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<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 a text string. 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 $x
refer to variable names "myTemp" and "x". See the
<A HREF = "variable.html">variable</A> command for details of how strings are
assigned to variables and how they are substituted for in input
scripts.
</P>
<P>(4) The line is broken into "words" separated by whitespace (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.
</P>
<P>(5) The first word is the command name. All successive words in the
line are arguments.
</P>
<P>(6) Text with spaces can be enclosed in double quotes so it will be
treated as a single argument. See the <A HREF = "dump_modify.html">dump modify</A>
or <A HREF = "fix_print.html">fix print</A> commands for examples. A '#' or '$'
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 = "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 = "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>Various computations can be specified for execution during a
simulation using the <A HREF = "compute.html">compute</A>,
<A HREF = "compute_modify.html">compute_modify</A>, and <A HREF = "variable.html">variable</A>
commands.
</P>
<P>Output options are set by the <A HREF = "thermo.html">thermo</A>, <A HREF = "dump.html">dump</A>,
and <A HREF = "restart.html">restart</A> commands.
</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 = "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 = "communicate.html">communicate</A>, <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 = "shape.html">shape</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>Computes:
</P>
<P><A HREF = "compute.html">compute</A>, <A HREF = "compute_modify.html">compute_modify</A>,
<A HREF = "uncompute.html">uncompute</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 = "displace_box.html">displace_box</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 = "if.html">if</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 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 = "change_box.html">change_box</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "communicate.html">communicate</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "displace_box.html">displace_box</A></TD><TD ><A HREF = "dump.html">dump</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "if.html">if</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 = "pair_coeff.html">pair_coeff</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shape.html">shape</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "temper.html">temper</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "undump.html">undump</A></TD></TR>
<TR ALIGN="center"><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>
</TD></TR></TABLE></DIV>
<HR>
<P>Fix styles. 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:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<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_atom.html">ave/atom</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_com.html">com</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV>
<HR>
<P>Compute styles. 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
description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_attribute_atom.html">attribute/atom</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_ebond_atom.html">ebond/atom</A></TD><TD ><A HREF = "compute_epair_atom.html">epair/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><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_sum.html">sum</A></TD><TD ><A HREF = "compute_sum_atom.html">sum/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_variable.html">variable</A></TD><TD ><A HREF = "compute_variable_atom.html">variable/atom</A>
+<TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><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_sum.html">sum</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_sum_atom.html">sum/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_variable.html">variable</A></TD><TD ><A HREF = "compute_variable_atom.html">variable/atom</A>
</TD></TR></TABLE></DIV>
<P>These are compute styles contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland</A>
</TD></TR></TABLE></DIV>
<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:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<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_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_airebo.html">airebo</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_colloid.html">colloid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/cut</A></TD><TD ><A HREF = "pair_coul.html">coul/long</A></TD><TD ><A HREF = "pair_dipole.html">dipole/cut</A></TD><TD ><A HREF = "pair_dpd.html">dpd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gran.html">gran/hertzian</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</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_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A>
</TD></TR></TABLE></DIV>
<P>These are pair styles contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_buck_coul.html">buck/coul</A></TD><TD ><A HREF = "pair_lj_coul.html">lj/coul</A>
</TD></TR></TABLE></DIV>
<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 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:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<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>
</TD></TR></TABLE></DIV>
<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:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<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>
<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>
</TD></TR></TABLE></DIV>
<HR>
<P>Improper_style potentials. 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 BORDER=1 >
<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>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic</A>
</TD></TR></TABLE></DIV>
<HR>
<P>Kspace solvers. See the <A HREF = "kspace_style.html">kspace_style</A> command for
an overview of Kspace solvers. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<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>
</TD></TR></TABLE></DIV>
<P>These are Kspace solvers contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">ewald/n</A>
</TD></TR></TABLE></DIV>
</HTML>
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index db4578bf8..292f72395 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -1,600 +1,601 @@
"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_howto.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
3. Commands :h3
This section describes how a LAMMPS input script is formatted and what
commands are used to define a LAMMPS simulation.
3.1 "LAMMPS input script"_#3_1
3.2 "Parsing rules"_#3_2
3.3 "Input script structure"_#3_3
3.4 "Commands listed by category"_#3_4
3.5 "Commands listed alphabetically"_#3_5 :all(b)
:line
3.1 LAMMPS input script :link(3_1),h4
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.
In many cases, the ordering of commands in an input script is not
important. However the following rules apply:
(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:
timestep 0.5
run 100
run 100 :pre
does something different than this sequence:
run 100
timestep 0.5
run 100 :pre
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.
(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.
(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
"read_data"_read_data.html command initializes the system by setting
up the simulation box and assigning atoms to processors. If default
values are not desired, the "processors"_processors.html and
"boundary"_boundary.html commands need to be used before read_data to
tell LAMMPS how to map processors to the simulation box.
Many input script errors are detected by LAMMPS and an ERROR or
WARNING message is printed. "This section"_Section_errors.html gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.
:line
3.2 Parsing rules :link(3_2),h4
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.
Here is how each line in the input script is parsed by LAMMPS:
(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.
(2) All characters from the first "#" character onward are treated as
comment and discarded.
(3) The line is searched repeatedly for $ characters which indicate
variables that are replaced with a text string. 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 $x
refer to variable names "myTemp" and "x". See the
"variable"_variable.html command for details of how strings are
assigned to variables and how they are substituted for in input
scripts.
(4) The line is broken into "words" separated by whitespace (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.
(5) The first word is the command name. All successive words in the
line are arguments.
(6) Text with spaces can be enclosed in double quotes so it will be
treated as a single argument. See the "dump modify"_dump_modify.html
or "fix print"_fix_print.html commands for examples. A '#' or '$'
character that in text between double quotes will not be treated as a
comment or substituted for as a variable.
:line
3.3 Input script structure :h4,link(3_3)
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
"this section"_Section_example.html, and animated on the "LAMMPS WWW
Site"_lws.
A LAMMPS input script typically has 4 parts:
Initialization
Atom definition
Settings
Run a simulation :ol
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.
(1) Initialization
Set parameters that need to be defined before atoms are created or
read-in from a file.
The relevant commands are "units"_units.html,
"dimension"_dimension.html, "newton"_newton.html,
"processors"_processors.html, "boundary"_boundary.html,
"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
If force-field parameters appear in the files that will be read, these
commands tell LAMMPS what kinds of force fields are being used:
"pair_style"_pair_style.html, "bond_style"_bond_style.html,
"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
"improper_style"_improper_style.html.
(2) Atom definition
There are 3 ways to define atoms in LAMMPS. Read them in from a data
or restart file via the "read_data"_read_data.html or
"read_restart"_read_restart.html commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: "lattice"_lattice.html,
"region"_region.html, "create_box"_create_box.html,
"create_atoms"_create_atoms.html. The entire set of atoms can be
duplicated to make a larger simulation using the
"replicate"_replicate.html command.
(3) Settings
Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters,
output options, etc.
