2006-09-22 00:22:34 +08:00
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"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_howto.html :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,Section_commands.html#comm)
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:line
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3. Commands :h3
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This section describes how a LAMMPS input script is formatted and what
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commands are used to define a LAMMPS simulation.
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3.1 "LAMMPS input script"_#3_1
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3.2 "Parsing rules"_#3_2
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3.3 "Input script structure"_#3_3
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3.4 "Commands listed by category"_#3_4
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3.5 "Commands listed alphabetically"_#3_5 :all(b)
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:line
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3.1 LAMMPS input script :link(3_1),h4
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LAMMPS executes by reading commands from a input script (text file),
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one line at a time. When the input script ends, LAMMPS exits. Each
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command causes LAMMPS to take some action. It may set an internal
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variable, read in a file, or run a simulation. Most commands have
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default settings, which means you only need to use the command if you
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wish to change the default.
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In many cases, the ordering of commands in an input script is not
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important. However the following rules apply:
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(1) LAMMPS does not read your entire input script and then perform a
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simulation with all the settings. Rather, the input script is read
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one line at a time and each command takes effect when it is read.
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Thus this sequence of commands:
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timestep 0.5
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run 100
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run 100 :pre
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does something different than this sequence:
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run 100
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timestep 0.5
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run 100 :pre
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In the first case, the specified timestep (0.5 fmsec) is used for two
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simulations of 100 timesteps each. In the 2nd case, the default
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timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
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fmsec timestep is used for the 2nd one.
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(2) Some commands are only valid when they follow other commands. For
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example you cannot set the temperature of a group of atoms until atoms
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have been defined and a group command is used to define which atoms
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belong to the group.
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(3) Sometimes command B will use values that can be set by command A.
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This means command A must precede command B in the input script if it
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is to have the desired effect. For example, the
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"read_data"_read_data.html command initializes the system by setting
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up the simulation box and assigning atoms to processors. If default
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values are not desired, the "processors"_processors.html and
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"boundary"_boundary.html commands need to be used before read_data to
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tell LAMMPS how to map processors to the simulation box.
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Many input script errors are detected by LAMMPS and an ERROR or
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WARNING message is printed. "This section"_Section_errors.html gives
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more information on what errors mean. The documentation for each
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command lists restrictions on how the command can be used.
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:line
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3.2 Parsing rules :link(3_2),h4
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Each non-blank line in the input script is treated as a command.
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LAMMPS commands are case sensitive. Command names are lower-case, as
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are specified command arguments. Upper case letters may be used in
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file names or user-chosen ID strings.
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Here is how each line in the input script is parsed by LAMMPS:
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(1) If the line ends with a "&" character (with no trailing
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whitespace), the command is assumed to continue on the next line. The
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next line is concatenated to the previous line by removing the "&"
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character and newline. This allows long commands to be continued
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across two or more lines.
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(2) All characters from the first "#" character onward are treated as
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comment and discarded.
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(3) The line is searched repeatedly for $ characters which indicate
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variables that are replaced with text. If the $ is followed by curly
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brackets, then the variable name is the text inside the curly
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brackets. If no curly brackets follow the $, then the variable name
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is the character immediately following the $. Thus $\{myTemp\} and $x
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refer to variable names "myTemp" and "x". See the
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"variable"_variable.html command for details of how values are
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assigned to variables and how they are substituted for in input
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scripts.
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(4) The line is broken into "words" separated by whitespace (tabs,
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spaces). Note that words can thus contain letters, digits,
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underscores, or punctuation characters.
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(5) The first word is the command name. All successive words in the
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line are arguments.
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(6) Text with spaces can be enclosed in double quotes so it will be
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treated as a single argument. See the "dump modify"_dump_modify.html
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or "fix print"_fix_print.html commands for examples. A '#' or '$'
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character that in text between double quotes will not be treated as a
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comment or substituted for as a variable.
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:line
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3.3 Input script structure :h4,link(3_3)
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This section describes the structure of a typical LAMMPS input script.
