forked from lijiext/lammps
372 lines
25 KiB
HTML
372 lines
25 KiB
HTML
<HTML>
|
|
<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>
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
<H3>3. Commands
|
|
</H3>
|
|
<P>This section describes how a LAMMPS input script is formatted and what
|
|
commands are used to define a LAMMPS simulation.
|
|
</P>
|
|
3.1 <A HREF = "#3_1">LAMMPS input script</A><BR>
|
|
3.2 <A HREF = "#3_2">Parsing rules</A><BR>
|
|
3.3 <A HREF = "#3_3">Input script structure</A><BR>
|
|
3.4 <A HREF = "#3_4">Commands listed by category</A><BR>
|
|
3.5 <A HREF = "#3_5">Commands listed alphabetically</A> <BR>
|
|
|
|
<HR>
|
|
|
|
<A NAME = "3_1"></A><H4>3.1 LAMMPS input script
|
|
</H4>
|
|
<P>LAMMPS executes by reading commands from a input script (text file),
|
|
one line at a time. When the input script ends, LAMMPS exits. Each
|
|
command causes LAMMPS 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.
|
|
</P>
|
|
<P>In many cases, the ordering of commands in an input script is not
|
|
important. However the following rules apply:
|
|
</P>
|
|
<P>(1) LAMMPS 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:
|
|
</P>
|
|
<PRE>timestep 0.5
|
|
run 100
|
|
run 100
|
|
</PRE>
|
|
<P>does something different than this sequence:
|
|
</P>
|
|
<PRE>run 100
|
|
timestep 0.5
|
|
run 100
|
|
</PRE>
|
|
<P>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.
|
|
</P>
|
|
<P>(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.
|
|
</P>
|
|
<P>(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
|
|
<A HREF = "read_data.html">read_data</A> command initializes the system by setting
|
|
up the simulation box and assigning atoms to processors. If default
|
|
values are not desired, the <A HREF = "processors.html">processors</A> and
|
|
<A HREF = "boundary.html">boundary</A> commands need to be used before read_data to
|
|
tell LAMMPS how to map processors to the simulation box.
|
|
</P>
|
|
<P>Many input script errors are detected by LAMMPS and an ERROR or
|
|
WARNING message is printed. <A HREF = "Section_errors.html">This section</A> gives
|
|
more information on what errors mean. The documentation for each
|
|
command lists restrictions on how the command can be used.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "3_2"></A><H4>3.2 Parsing rules
|
|
</H4>
|
|
<P>Each non-blank line in the input script is treated as a command.
|
|
LAMMPS 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.
|
|
</P>
|
|
<P>Here is how each line in the input script is parsed by LAMMPS:
|
|
</P>
|
|
<P>(1) If the line ends with a "&" character (with no trailing
|
|
whitespace), 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.
|
|
</P>
|
|
<P>(2) All characters from the first "#" character onward are treated as
|
|
comment and discarded.
|
|
</P>
|
|
<P>(3) The line is searched repeatedly for $ characters which indicate
|
|
variables that are replaced with text. 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 character immediately following the $. Thus ${myTemp} and $x
|
|
refer to variable names "myTemp" and "x". See the
|
|
<A HREF = "variable.html">variable</A> command for details of how values are
|
|
assigned to variables and how they are substituted for in input
|
|
scripts.
|
|
</P>
|
|
<P>(4) The line is broken into "words" separated by whitespace (tabs,
|
|
spaces). Note that words can thus contain letters, digits,
|
|
underscores, or punctuation characters.
|
|
</P>
|
|
<P>(5) The first word is the command name. All successive words in the
|
|
line are arguments.
|
|
</P>
|
|
<P>(6) Text with spaces can be enclosed in double quotes so it will be
|
|
treated as a single argument. See the <A HREF = "dump_modify.html">dump modify</A>
|
|
or <A HREF = "fix_print.html">fix print</A> commands for examples. A '#' or '$'
|
|
character that in text between double quotes will not be treated as a
|
|
comment or substituted for as a variable.
|
|
</P>
|
|
<HR>
|
|
|
|
<H4><A NAME = "3_3"></A>3.3 Input script structure
|
|
</H4>
|
|
<P>This section describes the structure of a typical LAMMPS input script.
|
|
The "examples" directory in the LAMMPS distribution contains many
|
|
sample input scripts; the corresponding problems are discussed in
|
|
<A HREF = "Section_example.html">this section</A>, and animated on the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
|
|
Site</A>.