Force field coefficients are set by these commands (they can also be
set in the read-in files): "pair_coeff"_pair_coeff.html,
"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
"dihedral_coeff"_dihedral_coeff.html,
"improper_coeff"_improper_coeff.html,
"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
"special_bonds"_special_bonds.html.
Various simulation parameters are set by these commands:
"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
"group"_group.html, "timestep"_timestep.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
"min_style"_min_style.html, "min_modify"_min_modify.html.
Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The "fix"_fix.html command comes in many flavors.
Various computations can be specified for execution during a
simulation using the "compute"_compute.html,
"compute_modify"_compute_modify.html, and "variable"_variable.html
commands.
Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
and "restart"_restart.html commands.
(4) Run a simulation
A molecular dynamics simulation is run using the "run"_run.html
command. Energy minimization (molecular statics) is performed using
the "minimize"_minimize.html command. A parallel tempering
(replica-exchange) simulation can be run using the
"temper"_temper.html command.
:line
3.4 Commands listed by category :link(3_4),h4
This section lists all LAMMPS commands, grouped by category. The
"next section"_#3_5 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.
Initialization:
"atom_modify"_atom_modify.html, "atom_style"_atom_style.html,
"boundary"_boundary.html, "dimension"_dimension.html,
"newton"_newton.html, "processors"_processors.html, "units"_units.html
Atom definition:
"create_atoms"_create_atoms.html, "create_box"_create_box.html,
"lattice"_lattice.html, "read_data"_read_data.html,
"read_restart"_read_restart.html, "region"_region.html,
"replicate"_replicate.html
Force fields:
"angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html,
"bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html,
"dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html,
"pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html,
"pair_style"_pair_style.html, "pair_write"_pair_write.html,
"special_bonds"_special_bonds.html
Settings:
"communicate"_communicate.html, "dipole"_dipole.html,
"group"_group.html, "mass"_mass.html, "min_modify"_min_modify.html,
"min_style"_min_style.html, "neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html, "reset_timestep"_reset_timestep.html,
"run_style"_run_style.html, "set"_set.html, "shape"_shape.html,
"timestep"_timestep.html, "velocity"_velocity.html
Fixes:
"fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html
Computes:
"compute"_compute.html, "compute_modify"_compute_modify.html,
"uncompute"_uncompute.html
Output:
"dump"_dump.html, "dump_modify"_dump_modify.html,
"restart"_restart.html, "thermo"_thermo.html,
"thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html,
"undump"_undump.html, "write_restart"_write_restart.html
Actions:
"delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html,
"displace_atoms"_displace_atoms.html,
"displace_box"_displace_box.html, "minimize"_minimize.html,
"run"_run.html, "temper"_temper.html
Miscellaneous:
"clear"_clear.html, "echo"_echo.html, "if"_if.html,
"include"_include.html, "jump"_jump.html, "label"_label.html,
"log"_log.html, "next"_next.html, "print"_print.html,
"shell"_shell.html, "variable"_variable.html
:line
3.5 Individual commands :h4,link(3_5),link(comm)
This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The "previous
section"_#3_4 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.
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,
"atom_modify"_atom_modify.html,
"atom_style"_atom_style.html,
"bond_coeff"_bond_coeff.html,
"bond_style"_bond_style.html,
"boundary"_boundary.html,
"change_box"_change_box.html,
"clear"_clear.html,
"communicate"_communicate.html,
"compute"_compute.html,
"compute_modify"_compute_modify.html,
"create_atoms"_create_atoms.html,
"create_box"_create_box.html,
"delete_atoms"_delete_atoms.html,
"delete_bonds"_delete_bonds.html,
"dielectric"_dielectric.html,
"dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"dimension"_dimension.html,
"dipole"_dipole.html,
"displace_atoms"_displace_atoms.html,
"displace_box"_displace_box.html,
"dump"_dump.html,
"dump_modify"_dump_modify.html,
"echo"_echo.html,
"fix"_fix.html,
"fix_modify"_fix_modify.html,
"group"_group.html,
"if"_if.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"include"_include.html,
"jump"_jump.html,
"kspace_modify"_kspace_modify.html,
"kspace_style"_kspace_style.html,
"label"_label.html,
"lattice"_lattice.html,
"log"_log.html,
"mass"_mass.html,
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
"neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html,
"newton"_newton.html,
"next"_next.html,
"pair_coeff"_pair_coeff.html,
"pair_modify"_pair_modify.html,
"pair_style"_pair_style.html,
"pair_write"_pair_write.html,
"print"_print.html,
"processors"_processors.html,
"read_data"_read_data.html,
"read_restart"_read_restart.html,
"region"_region.html,
"replicate"_replicate.html,
"reset_timestep"_reset_timestep.html,
"restart"_restart.html,
"run"_run.html,
"run_style"_run_style.html,
"set"_set.html,
"shape"_shape.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
"temper"_temper.html,
"thermo"_thermo.html,
"thermo_modify"_thermo_modify.html,
"thermo_style"_thermo_style.html,
"timestep"_timestep.html,
"uncompute"_uncompute.html,
"undump"_undump.html,
"unfix"_unfix.html,
"units"_units.html,
"variable"_variable.html,
"velocity"_velocity.html,
"write_restart"_write_restart.html :tb(c=6,ea=c)
:line
Fix styles. See the "fix"_fix.html command for one-line descriptions
of each style or click on the style itself for a full description:
"addforce"_fix_addforce.html,
"aveforce"_fix_aveforce.html,
"ave/atom"_fix_ave_atom.html,
"ave/spatial"_fix_ave_spatial.html,
"ave/time"_fix_ave_time.html,
"com"_fix_com.html,
"deform"_fix_deform.html,
"deposit"_fix_deposit.html,
"drag"_fix_drag.html,
"dt/reset"_fix_dt_reset.html,
"efield"_fix_efield.html,
"enforce2d"_fix_enforce2d.html,
"freeze"_fix_freeze.html,
"gran/diag"_fix_gran_diag.html,
"gravity"_fix_gravity.html,
"gyration"_fix_gyration.html,
"heat"_fix_heat.html,
"indent"_fix_indent.html,
"langevin"_fix_langevin.html,
"lineforce"_fix_lineforce.html,
"msd"_fix_msd.html,