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The "examples" directory in the LAMMPS distribution contains many
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sample input scripts; the corresponding problems are discussed in
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"this section"_Section_example.html, and animated on the "LAMMPS WWW
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Site"_lws.
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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 the
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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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2006-09-22 00:22:34 +08:00
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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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"temperature"_temperature.html, "temp_modify"_temp_modify.html,
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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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Output options are set by these commands: "thermo"_thermo.html,
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"dump"_dump.html, "restart"_restart.html.
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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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:line
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3.4 Commands listed by category :link(3_4),h4
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This section lists all LAMMPS commands, grouped by category. The
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"next section"_#3_5 lists the same commands alphabetically. Note that
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some style options for some commands are part of specific LAMMPS
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packages, which means they cannot be used unless the package was
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included when LAMMPS was built. Not all packages are included in a
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default LAMMPS build. These dependencies are listed as Restrictions
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in the command's documentation.
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Initialization:
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"atom_modify"_atom_modify.html, "atom_style"_atom_style.html,
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"boundary"_boundary.html, "dimension"_dimension.html,
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"newton"_newton.html, "processors"_processors.html, "units"_units.html
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Atom definition:
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"create_atoms"_create_atoms.html, "create_box"_create_box.html,
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"lattice"_lattice.html, "read_data"_read_data.html,
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"read_restart"_read_restart.html, "region"_region.html,
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"replicate"_replicate.html
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Force fields:
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"angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html,
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"bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html,
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"dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html,
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"dihedral_style"_dihedral_style.html,
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"improper_coeff"_improper_coeff.html,
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"improper_style"_improper_style.html,
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"kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html,
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"pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html,
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"pair_style"_pair_style.html, "pair_write"_pair_write.html,
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"special_bonds"_special_bonds.html
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Settings:
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"dipole"_dipole.html, "group"_group.html, "mass"_mass.html,
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"min_modify"_min_modify.html, "min_style"_min_style.html,
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"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html,
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"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
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"set"_set.html, "temp_modify"_temp_modify.html,
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"temperature"_temperature.html, "timestep"_timestep.html,
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"velocity"_velocity.html
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Fixes:
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"fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html
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Output:
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"dump"_dump.html, "dump_modify"_dump_modify.html,
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"restart"_restart.html, "thermo"_thermo.html,
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"thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html,
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"undump"_undump.html, "write_restart"_write_restart.html
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Actions:
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"delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html,
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"displace_atoms"_displace_atoms.html, "minimize"_minimize.html,
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"run"_run.html, "temper"_temper.html
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Miscellaneous:
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"clear"_clear.html, "echo"_echo.html, "include"_include.html,
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"jump"_jump.html, "label"_label.html, "log"_log.html,
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"next"_next.html, "print"_print.html, "shell"_shell.html,
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"variable"_variable.html
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:line
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3.5 Individual commands :h4,link(3_5),link(comm)
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This section lists all LAMMPS commands alphabetically, with a separate
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listing below of styles within certain commands. The "previous
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section"_#3_4 lists the same commands, grouped by category. Note that
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some style options for some commands are part of specific LAMMPS
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packages, which means they cannot be used unless the package was
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included when LAMMPS was built. Not all packages are included in a
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default LAMMPS build. These dependencies are listed as Restrictions
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in the command's documentation.