|
|
</P>
|
|
<P>A LAMMPS input script typically has 4 parts:
|
|
</P>
|
|
<OL><LI>Initialization
|
|
<LI>Atom definition
|
|
<LI>Settings
|
|
<LI>Run a simulation
|
|
</OL>
|
|
<P>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.
|
|
</P>
|
|
<P>(1) Initialization
|
|
</P>
|
|
<P>Set parameters that need to be defined before atoms are created or
|
|
read-in from a file.
|
|
</P>
|
|
<P>The relevant commands are <A HREF = "units.html">units</A>,
|
|
<A HREF = "dimension.html">dimension</A>, <A HREF = "newton.html">newton</A>,
|
|
<A HREF = "processors.html">processors</A>, <A HREF = "boundary.html">boundary</A>,
|
|
<A HREF = "atom_style.html">atom_style</A>, <A HREF = "atom_modify.html">atom_modify</A>.
|
|
</P>
|
|
<P>If force-field parameters appear in the files that will be read, these
|
|
commands tell LAMMPS what kinds of force fields are being used:
|
|
<A HREF = "pair_style.html">pair_style</A>, <A HREF = "bond_style.html">bond_style</A>,
|
|
<A HREF = "angle_style.html">angle_style</A>, <A HREF = "dihedral_style.html">dihedral_style</A>,
|
|
<A HREF = "improper_style.html">improper_style</A>.
|
|
</P>
|
|
<P>(2) Atom definition
|
|
</P>
|
|
<P>There are 3 ways to define atoms in LAMMPS. Read them in from a data
|
|
or restart file via the <A HREF = "read_data.html">read_data</A> or
|
|
<A HREF = "read_restart.html">read_restart</A> commands. These files can contain
|
|
molecular topology information. Or create atoms on a lattice (with no
|
|
molecular topology), using these commands: <A HREF = "lattice.html">lattice</A>,
|
|
<A HREF = "orient.html">orient</A>, <A HREF = "origin.html">origin</A>, <A HREF = "region.html">region</A>,
|
|
<A HREF = "create_box.html">create_box</A>, <A HREF = "create_atoms.html">create_atoms</A>. The
|
|
entire set of atoms can be duplicated to make a larger simulation
|
|
using the <A HREF = "replicate.html">replicate</A> command.
|
|
</P>
|
|
<P>(3) Settings
|
|
</P>
|
|
<P>Once atoms and molecular topology are defined, a variety of settings
|
|
can be specified: force field coefficients, simulation parameters,
|
|
output options, etc.
|
|
</P>
|
|
<P>Force field coefficients are set by these commands (they can also be
|
|
set in the read-in files): <A HREF = "pair_coeff.html">pair_coeff</A>,
|
|
<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "angle_coeff.html">angle_coeff</A>,
|
|
<A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
|
|
<A HREF = "improper_coeff.html">improper_coeff</A>,
|
|
<A HREF = "kspace_style.html">kspace_style</A>, <A HREF = "dielectric.html">dielectric</A>,
|
|
<A HREF = "special_bonds.html">special_bonds</A>.
|
|
</P>
|
|
<P>Various simulation parameters are set by these commands:
|
|
<A HREF = "temperature.html">temperature</A>, <A HREF = "temp_modify.html">temp_modify</A>,
|
|
<A HREF = "neighbor.html">neighbor</A>, <A HREF = "neigh_modify.html">neigh_modify</A>,
|
|
<A HREF = "group.html">group</A>, <A HREF = "timestep.html">timestep</A>,
|
|
<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
|
|
<A HREF = "min_style.html">min_style</A>, <A HREF = "min_modify.html">min_modify</A>.
|
|
</P>
|
|
<P>Fixes impose a variety of boundary conditions, time integration, and
|
|
diagnostic options. The <A HREF = "fix.html">fix</A> command comes in many flavors.
|
|
</P>
|
|
<P>Output options are set by these commands: <A HREF = "thermo.html">thermo</A>,
|
|
<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A>.