"momentum"_fix_momentum.html,
"nph"_fix_nph.html,
"npt"_fix_npt.html,
"npt/asphere"_fix_npt_asphere.html,
"nve"_fix_nve.html,
"nve/asphere"_fix_nve_asphere.html,
"nve/dipole"_fix_nve_dipole.html,
"nve/gran"_fix_nve_gran.html,
"nve/limit"_fix_nve_limit.html,
"nve/noforce"_fix_nve_noforce.html,
"nvt"_fix_nvt.html,
"nvt/asphere"_fix_nvt_asphere.html,
"nvt/sllod"_fix_nvt_sllod.html,
"orient/fcc"_fix_orient_fcc.html,
"planeforce"_fix_planeforce.html,
"poems"_fix_poems.html,
"pour"_fix_pour.html,
"print"_fix_print.html,
"rdf"_fix_rdf.html,
"recenter"_fix_recenter.html,
"rigid"_fix_rigid.html,
"setforce"_fix_setforce.html,
"shake"_fix_shake.html,
"spring"_fix_spring.html,
"spring/rg"_fix_spring_rg.html,
"spring/self"_fix_spring_self.html,
"temp/rescale"_fix_temp_rescale.html,
"tmd"_fix_tmd.html,
"viscosity"_fix_viscosity.html,
"viscous"_fix_viscous.html,
"wall/gran"_fix_wall_gran.html,
"wall/lj126"_fix_wall_lj126.html,
"wall/lj93"_fix_wall_lj93.html,
"wall/reflect"_fix_wall_reflect.html,
"wiggle"_fix_wiggle.html :tb(c=8,ea=c)
:line
Compute styles. See the "compute"_compute.html command for one-line
descriptions of each style or click on the style itself for a full
description:
"attribute/atom"_compute_attribute_atom.html,
"centro/atom"_compute_centro_atom.html,
"coord/atom"_compute_coord_atom.html,
"ebond/atom"_compute_ebond_atom.html,
"epair/atom"_compute_epair_atom.html,
"ke/atom"_compute_ke_atom.html,
+"pe"_compute_pe.html,
"pressure"_compute_pressure.html,
"rotate/dipole"_compute_rotate_dipole.html,
"rotate/gran"_compute_rotate_gran.html,
"stress/atom"_compute_stress_atom.html,
"sum"_compute_sum.html,
"sum/atom"_compute_sum_atom.html,
"temp"_compute_temp.html,
"temp/asphere"_compute_temp_asphere.html,
"temp/deform"_compute_temp_deform.html,
"temp/dipole"_compute_temp_dipole.html,
"temp/partial"_compute_temp_partial.html,
"temp/ramp"_compute_temp_ramp.html,
"temp/region"_compute_temp_region.html,
"variable"_compute_variable.html,
"variable/atom"_compute_variable_atom.html :tb(c=6,ea=c)
These are compute styles contributed by users, which can be used if
"LAMMPS is built with the appropriate package"_Section_start.html#2_3.
"ackland"_compute_ackland_atom.html :tb(c=6,ea=c)
:line
Pair_style potentials. 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_none.html,
"hybrid"_pair_hybrid.html,
"hybrid/overlay"_pair_hybrid.html,
"airebo"_pair_airebo.html,
"buck"_pair_buck.html,
"buck/coul/cut"_pair_buck.html,
"buck/coul/long"_pair_buck.html,
"colloid"_pair_colloid.html,
"coul/cut"_pair_coul.html,
"coul/long"_pair_coul.html,
"dipole/cut"_pair_dipole.html,
"dpd"_pair_dpd.html,
"eam"_pair_eam.html,
"eam/opt"_pair_eam.html,
"eam/alloy"_pair_eam.html,
"eam/alloy/opt"_pair_eam.html,
"eam/fs"_pair_eam.html,
"eam/fs/opt"_pair_eam.html,
"gayberne"_pair_gayberne.html,
"gran/hertzian"_pair_gran.html,
"gran/history"_pair_gran.html,
"gran/no_history"_pair_gran.html,
"lj/charmm/coul/charmm"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit"_pair_charmm.html,
"lj/charmm/coul/long"_pair_charmm.html,
"lj/charmm/coul/long/opt"_pair_charmm.html,
"lj/class2"_pair_class2.html,
"lj/class2/coul/cut"_pair_class2.html,
"lj/class2/coul/long"_pair_class2.html,
"lj/cut"_pair_lj.html,
"lj/cut/opt"_pair_lj.html,
"lj/cut/coul/cut"_pair_lj.html,
"lj/cut/coul/debye"_pair_lj.html,
"lj/cut/coul/long"_pair_lj.html,
"lj/cut/coul/long/tip4p"_pair_lj.html,
"lj/expand"_pair_lj_expand.html,
"lj/smooth"_pair_lj_smooth.html,
"lubricate"_pair_lubricate.html,
"meam"_pair_meam.html,
"morse"_pair_morse.html,
"morse/opt"_pair_morse.html,
"resquared"_pair_resquared.html,
"soft"_pair_soft.html,
"sw"_pair_sw.html,
"table"_pair_table.html,
"tersoff"_pair_tersoff.html,
"yukawa"_pair_yukawa.html :tb(c=4,ea=c)
These are pair styles contributed by users, which can be used if
"LAMMPS is built with the appropriate package"_Section_start.html#2_3.
"buck/coul"_pair_buck_coul.html,
"lj/coul"_pair_lj_coul.html :tb(c=4,ea=c)
:line
Bond_style potentials. 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_none.html,
"hybrid"_bond_hybrid.html,
"class2"_bond_class2.html,
"fene"_bond_fene.html,
"fene/expand"_bond_fene_expand.html,
"harmonic"_bond_harmonic.html,
"morse"_bond_morse.html,
"nonlinear"_bond_nonlinear.html,
"quartic"_bond_quartic.html :tb(c=4,ea=c,w=100)
:line
Angle_style potentials. 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_none.html,
"hybrid"_angle_hybrid.html,
"charmm"_angle_charmm.html,
"class2"_angle_class2.html,
"cosine"_angle_cosine.html,
"cosine/squared"_angle_cosine_squared.html,
"harmonic"_angle_harmonic.html :tb(c=4,ea=c,w=100)
:line
Dihedral_style potentials. 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_none.html,
"hybrid"_dihedral_hybrid.html,
"charmm"_dihedral_charmm.html,
"class2"_dihedral_class2.html,
"harmonic"_dihedral_harmonic.html,
"helix"_dihedral_helix.html,
"multi/harmonic"_dihedral_multi_harmonic.html,
"opls"_dihedral_opls.html :tb(c=4,ea=c,w=100)
:line
Improper_style potentials. 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_none.html,
"hybrid"_improper_hybrid.html,
"class2"_improper_class2.html,
"cvff"_improper_cvff.html,
"harmonic"_improper_harmonic.html :tb(c=4,ea=c,w=100)
:line
Kspace solvers. See the "kspace_style"_kspace_style.html command for
an overview of Kspace solvers. Click on the style itself for a full
description:
"ewald"_kspace_style.html,
"pppm"_kspace_style.html,
"pppm/tip4p"_kspace_style.html :tb(c=4,ea=c,w=100)
These are Kspace solvers contributed by users, which can be used if
"LAMMPS is built with the appropriate package"_Section_start.html#2_3.
"ewald/n"_kspace_style.html :tb(c=4,ea=c,w=100)
diff --git a/doc/compute.html b/doc/compute.html
index 8453388b5..7bd256009 100644
--- a/doc/compute.html
+++ b/doc/compute.html
@@ -1,126 +1,129 @@
<HTML>
<CENTER><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>
</CENTER>
<HR>
<H3>compute command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID style args
</PRE>
<UL><LI>ID = user-assigned name for the computation
<LI>group-ID = ID of the group of atoms to perform the computation on
<LI>style = one of a list of possible style names (see below)
<LI>args = arguments used by a particular style
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all temp
compute newtemp flow temp/partial 1 1 0
compute 3 all ke/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Create a computation that will be performed on a group of atoms.