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"angle_coeff"_angle_coeff.html,
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"angle_style"_angle_style.html,
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"atom_modify"_atom_modify.html,
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"atom_style"_atom_style.html,
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"bond_coeff"_bond_coeff.html,
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"bond_style"_bond_style.html,
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"boundary"_boundary.html,
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"clear"_clear.html,
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"create_atoms"_create_atoms.html,
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"create_box"_create_box.html,
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"delete_atoms"_delete_atoms.html,
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"delete_bonds"_delete_bonds.html,
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|
"dielectric"_dielectric.html,
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|
"dihedral_coeff"_dihedral_coeff.html,
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"dihedral_style"_dihedral_style.html,
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"dimension"_dimension.html,
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"dipole"_dipole.html,
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"displace_atoms"_displace_atoms.html,
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"dump"_dump.html,
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"dump_modify"_dump_modify.html,
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"echo"_echo.html,
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|
"fix"_fix.html,
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|
"fix_modify"_fix_modify.html,
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"group"_group.html,
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"improper_coeff"_improper_coeff.html,
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"improper_style"_improper_style.html,
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"include"_include.html,
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"jump"_jump.html,
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"kspace_modify"_kspace_modify.html,
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"kspace_style"_kspace_style.html,
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"label"_label.html,
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"lattice"_lattice.html,
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"log"_log.html,
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"mass"_mass.html,
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"minimize"_minimize.html,
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"min_modify"_min_modify.html,
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"min_style"_min_style.html,
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"neigh_modify"_neigh_modify.html,
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"neighbor"_neighbor.html,
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"newton"_newton.html,
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"next"_next.html,
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"pair_coeff"_pair_coeff.html,
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"pair_modify"_pair_modify.html,
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|
"pair_style"_pair_style.html,
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|
"pair_write"_pair_write.html,
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"print"_print.html,
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"processors"_processors.html,
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"read_data"_read_data.html,
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"read_restart"_read_restart.html,
|
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"region"_region.html,
