2006-09-22 00:22:34 +08:00
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<CENTER><A HREF = "Section_start.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_howto.html">Next Section</A>
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<HR>
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<H3>3. Commands
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</H3>
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<P>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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</P>
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3.1 <A HREF = "#3_1">LAMMPS input script</A><BR>
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3.2 <A HREF = "#3_2">Parsing rules</A><BR>
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3.3 <A HREF = "#3_3">Input script structure</A><BR>
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3.4 <A HREF = "#3_4">Commands listed by category</A><BR>
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3.5 <A HREF = "#3_5">Commands listed alphabetically</A> <BR>
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<HR>
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<A NAME = "3_1"></A><H4>3.1 LAMMPS input script
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</H4>
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<P>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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</P>
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<P>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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</P>
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<P>(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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</P>
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<PRE>timestep 0.5
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run 100
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run 100
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</PRE>
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<P>does something different than this sequence:
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</P>
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<PRE>run 100
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timestep 0.5
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run 100
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</PRE>
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<P>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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</P>
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<P>(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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</P>
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<P>(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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<A HREF = "read_data.html">read_data</A> 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 <A HREF = "processors.html">processors</A> and
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<A HREF = "boundary.html">boundary</A> 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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</P>
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<P>Many input script errors are detected by LAMMPS and an ERROR or
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WARNING message is printed. <A HREF = "Section_errors.html">This section</A> 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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</P>
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<HR>
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<A NAME = "3_2"></A><H4>3.2 Parsing rules
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</H4>
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<P>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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</P>
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<P>Here is how each line in the input script is parsed by LAMMPS:
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</P>
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<P>(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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</P>
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<P>(2) All characters from the first "#" character onward are treated as
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comment and discarded.
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</P>
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<P>(3) The line is searched repeatedly for $ characters which indicate
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variables that are replaced with a text string. If the $ is followed
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by curly 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 $x
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refer to variable names "myTemp" and "x". See the
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<A HREF = "variable.html">variable</A> command for details of how strings are
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assigned to variables and how they are substituted for in input
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scripts.
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</P>
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<P>(4) The line is broken into "words" separated by whitespace (tabs,
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spaces). Note that words can thus contain letters, digits,
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underscores, or punctuation characters.
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</P>
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<P>(5) The first word is the command name. All successive words in the
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line are arguments.
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</P>
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<P>(6) Text with spaces can be enclosed in double quotes so it will be
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treated as a single argument. See the <A HREF = "dump_modify.html">dump modify</A>
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or <A HREF = "fix_print.html">fix print</A> commands for examples. A '#' or '$'
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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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</P>
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<HR>
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<H4><A NAME = "3_3"></A>3.3 Input script structure
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</H4>
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<P>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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<A HREF = "Section_example.html">this section</A>, and animated on the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
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Site</A>.
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</P>
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<P>A LAMMPS input script typically has 4 parts:
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</P>
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<OL><LI>Initialization
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<LI>Atom definition
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<LI>Settings
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<LI>Run a simulation
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</OL>
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<P>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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</P>
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<P>(1) Initialization
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</P>
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<P>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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</P>
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<P>The relevant commands are <A HREF = "units.html">units</A>,
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<A HREF = "dimension.html">dimension</A>, <A HREF = "newton.html">newton</A>,
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<A HREF = "processors.html">processors</A>, <A HREF = "boundary.html">boundary</A>,
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<A HREF = "atom_style.html">atom_style</A>, <A HREF = "atom_modify.html">atom_modify</A>.
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</P>
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<P>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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<A HREF = "pair_style.html">pair_style</A>, <A HREF = "bond_style.html">bond_style</A>,
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<A HREF = "angle_style.html">angle_style</A>, <A HREF = "dihedral_style.html">dihedral_style</A>,
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<A HREF = "improper_style.html">improper_style</A>.