</P>
<P>In LAMMPS, a "compute" is used in several ways. There are two kinds
of computes, "global" computes that calculate one or more values for
the entire group of atoms, and "per-atom" computes that calculate one
or more values for each atom in the group. The latter has the word
"atom" in its style name.
</P>
<P>The results of global computes can be output via the <A HREF = "thermo_style.html">thermo_style
custom</A> or <A HREF = "fix_ave_time.html">fix ave/time</A> command.
Or the values can be referenced in a <A HREF = "variable.html">variable equal</A>
command. The results of computes that calculate a global temperature
or pressure can be used by fixes that do thermostatting or
barostatting and when atom velocities are created.
</P>
<P>The results of per-atom computes can be output via the <A HREF = "dump.html">dump
custom</A> command or the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command. Or the per-atom values can
be time-averaged via the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command and
then output via the <A HREF = "dump.html">dump custom</A> or <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> commands.
</P>
<P>See this <A HREF = "Section_howto.html#4_15">howto section</A> for a summary of
various LAMMPS output options.
</P>
-<P>LAMMPS creates its own global computes for thermodynamic output. Two
-computes are always created, named "thermo_temp" and
-"thermo_pressure", as if these commands had been invoked:
+<P>LAMMPS creates its own global computes for thermodynamic output.
+Three computes are always created, named "thermo_temp",
+"thermo_pressure", and"thermo_pe", as if these commands had been
+invoked in the input script:
</P>
<PRE>compute thermo_temp all temp
-compute thermo_pressure all pressure thermo_temp
+compute thermo_pressure all pressure thermo_temp
+compute thermo_pe all pe
</PRE>
<P>Additional computes are created if the thermo style requires it. See
the documentation for the <A HREF = "thermo_style.html">thermo_style</A> command.
</P>
<P>The dumping of atom snapshots and fixes that compute temperature or
pressure also create computes as required. These are discussed in the
documentation for the <A HREF = "dump.html">dump custom</A> and specific
<A HREF = "fix.html">fix</A> commands.
</P>
<P>In all these cases, the default computes can be replaced by computes
defined by the user in the input script, as described by the
<A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_modify.html">fix modify</A>, and
<A HREF = "dump.html">dump</A> commands.
</P>
<P>Properties of either a default of user-defined compute can be modified
via the <A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P>Computes can be deleted with the <A HREF = "uncompute.html">uncompute</A> command.
</P>
<P>Code for new computes can be added to LAMMPS (see <A HREF = "Section_modify.html">this
section</A> of the manaul) and the results of their
calculations accessed in the various ways described above.
</P>
<P>Each compute style has its own doc page which describes its arguments
and what it does. Here is an alphabetic list of compute styles
defined in LAMMPS:
</P>
<UL><LI><A HREF = "compute_attribute_atom.html">attribute/atom</A> - attribute (x,v,f,etc) of each atom
<LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
<LI><A HREF = "compute_coord_atom.html">coord/atom</A> - coordination number for each atom
<LI><A HREF = "compute_ebond_atom.html">ebond/atom</A> - bond energy for each atom
<LI><A HREF = "compute_epair_atom.html">epair/atom</A> - pairwise energy for each atom
<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
+<LI><A HREF = "compute_pe.html">pe</A> - potential energy
<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
<LI><A HREF = "compute_rotate_dipole.html">rotate/dipole</A> - rotational energy of dipolar atoms
<LI><A HREF = "compute_rotate_gran.html">rotate/gran</A> - rotational energy of granular atoms
<LI><A HREF = "compute_stress_atom.html">stress/atom</A> - stress tensor for each atom
<LI><A HREF = "compute_sum.html">sum</A> - sum per-atom quantities to a global value
<LI><A HREF = "compute_sum_atom.html">sum/atom</A> - sum per-atom quantities to per-atom values
<LI><A HREF = "compute_temp.html">temp</A> - temperature of group of atoms
<LI><A HREF = "compute_temp_asphere.html">temp/asphere</A> - temperature of aspherical particles
<LI><A HREF = "compute_temp_deform.html">temp/deform</A> - temperature excluding box deformation velocity
<LI><A HREF = "compute_temp_dipole.html">temp/dipole</A> - temperature of point dipolar particles
<LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
<LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature excluding ramped velocity component
<LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
<LI><A HREF = "compute_variable.html">variable</A> - calculate a scalar value from a variable
<LI><A HREF = "compute_variable_atom.html">variable/atom</A> - calculate a formula for each atom
</UL>
<P>There are also additional compute styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the compute section of <A HREF = "Section_commands.html#3_5">this
page</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "uncompute.html">uncompute</A>, <A HREF = "compute_modify.html">compute_modify</A>, <A HREF = "fix_ave_atom.html">fix
ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
<A HREF = "fix_ave_time.html">fix ave/time</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute.txt b/doc/compute.txt
index 01092a087..d324e12cd 100644
--- a/doc/compute.txt
+++ b/doc/compute.txt
@@ -1,121 +1,124 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute command :h3
[Syntax:]
compute ID group-ID style args :pre
ID = user-assigned name for the computation
group-ID = ID of the group of atoms to perform the computation on
style = one of a list of possible style names (see below)
args = arguments used by a particular style :ul
[Examples:]
compute 1 all temp
compute newtemp flow temp/partial 1 1 0
compute 3 all ke/atom :pre
[Description:]
Create a computation that will be performed on a group of atoms.
In LAMMPS, a "compute" is used in several ways. There are two kinds
of computes, "global" computes that calculate one or more values for
the entire group of atoms, and "per-atom" computes that calculate one
or more values for each atom in the group. The latter has the word
"atom" in its style name.
The results of global computes can be output via the "thermo_style
custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command.
Or the values can be referenced in a "variable equal"_variable.html
command. The results of computes that calculate a global temperature
or pressure can be used by fixes that do thermostatting or
barostatting and when atom velocities are created.
The results of per-atom computes can be output via the "dump
custom"_dump.html command or the "fix
ave/spatial"_fix_ave_spatial.html command. Or the per-atom values can
be time-averaged via the "fix ave/atom"_fix_ave_atom.html command and
then output via the "dump custom"_dump.html or "fix
ave/spatial"_fix_ave_spatial.html commands.
See this "howto section"_Section_howto.html#4_15 for a summary of
various LAMMPS output options.
-LAMMPS creates its own global computes for thermodynamic output. Two
-computes are always created, named "thermo_temp" and
-"thermo_pressure", as if these commands had been invoked:
+LAMMPS creates its own global computes for thermodynamic output.
+Three computes are always created, named "thermo_temp",
+"thermo_pressure", and"thermo_pe", as if these commands had been
+invoked in the input script:
compute thermo_temp all temp
-compute thermo_pressure all pressure thermo_temp :pre
+compute thermo_pressure all pressure thermo_temp
+compute thermo_pe all pe :pre
Additional computes are created if the thermo style requires it. See
the documentation for the "thermo_style"_thermo_style.html command.