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"replicate"_replicate.html,
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"reset_timestep"_reset_timestep.html,
|
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|
"restart"_restart.html,
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"run"_run.html,
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"run_style"_run_style.html,
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"set"_set.html,
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"shell"_shell.html,
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|
"special_bonds"_special_bonds.html,
|
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|
"temp_modify"_temp_modify.html,
|
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|
"temper"_temper.html,
|
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|
"temperature"_temperature.html,
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|
"thermo"_thermo.html,
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|
"thermo_modify"_thermo_modify.html,
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|
"thermo_style"_thermo_style.html,
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|
"timestep"_timestep.html,
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|
"undump"_undump.html,
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|
|
"unfix"_unfix.html,
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|
|
"units"_units.html,
|
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|
|
"variable"_variable.html,
|
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|
|
"velocity"_velocity.html,
|
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|
"write_restart"_write_restart.html :tb(c=6,ea=c)
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|
Fix styles. See the "fix"_fix.html command for one-line descriptions
|
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|
|
|
or click on the command itself for a full description:
|
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|
|
"fix addforce"_fix_addforce.html,
|
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|
|
|
"fix aveforce"_fix_aveforce.html,
|
|
|
|
|
"fix com"_fix_com.html,
|
2006-12-13 08:37:25 +08:00
|
|
|
"fix deposit"_fix_deposit.html,
|
2006-09-22 00:22:34 +08:00
|
|
|
"fix drag"_fix_drag.html,
|
|
|
|
|
"fix efield"_fix_efield.html,
|
|
|
|
|
"fix enforce2d"_fix_enforce2d.html,
|
|
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|
|
"fix freeze"_fix_freeze.html,
|
|
|
|
|
"fix gran/diag"_fix_gran_diag.html,
|
|
|
|
|
"fix gravity"_fix_gravity.html,
|
|
|
|
|
"fix gyration"_fix_gyration.html,
|
|
|
|
|
"fix indent"_fix_indent.html,
|
|
|
|
|
"fix langevin"_fix_langevin.html,
|
|
|
|
|
"fix lineforce"_fix_lineforce.html,
|
|
|
|
|
"fix msd"_fix_msd.html,
|
|
|
|
|
"fix momentum"_fix_momentum.html,
|
|
|
|
|
"fix nph"_fix_nph.html,
|
|
|
|
|
"fix npt"_fix_npt.html,
|
|
|
|
|
"fix nve"_fix_nve.html,
|
|
|
|
|
"fix nve/gran"_fix_nve_gran.html,
|
|
|
|
|
"fix nvt"_fix_nvt.html,
|
|
|
|
|
"fix orient/fcc"_fix_orient_fcc.html,
|
|
|
|
|
"fix planeforce"_fix_planeforce.html,
|
|
|
|
|
"fix poems"_fix_poems.html,
|
2006-12-13 08:37:25 +08:00
|
|
|
"fix pour"_fix_pour.html,
|
2006-09-22 00:22:34 +08:00
|
|
|
"fix print"_fix_print.html,
|
|
|
|
|
"fix rdf"_fix_rdf.html,
|
|
|
|
|
"fix recenter"_fix_recenter.html,
|
|
|
|
|
"fix rigid"_fix_rigid.html,
|
|
|
|
|
"fix setforce"_fix_setforce.html,
|
|
|
|
|
"fix shake"_fix_shake.html,
|
|
|
|
|
"fix spring"_fix_spring.html,
|
|
|
|
|
"fix spring/rg"_fix_spring_rg.html,
|
|
|
|
|
"fix spring/self"_fix_spring_self.html,
|
|
|
|
|
"fix temp/rescale"_fix_temp_rescale.html,
|
|
|
|
|
"fix tmd"_fix_tmd.html,
|
|
|
|
|
"fix uniaxial"_fix_uniaxial.html,
|
|
|
|
|
"fix vcm"_fix_vcm.html,
|
|
|
|
|
"fix viscous"_fix_viscous.html,
|
|
|
|
|
"fix volume/rescale"_fix_volume_rescale.html,
|
|
|
|
|
"fix wall/gran"_fix_wall_gran.html,
|
|
|
|
|
"fix wall/lj93"_fix_wall_lj93.html,
|
2006-11-14 06:18:34 +08:00
|
|
|
"fix wall/lj126"_fix_wall_lj126.html,
|
2006-09-22 00:22:34 +08:00
|
|
|
"fix wall/reflect"_fix_wall_reflect.html,
|
|
|
|
|