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</P>
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<P>(2) Atom definition
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</P>
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<P>There are 3 ways to define atoms in LAMMPS. Read them in from a data
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or restart file via the <A HREF = "read_data.html">read_data</A> or
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<A HREF = "read_restart.html">read_restart</A> 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: <A HREF = "lattice.html">lattice</A>,
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2006-11-14 06:18:34 +08:00
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<A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
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<A HREF = "create_atoms.html">create_atoms</A>. The entire set of atoms can be
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duplicated to make a larger simulation using the
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<A HREF = "replicate.html">replicate</A> command.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>(3) Settings
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</P>
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<P>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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</P>
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<P>Force field coefficients are set by these commands (they can also be
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set in the read-in files): <A HREF = "pair_coeff.html">pair_coeff</A>,
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<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "angle_coeff.html">angle_coeff</A>,
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<A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
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<A HREF = "improper_coeff.html">improper_coeff</A>,
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<A HREF = "kspace_style.html">kspace_style</A>, <A HREF = "dielectric.html">dielectric</A>,
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<A HREF = "special_bonds.html">special_bonds</A>.
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</P>
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<P>Various simulation parameters are set by these commands:
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<A HREF = "neighbor.html">neighbor</A>, <A HREF = "neigh_modify.html">neigh_modify</A>,
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<A HREF = "group.html">group</A>, <A HREF = "timestep.html">timestep</A>,
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<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
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<A HREF = "min_style.html">min_style</A>, <A HREF = "min_modify.html">min_modify</A>.
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</P>
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<P>Fixes impose a variety of boundary conditions, time integration, and
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diagnostic options. The <A HREF = "fix.html">fix</A> command comes in many flavors.
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</P>
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<P>Various computations can be specified for execution during a
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simulation using the <A HREF = "compute.html">compute</A>,
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<A HREF = "compute_modify.html">compute_modify</A>, and <A HREF = "variable.html">variable</A>
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commands.
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</P>
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<P>Output options are set by the <A HREF = "thermo.html">thermo</A>, <A HREF = "dump.html">dump</A>,
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and <A HREF = "restart.html">restart</A> commands.
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</P>
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<P>(4) Run a simulation
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</P>
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<P>A molecular dynamics simulation is run using the <A HREF = "run.html">run</A>
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command. Energy minimization (molecular statics) is performed using
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the <A HREF = "minimize.html">minimize</A> command. A parallel tempering
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(replica-exchange) simulation can be run using the
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<A HREF = "temper.html">temper</A> command.
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</P>
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<HR>
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<A NAME = "3_4"></A><H4>3.4 Commands listed by category
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</H4>
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<P>This section lists all LAMMPS commands, grouped by category. The
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<A HREF = "#3_5">next section</A> 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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</P>
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<P>Initialization:
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</P>
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<P><A HREF = "atom_modify.html">atom_modify</A>, <A HREF = "atom_style.html">atom_style</A>,
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<A HREF = "boundary.html">boundary</A>, <A HREF = "dimension.html">dimension</A>,
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<A HREF = "newton.html">newton</A>, <A HREF = "processors.html">processors</A>, <A HREF = "units.html">units</A>
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</P>
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<P>Atom definition:
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</P>
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<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "create_box.html">create_box</A>,