The dumping of atom snapshots and fixes that compute temperature or
pressure also create computes as required. These are discussed in the
documentation for the "dump custom"_dump.html and specific
"fix"_fix.html commands.
In all these cases, the default computes can be replaced by computes
defined by the user in the input script, as described by the
"thermo_modify"_thermo_modify.html, "fix modify"_fix_modify.html, and
"dump"_dump.html commands.
Properties of either a default of user-defined compute can be modified
via the "compute_modify"_compute_modify.html command.
Computes can be deleted with the "uncompute"_uncompute.html command.
Code for new computes can be added to LAMMPS (see "this
section"_Section_modify.html of the manaul) and the results of their
calculations accessed in the various ways described above.
Each compute style has its own doc page which describes its arguments
and what it does. Here is an alphabetic list of compute styles
defined in LAMMPS:
"attribute/atom"_compute_attribute_atom.html - attribute (x,v,f,etc) of each atom
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
"coord/atom"_compute_coord_atom.html - coordination number for each atom
"ebond/atom"_compute_ebond_atom.html - bond energy for each atom
"epair/atom"_compute_epair_atom.html - pairwise energy for each atom
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
+"pe"_compute_pe.html - potential energy
"pressure"_compute_pressure.html - total pressure and pressure tensor
"rotate/dipole"_compute_rotate_dipole.html - rotational energy of dipolar atoms
"rotate/gran"_compute_rotate_gran.html - rotational energy of granular atoms
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
"sum"_compute_sum.html - sum per-atom quantities to a global value
"sum/atom"_compute_sum_atom.html - sum per-atom quantities to per-atom values
"temp"_compute_temp.html - temperature of group of atoms
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
"temp/dipole"_compute_temp_dipole.html - temperature of point dipolar particles
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
"temp/region"_compute_temp_region.html - temperature of a region of atoms
"variable"_compute_variable.html - calculate a scalar value from a variable
"variable/atom"_compute_variable_atom.html - calculate a formula for each atom :ul
There are also additional compute styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the compute section of "this
page"_Section_commands.html#3_5.
[Restrictions:] none
[Related commands:]
"uncompute"_uncompute.html, "compute_modify"_compute_modify.html, "fix
ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html,
"fix ave/time"_fix_ave_time.html
[Default:] none
diff --git a/doc/compute_modify.html b/doc/compute_modify.html
index 176b74e1f..8ca891cc8 100644
--- a/doc/compute_modify.html
+++ b/doc/compute_modify.html
@@ -1,66 +1,76 @@
<HTML>
<CENTER><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>
</CENTER>
<HR>
<H3>compute_modify command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute_modify compute-ID keyword value ...
</PRE>
<UL><LI>compute-ID = ID of the compute to modify
<LI>one or more keyword/value pairs may be listed
<LI>keyword = <I>extra</I> or <I>dynamic</I>
<PRE> <I>extra</I> value = N
N = # of extra degrees of freedom to subtract
<I>dynamic</I> value = <I>yes</I> or <I>no</I>
- yes/no = do or do not recompute the number of atoms contributing to the temperature
+ yes/no = do or do not recompute the number of atoms contributing to the temperature
+ <I>thermo</I> value = <I>yes</I> or <I>no</I>
+ yes/no = do or do not add contributions from fixes to the potential energy
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute_modify myTemp extra 0
compute_modify newtemp dynamic yes extra 600
</PRE>
<P><B>Description:</B>
</P>
<P>Modify one or more parameters of a previously defined compute. Not
all compute styles support all parameters.
</P>
<P>The <I>extra</I> keyword refers to how many degrees-of-freedom are
subtracted (typically from 3N) as a normalizing factor in a
temperature computation. Only computes that compute a temperature use
this option. The default is 3 which is a correction factor for an
ensemble of velocities with zero total linear momentum.
</P>
<P>The <I>dynamic</I> keyword determines whether the number of atoms N in the
compute group is re-computed each time a temperature is computed.
Only compute styles that compute a temperature use this option. By
default, N is assumed to be constant. If you are adding atoms to the
system (see the <A HREF = "fix_pour.html">fix pour</A> or <A HREF = "fix_deposit.html">fix
deposit</A> commands) or expect atoms to be lost
(e.g. due to evaporation), then this option can be used to insure the
temperature is correctly normalized.
</P>
+<P>The <I>thermo</I> keyword determines whether the potential energy
+contribution calculated by some <A HREF = "fix.html">fixes</A> is added to the
+potential energy calculated by the compute. Only the compute of style
+<I>pe</I> uses this option. See the doc pages for <A HREF = "fix.html">individual
+fixes</A> for details.
+</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute.html">compute</A>
</P>
<P><B>Default:</B>
</P>
-<P>The option defaults are extra = 3 and dynamic = no.
+<P>The option defaults are extra = 3 and dynamic = no. Thermo is <I>yes</I> if
+the compute of style <I>pe</I> was defined with no extra keywords; otherwise
+it is <I>no</I>.
</P>
</HTML>
diff --git a/doc/compute_modify.txt b/doc/compute_modify.txt
index 795c28cda..293eef16d 100644
--- a/doc/compute_modify.txt
+++ b/doc/compute_modify.txt
@@ -1,57 +1,67 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute_modify command :h3
[Syntax:]
compute_modify compute-ID keyword value ... :pre
compute-ID = ID of the compute to modify :ulb,l
one or more keyword/value pairs may be listed :l
keyword = {extra} or {dynamic} :l
{extra} value = N
N = # of extra degrees of freedom to subtract
{dynamic} value = {yes} or {no}
- yes/no = do or do not recompute the number of atoms contributing to the temperature :pre
+ yes/no = do or do not recompute the number of atoms contributing to the temperature
+ {thermo} value = {yes} or {no}
+ yes/no = do or do not add contributions from fixes to the potential energy :pre
:ule
[Examples:]
compute_modify myTemp extra 0
compute_modify newtemp dynamic yes extra 600 :pre
[Description:]
Modify one or more parameters of a previously defined compute. Not
all compute styles support all parameters.
The {extra} keyword refers to how many degrees-of-freedom are
subtracted (typically from 3N) as a normalizing factor in a
temperature computation. Only computes that compute a temperature use
this option. The default is 3 which is a correction factor for an
ensemble of velocities with zero total linear momentum.
The {dynamic} keyword determines whether the number of atoms N in the
compute group is re-computed each time a temperature is computed.
Only compute styles that compute a temperature use this option. By
default, N is assumed to be constant. If you are adding atoms to the
system (see the "fix pour"_fix_pour.html or "fix
deposit"_fix_deposit.html commands) or expect atoms to be lost
(e.g. due to evaporation), then this option can be used to insure the
temperature is correctly normalized.
+The {thermo} keyword determines whether the potential energy
+contribution calculated by some "fixes"_fix.html is added to the
+potential energy calculated by the compute. Only the compute of style
+{pe} uses this option. See the doc pages for "individual
+fixes"_fix.html for details.