"fix wiggle"_fix_wiggle.html :tb(c=6,ea=c)
|
|
|
|
|
|
|
|
|
|
Pair styles. See the "pair_style"_pair_style.html command for an
|
|
|
|
|
overview of pair potentials. Click on the style itself for a full
|
|
|
|
|
description:
|
|
|
|
|
|
|
|
|
|
"none"_pair_style_none.html,
|
|
|
|
|
"hybrid"_pair_style_hybrid.html,
|
|
|
|
|
"buck"_pair_style_buck.html,
|
|
|
|
|
"buck/coul/cut"_pair_style_buck.html,
|
|
|
|
|
"buck/coul/long"_pair_style_buck.html,
|
|
|
|
|
"dpd"_pair_style_dpd.html,
|
|
|
|
|
"eam"_pair_style_eam.html,
|
|
|
|
|
"eam/alloy"_pair_style_eam.html,
|
|
|
|
|
"eam/fs"_pair_style_eam.html,
|
|
|
|
|
"gran/hertzian"_pair_style_gran.html,
|
|
|
|
|
"gran/history"_pair_style_gran.html,
|
|
|
|
|
"gran/no_history"_pair_style_gran.html,
|
|
|
|
|
"lj/charmm/coul/charmm"_pair_style_charmm.html,
|
|
|
|
|
"lj/charmm/coul/charmm/implicit"_pair_style_charmm.html,
|
|
|
|
|
"lj/charmm/coul/long"_pair_style_charmm.html,
|
|
|
|
|
"lj/class2"_pair_style_class2.html,
|
|
|
|
|
"lj/class2/coul/cut"_pair_style_class2.html,
|
|
|
|
|
"lj/class2/coul/long"_pair_style_class2.html,
|
|
|
|
|
"lj/cut"_pair_style_lj.html,
|
|
|
|
|
"lj/cut/coul/cut"_pair_style_lj.html,
|
|
|
|
|
"lj/cut/coul/debye"_pair_style_lj.html,
|
|
|
|
|
"lj/cut/coul/long"_pair_style_lj.html,
|
|
|
|
|
"lj/cut/coul/long/tip4p"_pair_style_lj.html,
|
|
|
|
|
"lj/expand"_pair_style_lj_expand.html,
|
|
|
|
|
"lj/smooth"_pair_style_lj_smooth.html,
|
2007-01-30 07:28:45 +08:00
|
|
|
"meam"_pair_style_meam.html,
|
2006-09-22 00:22:34 +08:00
|
|
|
"morse"_pair_style_morse.html,
|
|
|
|
|
"soft"_pair_style_soft.html,
|
2006-11-29 01:00:29 +08:00
|
|
|
"sw"_pair_style_sw.html,
|
2006-09-22 00:22:34 +08:00
|
|
|
"table"_pair_style_table.html,
|
2006-11-29 01:00:29 +08:00
|
|
|
"tersoff"_pair_style_tersoff.html,
|
2006-09-22 00:22:34 +08:00
|
|
|
"yukawa"_pair_style_yukawa.html :tb(c=4,ea=c)
|
|
|
|
|
|
|
|
|
|
Bond styles. See the "bond_style"_bond_style.html command for an
|
|
|
|
|
overview of bond potentials. Click on the style itself for a full
|
|
|
|
|
description:
|
|
|
|
|
|
|
|
|
|
"none"_bond_style_none.html,
|
|
|
|
|
"hybrid"_bond_style_hybrid.html,
|
|
|
|
|
"class2"_bond_style_class2.html,
|
|
|
|
|
"fene"_bond_style_fene.html,
|
|
|
|
|
"fene/expand"_bond_style_fene_expand.html,
|
|
|
|
|
"harmonic"_bond_style_harmonic.html,
|
|
|
|
|
"morse"_bond_style_morse.html,
|
|
|
|
|
"nonlinear"_bond_style_nonlinear.html,
|
|
|
|
|
"quartic"_bond_style_quartic.html :tb(c=4,ea=c,w=100)
|
|
|
|
|
|
|
|
|
|
Angle styles. See the "angle_style"_angle_style.html command for an
|
|
|
|
|
overview of angle potentials. Click on the style itself for a full
|
|
|
|
|
description:
|
|
|
|
|
|
|
|
|
|
"none"_angle_style_none.html,
|
|
|
|
|
"hybrid"_angle_style_hybrid.html,
|
|
|
|
|
"charmm"_angle_style_charmm.html,
|
|
|
|
|
"class2"_angle_style_class2.html,
|
|
|
|
|
"cosine"_angle_style_cosine.html,
|
|
|
|
|
"cosine/squared"_angle_style_cosine_squared.html,
|
|
|
|
|
"harmonic"_angle_style_harmonic.html :tb(c=6,ea=c,w=100)
|
|
|
|
|
|
|
|
|
|
Dihedral styles. See the "dihedral_style"_dihedral_style.html command
|
|
|
|
|
for an overview of dihedral potentials. Click on the style itself for
|
|
|
|
|
a full description:
|
|
|
|
|
|
|
|
|
|
"none"_dihedral_style_none.html,
|
|
|
|
|
"hybrid"_dihedral_style_hybrid.html,
|
|
|
|
|
"charmm"_dihedral_style_charmm.html,
|
|
|
|
|
"class2"_dihedral_style_class2.html,
|
|
|
|
|
"harmonic"_dihedral_style_harmonic.html,
|
|
|
|
|
"helix"_dihedral_style_helix.html,
|
|
|
|
|
"multi/harmonic"_dihedral_style_multi_harmonic.html,
|
|
|
|
|
"opls"_dihedral_style_opls.html :tb(c=7,ea=c,w=100)
|
|
|
|
|
|
|
|
|
|
Improper styles. See the "improper_style"_improper_style.html command for an
|
|
|
|
|
overview of improper potentials. Click on the style itself for a full
|
|
|
|
|
description:
|
|
|
|
|
|
|
|
|
|
"none"_improper_style_none.html,
|
|
|
|
|
"hybrid"_improper_style_hybrid.html,
|
|
|
|
|
"class2"_improper_style_class2.html,
|
|
|
|
|
"cvff"_improper_style_cvff.html,
|
|
|
|
|
"harmonic"_improper_style_harmonic.html :tb(c=4,ea=c,w=100)
|