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<A HREF = "lattice.html">lattice</A>, <A HREF = "read_data.html">read_data</A>,
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<A HREF = "read_restart.html">read_restart</A>, <A HREF = "region.html">region</A>,
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<A HREF = "replicate.html">replicate</A>
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</P>
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<P>Force fields:
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</P>
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<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_style.html">angle_style</A>,
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<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "bond_style.html">bond_style</A>,
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<A HREF = "dielectric.html">dielectric</A>, <A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
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<A HREF = "dihedral_style.html">dihedral_style</A>,
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<A HREF = "improper_coeff.html">improper_coeff</A>,
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<A HREF = "improper_style.html">improper_style</A>,
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<A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "kspace_style.html">kspace_style</A>,
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<A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_modify.html">pair_modify</A>,
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<A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_write.html">pair_write</A>,
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<A HREF = "special_bonds.html">special_bonds</A>
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</P>
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<P>Settings:
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</P>
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<P><A HREF = "dipole.html">dipole</A>, <A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>,
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<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
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<A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
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<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
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<A HREF = "set.html">set</A>, <A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
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</P>
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<P>Fixes:
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</P>
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<P><A HREF = "fix.html">fix</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "unfix.html">unfix</A>
|
|
|
|
|
</P>
|
2007-02-10 05:37:30 +08:00
|
|
|
<P>Computes:
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "compute.html">compute</A>, <A HREF = "compute_modify.html">compute_modify</A>,
|
|
|
|
|
<A HREF = "uncompute.html">uncompute</A>
|
|
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P>Output:
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_modify.html">dump_modify</A>,
|
|
|
|
|
<A HREF = "restart.html">restart</A>, <A HREF = "thermo.html">thermo</A>,
|
|
|
|
|
<A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "thermo_style.html">thermo_style</A>,
|
|
|
|
|
<A HREF = "undump.html">undump</A>, <A HREF = "write_restart.html">write_restart</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P>Actions:
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
|
|
|
|
|
<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "minimize.html">minimize</A>,
|
|
|
|
|
<A HREF = "run.html">run</A>, <A HREF = "temper.html">temper</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P>Miscellaneous:
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "clear.html">clear</A>, <A HREF = "echo.html">echo</A>, <A HREF = "include.html">include</A>,
|
|
|
|
|
<A HREF = "jump.html">jump</A>, <A HREF = "label.html">label</A>, <A HREF = "log.html">log</A>,
|
|
|
|
|
<A HREF = "next.html">next</A>, <A HREF = "print.html">print</A>, <A HREF = "shell.html">shell</A>,
|
|
|
|
|
<A HREF = "variable.html">variable</A>
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<H4><A NAME = "3_5"></A><A NAME = "comm"></A>3.5 Individual commands
|
|
|
|
|
</H4>
|
|
|
|
|
<P>This section lists all LAMMPS commands alphabetically, with a separate
|
|
|
|
|
listing below of styles within certain commands. The <A HREF = "#3_4">previous
|
|
|
|
|
section</A> 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.
|
|
|
|
|
</P>
|
|
|
|
|
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD><TD ><A HREF = "bond_style.html">bond_style</A></TD></TR>
|
2007-02-10 05:37:30 +08:00
|
|
|
<TR ALIGN="center"><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "dipole.html">dipole</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "echo.html">echo</A></TD><TD ><A HREF = "fix.html">fix</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD><TD ><A HREF = "label.html">label</A></TD><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "print.html">print</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
|
2006-09-22 00:22:34 +08:00
|
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
|
|
2007-02-10 05:37:30 +08:00
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P>Fix commands. See the <A HREF = "fix.html">fix</A> command for one-line
|
|
|
|
|
descriptions of each style or click on the style itself for a full
|
|
|
|
|
description:
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
2007-02-21 08:18:01 +08:00
|
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gran_diag.html">gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_uniaxial.html">uniaxial</A></TD></TR>
|
2007-02-22 07:10:35 +08:00
|
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
|
2006-09-22 00:22:34 +08:00
|
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
|
|
2007-02-10 05:37:30 +08:00
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P>Compute commands. See the <A HREF = "compute.html">compute</A> command for one-line
|
|
|
|
|
descriptions of each style or click on the style itself for a full
|
2006-09-22 00:22:34 +08:00