+
[Restrictions:] none
[Related commands:]
"compute"_compute.html
[Default:]
-The option defaults are extra = 3 and dynamic = no.
+The option defaults are extra = 3 and dynamic = no. Thermo is {yes} if
+the compute of style {pe} was defined with no extra keywords; otherwise
+it is {no}.
diff --git a/doc/compute_pe.html b/doc/compute_pe.html
new file mode 100644
index 000000000..cf2033800
--- /dev/null
+++ b/doc/compute_pe.html
@@ -0,0 +1,64 @@
+<HTML>
+<CENTER><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>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute pe command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID pe keyword ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>pe = style name of this compute command
+<LI>zero of more keywords may be appended
+<LI>keyword = <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>kspace</I>
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all pe
+compute molPE all bond angle dihedral improper
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the potential energy of the
+entire system of atoms. The specified group must be "all". See the
+<A HREF = "compute_epair_atom.html">compute epair/atom</A> <A HREF = "compute_ebond_atom.html">compute
+ebond/atom</A> or commands if you want per-atom
+energies. These per-atom values could be summed for a group of atoms
+via the <A HREF = "compute_sum.html">compute sum</A> command.
+</P>
+<P>The energy is calulated by the various pair, bond, etc potentials
+defined for the simulation. If no extra keywords are listed, then the
+potential energy is the sum of pair, bond, angle, dihedral, improper,
+and kspace (long-range) energy. If any extra keywords are listed,
+then only those components are summed to compute the potential energy.
+</P>
+<P>Various fixes can contribute to the total potential energy of the
+system. See the doc pages for <A HREF = "fix.html">individual fixes</A> for
+details. The <I>thermo</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command determines whether these
+contributions are added into the computed potential energy. If no
+keywords are specified the default is <I>yes</I>. If any keywords are
+specified, the default is <I>no</I>.
+</P>
+<P>A compute of this style with the ID of "thermo_pe" is created when
+LAMMPS starts up, as if this command were in the input script:
+</P>
+<PRE>compute thermo_pe all pe
+</PRE>
+<P>See the "thermo_style" command for more details.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B> none
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/compute_pe.txt b/doc/compute_pe.txt
new file mode 100644
index 000000000..e5f77a8b1
--- /dev/null
+++ b/doc/compute_pe.txt
@@ -0,0 +1,59 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute pe command :h3
+
+[Syntax:]
+
+compute ID group-ID pe keyword ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+pe = style name of this compute command
+zero of more keywords may be appended
+keyword = {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} :ul
+
+[Examples:]
+
+compute 1 all pe
+compute molPE all bond angle dihedral improper :pre
+
+[Description:]
+
+Define a computation that calculates the potential energy of the
+entire system of atoms. The specified group must be "all". See the
+"compute epair/atom"_compute_epair_atom.html "compute
+ebond/atom"_compute_ebond_atom.html or commands if you want per-atom
+energies. These per-atom values could be summed for a group of atoms
+via the "compute sum"_compute_sum.html command.
+
+The energy is calulated by the various pair, bond, etc potentials
+defined for the simulation. If no extra keywords are listed, then the
+potential energy is the sum of pair, bond, angle, dihedral, improper,
+and kspace (long-range) energy. If any extra keywords are listed,
+then only those components are summed to compute the potential energy.
+
+Various fixes can contribute to the total potential energy of the
+system. See the doc pages for "individual fixes"_fix.html for
+details. The {thermo} option of the
+"compute_modify"_compute_modify.html command determines whether these
+contributions are added into the computed potential energy. If no
+keywords are specified the default is {yes}. If any keywords are
+specified, the default is {no}.
+
+A compute of this style with the ID of "thermo_pe" is created when
+LAMMPS starts up, as if this command were in the input script:
+
+compute thermo_pe all pe :pre
+
+See the "thermo_style" command for more details.
+
+[Restrictions:] none
+
+[Related commands:] none
+
+[Default:] none
diff --git a/doc/compute_pressure.html b/doc/compute_pressure.html
index 5c68cec50..af675c03a 100644
--- a/doc/compute_pressure.html
+++ b/doc/compute_pressure.html
@@ -1,73 +1,81 @@
<HTML>
<CENTER><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>
</CENTER>
<HR>
<H3>compute pressure command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID pressure compute-ID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>pressure = style name of this compute command
<LI>compute-ID = ID of compute that calculates temperature
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all pressure myTemp
</PRE>
<P><B>Description:</B>
</P>
-<P>Define a computation that calculates the pressure of atoms averaged
-over the entire system. The specified group must be "all". See the
-<A HREF = "dump.html">dump custom</A> command for how to dump the per-atom stress
-tensor if you want more localized information about pressure (stress)
-in your system.
+<P>Define a computation that calculates the pressure of the entire system
+of atoms. The specified group must be "all". See the <A HREF = "compute_stress_atom.html">compute
+stress/atom</A> command if you want per-atom
+pressure (stress). These per-atom values could be summed for a group
+of atoms via the <A HREF = "compute_sum.html">compute sum</A> command.
</P>
-<P>The pressure is computed by the standard formula
+<P>The pressure is computed by the formula
</P>
<CENTER><IMG SRC = "Eqs/pressure.jpg">
</CENTER>
<P>where N is the number of atoms in the system (see discussion of DOF
below), Kb is the Boltzmann constant, T is the temperature, d is the
dimensionality of the system (2 or 3 for 2d/3d), V is the system
volume (or area in 2d), and the second term is the virial, computed
within LAMMPS for all pairwise as well as 2-body, 3-body, 4-body, and
long-range interactions. <A HREF = "fix.html">Fixes</A> that impose constraints
(e.g. the <A HREF = "fix_shake.html">fix shake</A> command) also contribute to the
virial term.
</P>
<P>A 6-component pressure tensor is also calculated by this compute which
can be output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.
The formula for the components of the tensor is the same as in above
formula, except that the first term uses the components of the kinetic
energy tensor (vx * vy instead of v^2 for temperature) and the second
term uses Rx * Fy for the Wxy component of the virial tensor, etc.
</P>
<P>The temperature and kinetic energy tensor is not calculated by this
compute, but rather by the temperature compute specified as the last
argument of the command. Normally this compute should calculate the
temperature of all atoms for consistency with the virial term, but any
compute style that calculates temperature can be used, e.g. one that
excludes frozen atoms or other degrees of freedom.
</P>
<P>Note that the N is the above formula is really degrees-of-freedom/d
where the DOF is specified by the temperature compute. See the
various <A HREF = "compute.html">compute temperature</A> styles for details.
</P>
+<P>A compute of this style with the ID of "thermo_press" is created when
+LAMMPS starts up, as if this command were in the input script:
+</P>
+<PRE>compute thermo_press all pressure thermo_temp
+</PRE>
+<P>where "thermo_temp" is the ID of a similarly defined compute of style
+"temp". See the "thermo_style" command for more details.
