specified for execution during a
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simulation using the "compute"_compute.html,
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"compute_modify"_compute_modify.html, and "variable"_variable.html
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commands.
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Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
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and "restart"_restart.html commands.
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(4) Run a simulation
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A molecular dynamics simulation is run using the "run"_run.html
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command. Energy minimization (molecular statics) is performed using
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the "minimize"_minimize.html command. A parallel tempering
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(replica-exchange) simulation can be run using the
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"temper"_temper.html command.
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