|
|
</P>
|
|
<P>(4) Run a simulation
|
|
</P>
|
|
<P>A molecular dynamics simulation is run using the <A HREF = "run.html">run</A>
|
|
command. Energy minimization (molecular statics) is performed using
|
|
the <A HREF = "minimize.html">minimize</A> command. A parallel tempering
|
|
(replica-exchange) simulation can be run using the
|
|
<A HREF = "temper.html">temper</A> command.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "3_4"></A><H4>3.4 Commands listed by category
|
|
</H4>
|
|
<P>This section lists all LAMMPS commands, grouped by category. The
|
|
<A HREF = "#3_5">next section</A> lists the same commands alphabetically. 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>
|
|
<P>Initialization:
|
|
</P>
|
|
<P><A HREF = "atom_modify.html">atom_modify</A>, <A HREF = "atom_style.html">atom_style</A>,
|
|
<A HREF = "boundary.html">boundary</A>, <A HREF = "dimension.html">dimension</A>,
|
|
<A HREF = "newton.html">newton</A>, <A HREF = "processors.html">processors</A>, <A HREF = "units.html">units</A>
|
|
</P>
|
|
<P>Atom definition:
|
|
</P>
|
|
<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "create_box.html">create_box</A>,
|
|
<A HREF = "lattice.html">lattice</A>, <A HREF = "orient.html">orient</A>, <A HREF = "origin.html">origin</A>,
|
|
<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>,
|
|
<A HREF = "region.html">region</A>, <A HREF = "replicate.html">replicate</A>
|
|
</P>
|
|
<P>Force fields:
|
|
</P>
|
|
<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_style.html">angle_style</A>,
|
|
<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "bond_style.html">bond_style</A>,
|
|
<A HREF = "dielectric.html">dielectric</A>, <A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
|
|
<A HREF = "dihedral_style.html">dihedral_style</A>,
|
|
<A HREF = "improper_coeff.html">improper_coeff</A>,
|
|
<A HREF = "improper_style.html">improper_style</A>,
|
|
<A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "kspace_style.html">kspace_style</A>,
|
|
<A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_modify.html">pair_modify</A>,
|
|
<A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_write.html">pair_write</A>,
|
|
<A HREF = "special_bonds.html">special_bonds</A>
|
|
</P>
|
|
<P>Settings:
|
|
</P>
|
|
<P><A HREF = "dipole.html">dipole</A>, <A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>,
|
|
<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
|
|
<A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
|
|
<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
|
|
<A HREF = "set.html">set</A>, <A HREF = "temp_modify.html">temp_modify</A>,
|
|
<A HREF = "temperature.html">temperature</A>, <A HREF = "timestep.html">timestep</A>,
|
|
<A HREF = "velocity.html">velocity</A>
|
|
</P>
|
|
<P>Fixes:
|
|
</P>
|
|
<P><A HREF = "fix.html">fix</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "unfix.html">unfix</A>
|
|
</P>
|
|
<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>
|
|
<TR ALIGN="center"><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD></TR>
|
|
<TR ALIGN="center"><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><TD ><A HREF = "dipole.html">dipole</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD></TR>
|
|
<TR ALIGN="center"><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><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD></TR>
|
|
<TR ALIGN="center"><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><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD></TR>
|
|
<TR ALIGN="center"><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><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD></TR>
|
|
<TR ALIGN="center"><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><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "orient.html">orient</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "origin.html">origin</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 = "temp_modify.html">temp_modify</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "temperature.html">temperature</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></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "timestep.html">timestep</A></TD><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></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "write_restart.html">write_restart</A>
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
<P>Fix styles. See the <A HREF = "fix.html">fix</A> command for one-line descriptions
|
|
or click on the command itself for a full description:
|
|
</P>
|
|
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">fix addforce</A></TD><TD ><A HREF = "fix_aveforce.html">fix aveforce</A></TD><TD ><A HREF = "fix_com.html">fix com</A></TD><TD ><A HREF = "fix_drag.html">fix drag</A></TD><TD ><A HREF = "fix_efield.html">fix efield</A></TD><TD ><A HREF = "fix_enforce2d.html">fix enforce2d</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_freeze.html">fix freeze</A></TD><TD ><A HREF = "fix_gran_diag.html">fix gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">fix gravity</A></TD><TD ><A HREF = "fix_gyration.html">fix gyration</A></TD><TD ><A HREF = "fix_indent.html">fix indent</A></TD><TD ><A HREF = "fix_insert.html">fix insert</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_langevin.html">fix langevin</A></TD><TD ><A HREF = "fix_lineforce.html">fix lineforce</A></TD><TD ><A HREF = "fix_msd.html">fix msd</A></TD><TD ><A HREF = "fix_momentum.html">fix momentum</A></TD><TD ><A HREF = "fix_nph.html">fix nph</A></TD><TD ><A HREF = "fix_npt.html">fix npt</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_nve.html">fix nve</A></TD><TD ><A HREF = "fix_nve_gran.html">fix nve/gran</A></TD><TD ><A HREF = "fix_nvt.html">fix nvt</A></TD><TD ><A HREF = "fix_orient_fcc.html">fix orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">fix planeforce</A></TD><TD ><A HREF = "fix_poems.html">fix poems</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_print.html">fix print</A></TD><TD ><A HREF = "fix_rdf.html">fix rdf</A></TD><TD ><A HREF = "fix_recenter.html">fix recenter</A></TD><TD ><A HREF = "fix_rigid.html">fix rigid</A></TD><TD ><A HREF = "fix_setforce.html">fix setforce</A></TD><TD ><A HREF = "fix_shake.html">fix shake</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_spring.html">fix spring</A></TD><TD ><A HREF = "fix_spring_rg.html">fix spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">fix spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">fix temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">fix tmd</A></TD><TD ><A HREF = "fix_uniaxial.html">fix uniaxial</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_vcm.html">fix vcm</A></TD><TD ><A HREF = "fix_viscous.html">fix viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">fix volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">fix wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">fix wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">fix wall/reflect</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "fix_wiggle.html">fix wiggle</A>
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
<P>Pair styles. 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:
|
|
</P>
|
|
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_style_none.html">none</A></TD><TD ><A HREF = "pair_style_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_style_buck.html">buck</A></TD><TD ><A HREF = "pair_style_buck.html">buck/coul/cut</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_style_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_style_dpd.html">dpd</A></TD><TD ><A HREF = "pair_style_eam.html">eam</A></TD><TD ><A HREF = "pair_style_eam.html">eam/alloy</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_style_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_style_gran.html">gran/hertzian</A></TD><TD ><A HREF = "pair_style_gran.html">gran/history</A></TD><TD ><A HREF = "pair_style_gran.html">gran/no_history</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_style_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_style_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_style_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_style_class2.html">lj/class2</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_style_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_style_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_style_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_style_lj.html">lj/cut/coul/cut</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_style_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_style_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_style_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_style_lj_expand.html">lj/expand</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_style_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_style_morse.html">morse</A></TD><TD ><A HREF = "pair_style_soft.html">soft</A></TD><TD ><A HREF = "pair_style_table.html">table</A></TD></TR>
|
|
<TR ALIGN="center"><TD ><A HREF = "pair_style_yukawa.html">yukawa</A>
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
<P>Bond styles. 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_style_none.html">none</A></TD><TD WIDTH="100"><A HREF = "bond_style_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "bond_style_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "bond_style_fene.html">fene</A></TD></TR>
|
|
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_style_fene_expand.html">fene/expand</A></TD><TD WIDTH="100"><A HREF = "bond_style_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "bond_style_morse.html">morse</A></TD><TD WIDTH="100"><A HREF = "bond_style_nonlinear.html">nonlinear</A></TD></TR>
|
|
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_style_quartic.html">quartic</A>
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
<P>Angle styles. 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:
|
|
</P>
|
|
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
|
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_style_none.html">none</A></TD><TD WIDTH="100"><A HREF = "angle_style_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "angle_style_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "angle_style_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "angle_style_cosine.html">cosine</A></TD><TD WIDTH="100"><A HREF = "angle_style_cosine_squared.html">cosine/squared</A></TD></TR>
|
|
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_style_harmonic.html">harmonic</A>
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
<P>Dihedral styles. 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:
|
|
</P>
|
|
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
|
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_style_none.html">none</A></TD><TD WIDTH="100"><A HREF = "dihedral_style_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "dihedral_style_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "dihedral_style_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "dihedral_style_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_style_helix.html">helix</A></TD><TD WIDTH="100"><A HREF = "dihedral_style_multi_harmonic.html">multi/harmonic</A></TD></TR>
|
|
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_style_opls.html">opls</A>
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
<P>Improper styles. See the <A HREF = "improper_style.html">improper_style</A> command for an
|
|
overview of improper 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 = "improper_style_none.html">none</A></TD><TD WIDTH="100"><A HREF = "improper_style_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "improper_style_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "improper_style_cvff.html">cvff</A></TD></TR>
|
|
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_style_harmonic.html">harmonic</A>
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
</HTML>
|