+</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "themo_style.html">thermo_style</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_pressure.txt b/doc/compute_pressure.txt
index 726f658a3..830359bcd 100644
--- a/doc/compute_pressure.txt
+++ b/doc/compute_pressure.txt
@@ -1,68 +1,76 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute pressure command :h3
[Syntax:]
compute ID group-ID pressure compute-ID :pre
ID, group-ID are documented in "compute"_compute.html command
pressure = style name of this compute command
compute-ID = ID of compute that calculates temperature :ul
[Examples:]
compute 1 all pressure myTemp :pre
[Description:]
-Define a computation that calculates the pressure of atoms averaged
-over the entire system. The specified group must be "all". See the
-"dump custom"_dump.html command for how to dump the per-atom stress
-tensor if you want more localized information about pressure (stress)
-in your system.
+Define a computation that calculates the pressure of the entire system
+of atoms. The specified group must be "all". See the "compute
+stress/atom"_compute_stress_atom.html command if you want per-atom
+pressure (stress). These per-atom values could be summed for a group
+of atoms via the "compute sum"_compute_sum.html command.
-The pressure is computed by the standard formula
+The pressure is computed by the formula
:c,image(Eqs/pressure.jpg)
where N is the number of atoms in the system (see discussion of DOF
below), Kb is the Boltzmann constant, T is the temperature, d is the
dimensionality of the system (2 or 3 for 2d/3d), V is the system
volume (or area in 2d), and the second term is the virial, computed
within LAMMPS for all pairwise as well as 2-body, 3-body, 4-body, and
long-range interactions. "Fixes"_fix.html that impose constraints
(e.g. the "fix shake"_fix_shake.html command) also contribute to the
virial term.
A 6-component pressure tensor is also calculated by this compute which
can be output by the "thermo_style custom"_thermo_style.html command.
The formula for the components of the tensor is the same as in above
formula, except that the first term uses the components of the kinetic
energy tensor (vx * vy instead of v^2 for temperature) and the second
term uses Rx * Fy for the Wxy component of the virial tensor, etc.
The temperature and kinetic energy tensor is not calculated by this
compute, but rather by the temperature compute specified as the last
argument of the command. Normally this compute should calculate the
temperature of all atoms for consistency with the virial term, but any
compute style that calculates temperature can be used, e.g. one that
excludes frozen atoms or other degrees of freedom.
Note that the N is the above formula is really degrees-of-freedom/d
where the DOF is specified by the temperature compute. See the
various "compute temperature"_compute.html styles for details.
+A compute of this style with the ID of "thermo_press" is created when
+LAMMPS starts up, as if this command were in the input script:
+
+compute thermo_press all pressure thermo_temp :pre
+
+where "thermo_temp" is the ID of a similarly defined compute of style
+"temp". See the "thermo_style" command for more details.
+
[Restrictions:] none
[Related commands:]
"compute temp"_compute_temp.html, "thermo_style"_themo_style.html
[Default:] none
diff --git a/doc/compute_temp.html b/doc/compute_temp.html
index cdad72776..8e466ef4a 100644
--- a/doc/compute_temp.html
+++ b/doc/compute_temp.html
@@ -1,64 +1,71 @@
<HTML>
<CENTER><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>
</CENTER>
<HR>
<H3>compute temp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all temp
compute myTemp mobile temp
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
atoms. A compute of this style can be used by any command that
computes a temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
</P>
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature.
</P>
<P>A 6-component kinetic energy tensor is also calculated by this compute
for use in the computation of a pressure tensor. The formula for the
components of the tensor is the same as the above formula, except that
v^2 is replaced by vx * vy for the xy component, etc.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
</P>
<P>This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
</P>
+<P>A compute of this style with the ID of "thermo_temp" is created when
+LAMMPS starts up, as if this command were in the input script:
+</P>
+<PRE>compute thermo_temp all temp
+</PRE>
+<P>See the "thermo_style" command for more details.
+</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp_partial.html">compute temp/partial</A>, <A HREF = "compute_temp_region.html">compute
temp/region</A>, <A HREF = "compute_pressure.html">compute
pressure</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_temp.txt b/doc/compute_temp.txt
index 2bbe0bd24..a21c85cc4 100644
--- a/doc/compute_temp.txt
+++ b/doc/compute_temp.txt
@@ -1,59 +1,66 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp command :h3
[Syntax:]
compute ID group-ID temp :pre
ID, group-ID are documented in "compute"_compute.html command
temp = style name of this compute command :ul
[Examples:]
compute 1 all temp
compute myTemp mobile temp :pre
[Description:]
Define a computation that calculates the temperature of a group of
atoms. A compute of this style can be used by any command that
computes a temperature, e.g. "thermo_modify"_thermo_modify.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature.
A 6-component kinetic energy tensor is also calculated by this compute
for use in the computation of a pressure tensor. The formula for the
components of the tensor is the same as the above formula, except that
v^2 is replaced by vx * vy for the xy component, etc.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the {dynamic} option of the
"compute_modify"_compute_modify.html command if this is not the case.
This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as "fix shake"_fix_shake.html and
"fix rigid"_fix_rigid.html. This means the temperature of groups of
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
+A compute of this style with the ID of "thermo_temp" is created when
+LAMMPS starts up, as if this command were in the input script:
+
+compute thermo_temp all temp :pre
+
+See the "thermo_style" command for more details.
+
[Restrictions:] none
[Related commands:]
"compute temp/partial"_compute_temp_partial.html, "compute
temp/region"_compute_temp_region.html, "compute
pressure"_compute_pressure.html
[Default:] none
diff --git a/doc/thermo_style.html b/doc/thermo_style.html
index 542d12bb9..82cae6b80 100644
--- a/doc/thermo_style.html
+++ b/doc/thermo_style.html
@@ -1,288 +1,302 @@
<HTML>
<CENTER><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>
</CENTER>
<HR>
<H3>thermo_style command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>thermo_style style args
</PRE>
<UL><LI>style = <I>one</I> or <I>multi</I> or <I>granular</I> or <I>custom</I>
<LI>args = list of arguments for a particular style
<PRE> <I>one</I> args = none
<I>multi</I> args = none
<I>granular</I> args = none
<I>custom</I> args = list of attributes
possible attributes = step, atoms, cpu, temp, press,
pe, ke, etotal, enthalpy,
evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
emol, elong, etail,
vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
pxx, pyy, pzz, pxy, pxz, pyz
drot, grot,
c_ID, c_ID[n], f_ID, f_ID[n], v_name
step = timestep
atoms = # of atoms
cpu = elapsed CPU time
temp = temperature
press = pressure
pe = total potential energy
ke = kinetic energy
etotal = total energy (pe + ke)
enthalpy = enthalpy (pe + press*vol)
evdwl = VanderWaal pairwise energy
ecoul = Coulombic pairwise energy
epair = pairwise energy (evdwl + ecoul + elong + etail)
ebond = bond energy
eangle = angle energy
edihed = dihedral energy
eimp = improper energy
emol = molecular energy (ebond + eangle + edihed + eimp)
elong = long-range kspace energy
etail = VanderWaal energy long-range tail correction
vol = volume
lx,ly,lz = box lengths in x,y,z
xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
drot = rotational energy of dipolar atoms
grot = rotational energy of granular atoms
c_ID = scalar quantity calculated by a compute identified by its ID
c_ID[N] = Nth vector quantity calculated by a compute identified by its ID
f_ID = scalar quantity calculated by a fix identified by its ID
f_ID[N] = Nth vector quantity calculated by a fix identified by its ID
v_name = current value of a variable identified by the variable name
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>thermo_style multi
thermo_style custom step temp pe etotal press vol
thermo_style custom step temp etotal c_myTemp v_abc
</PRE>
<P><B>Description:</B>
</P>
<P>Set the style and content for printing thermodynamic data to the
screen and log file.