|
|
|
description:
|
|
|
|
|
</P>
|
|
|
|
|
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
2007-02-10 05:37:30 +08:00
|
|
|
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_epair_atom.html">epair/atom</A></TD><TD ><A HREF = "compute_etotal_atom.html">etotal/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD></TR>
|
2007-02-21 08:18:01 +08:00
|
|
|
<TR ALIGN="center"><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A><A HREF = "compute_variable_atom.html">variable/atom</A>
|
2006-09-22 00:22:34 +08:00
|
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
|
|
2007-02-10 05:37:30 +08:00
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P>Pair_style potentials. See the <A HREF = "pair_style.html">pair_style</A> command
|
|
|
|
|
for an overview of pair potentials. Click on the style itself for a
|
|
|
|
|
full description:
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
2007-02-10 05:37:30 +08:00
|
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hertzian</A></TD><TD ><A HREF = "pair_gran.html">gran/history</A></TD><TD ><A HREF = "pair_gran.html">gran/no_history</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A>
|
2006-09-22 00:22:34 +08:00
|
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
|
|
2007-02-10 05:37:30 +08:00
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P>Bond_style potentials. See the <A HREF = "bond_style.html">bond_style</A> command
|
|
|
|
|
for an overview of bond potentials. Click on the style itself for a
|
|
|
|
|
full description:
|
|
|
|
|
</P>
|
|
|
|
|
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
|
|
|
|
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_none.html">none</A></TD><TD WIDTH="100"><A HREF = "bond_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "bond_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "bond_fene.html">fene</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_fene_expand.html">fene/expand</A></TD><TD WIDTH="100"><A HREF = "bond_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "bond_morse.html">morse</A></TD><TD WIDTH="100"><A HREF = "bond_nonlinear.html">nonlinear</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_quartic.html">quartic</A>
|
|
|
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P>Angle_style potentials. See the <A HREF = "angle_style.html">angle_style</A>
|
|
|
|
|
command for an overview of angle potentials. Click on the style
|
|
|
|
|
itself for a full description:
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
2007-02-10 05:37:30 +08:00
|
|
|
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_none.html">none</A></TD><TD WIDTH="100"><A HREF = "angle_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "angle_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "angle_class2.html">class2</A></TD></TR>
|
|
|
|
|
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_cosine.html">cosine</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_squared.html">cosine/squared</A></TD><TD WIDTH="100"><A HREF = "angle_harmonic.html">harmonic</A>
|
2006-09-22 00:22:34 +08:00
|
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
|
|
2007-02-10 05:37:30 +08:00
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P>Dihedral_style potentials. See the
|
|
|
|
|
<A HREF = "dihedral_style.html">dihedral_style</A> command for an overview of
|
|
|
|
|
dihedral potentials. Click on the style itself for a full
|
|
|
|
|
description:
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
2007-02-10 05:37:30 +08:00
|
|
|
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_none.html">none</A></TD><TD WIDTH="100"><A HREF = "dihedral_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "dihedral_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "dihedral_class2.html">class2</A></TD></TR>
|
|
|
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_helix.html">helix</A></TD><TD WIDTH="100"><A HREF = "dihedral_multi_harmonic.html">multi/harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_opls.html">opls</A>
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2006-09-22 00:22:34 +08:00
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</TD></TR></TABLE></DIV>
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2007-02-10 05:37:30 +08:00
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<HR>
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<P>Improper_style potentials. See the
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<A HREF = "improper_style.html">improper_style</A> command for an overview of
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improper potentials. Click on the style itself for a full
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2006-09-22 00:22:34 +08:00
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description:
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</P>
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<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
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2007-02-10 05:37:30 +08:00
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_none.html">none</A></TD><TD WIDTH="100"><A HREF = "improper_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "improper_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "improper_cvff.html">cvff</A></TD></TR>
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic</A>
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2006-09-22 00:22:34 +08:00
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</TD></TR></TABLE></DIV>
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2007-02-23 00:59:04 +08:00
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<HR>
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<P>Kspace solvers. All of these solver styles are discussed as part of
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the <A HREF = "kspace_style.html">kspace_style</A> command:
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</P>
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<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">ewald</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/tip4p</A>
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</TD></TR></TABLE></DIV>
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2006-09-22 00:22:34 +08:00
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</HTML>
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