</P>
<P>Style <I>one</I> prints a one-line summary of thermodynamic info that is
the equivalent of "thermo_style custom step temp epair emol etotal
press". The line contains only numeric values.
</P>
<P>Style <I>multi</I> prints a multiple-line listing of thermodynamic info
that is the equivalent of "thermo_style custom etotal ke temp pe ebond
eangle edihed eimp evdwl ecoul elong press". The listing contains
numeric values and a string ID for each quantity.
</P>
<P>Style <I>granular</I> is used with <A HREF = "atom_style.html">atom style</A> granular
and prints a one-line numeric summary that is the equivalent of
"thermo_style custom step atoms ke grot".
</P>
<P>Style <I>custom</I> is the most general setting and allows you to specify
which of the keywords listed above you want printed on each
thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are
references to <A HREF = "compute.html">computes</A>, <A HREF = "fix.html">fixes</A>, and
<A HREF = "variable.html"">variables</A> that have been defined elsewhere in the
input script or can even be new styles which users have added to
LAMMPS (see the <A HREF = "Section_modify.html">Section_modify</A> section of the
documentation). Thus the <I>custom</I> style provides a flexible means of
outputting essentially any desired quantity as a simulation proceeds.
</P>
<P>All styles except <I>custom</I> have <I>vol</I> appended to their list of
outputs if the simulation box volume changes during the simulation.
</P>
<P>The values printed by the various keywords are instantaneous values,
calculated on the current timestep. Time-averaged quantities, which
include values from previous timesteps, can be output by using the
f_ID keyword and accessing a fix that does time-averaging such as the
<A HREF = "fix_ave_time.html">fix ave/time</A> command.
</P>
<P>Options invoked by the <A HREF = "thermo_modify.html">thermo_modify</A> command can
be used to set the one- or multi-line format of the print-out, the
normalization of energy quantities (total or per-atom), and the
numeric precision of each printed value.
</P>
<P>IMPORTANT NOTE: When you specify a "thermo_style<A HREF = "thermo_modify.html"> command, all
thermodynamic settings are restored to their default values, including
those previously set by a :thermo_modify</A> command.
Thus if your input script specifies a thermo_style command, you should
use the thermo_modify command after it.
</P>
<HR>
<P>Several of the thermodynamic quantities require a temperature to be
computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc". By
default this is done by using the "thermo_temp" compute which is
-created by LAMMPS as if this command had been issued:
+created when LAMMPS starts up, as if this command had been issued:
</P>
<PRE>compute thermo_temp all temp
</PRE>
<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details. Note
that the ID of this compute is <I>thermo_temp</I> and the group is <I>all</I>.
You can change the attributes of this temperature (e.g. its
degrees-of-freedom) via the <A HREF = "compute_modify.html">compute_modify</A>
command. Alternatively, you can directly assign a new compute (that
calculates temperature) which you have defined, to be used for
calculating any thermodynamic quantity that requires a temperature.
This is done via the <A HREF = "thermo_modify.html">thermo_modify</A> command.
</P>
<P>Several of the thermodynamic quantities require a pressure to be
-computed: "press", "enthalpy", "pxx etc", "pave". By default this is
-done by using the "thermo_pressure" compute which is created by LAMMPS
-as if this command had been issued:
+computed: "press", "enthalpy", "pxx", etc. By default this is done by
+using the "thermo_pressure" compute which is created when LAMMPS
+starts up, as if this command had been issued:
</P>
<PRE>compute thermo_pressure all pressure thermo_temp
</PRE>
<P>See the <A HREF = "compute_pressure.html">compute pressure</A> command for details.
Note that the ID of this compute is <I>thermo_pressure</I> and the group is
<I>all</I>. You can change the attributes of this pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command. Alternatively, you can
directly assign a new compute (that calculates pressure) which you
have defined, to be used for calculating any thermodynamic quantity
that requires a pressure. This is done via the
<A HREF = "thermo_modify.html">thermo_modify</A> command.
</P>
+<P>Several of the thermodynamic quantities require a potential energy to
+be computed: "pe", "etotal", "ebond", etc. This is done by using the
+"thermo_pe" compute which is created when LAMMPS starts up, as if this
+command had been issued:
+</P>
+<PRE>compute thermo_pe all pe
+</PRE>
+<P>See the <A HREF = "compute_pe.html">compute pe</A> command for details. Note that
+the ID of this compute is <I>thermo_pe</I> and the group is <I>all</I>. You can
+change the attributes of this potential energy via the
+<A HREF = "compute_modify.html">compute_modify</A> command.
+</P>
<P>The <I>drot</I> keyword requires a rotational energy to be computed for
point dipole particles. To do this, a compute of style
"rotate/dipole" is created, as if this command had been issued:
</P>
<PRE>compute thermo_rotate_dipole all rotate/dipole
</PRE>
<P>See the <A HREF = "compute_rotate_dipole.html">compute rotate/dipole</A> command for
details. Note that the ID of the new compute is
<I>thermo_rotate_dipole</I> and the group is <I>all</I>. You can change the
attributes of this computation via the
<A HREF = "compute_modify.html">compute_modify</A> command. Alternatively, you can
directly assign a new compute which you have defined, to be used for
<I>drot</I>. This is done via the <A HREF = "thermo_modify.html">thermo_modify</A>
command. For example, this could be useful if you wish to exclude
certain particles from the compuation.
</P>
<P>The <I>grot</I> keyword requires a rotational energy to be computed for
granular particles. To do this, a compute of style "rotate/gran" is
created, as if this command had been issued:
</P>
<PRE>compute thermo_rotate_gran all rotate/gran
</PRE>
<P>See the <A HREF = "compute_rotate_gran.html">compute rotate/gran</A> command for
details. Note that the ID of the new compute is <I>thermo_rotate_gran</I>
and the group is <I>all</I>. You can change the attributes of this
computation via the <A HREF = "compute_modify.html">compute_modify</A> command.
Alternatively, you can directly assign a new compute which you have
defined, to be used for <I>grot</I>. This is done via the
<A HREF = "thermo_modify.html">thermo_modify</A> command. For example, this could
be useful if you wish to exclude frozen particles from the compuation.
</P>
<HR>
<P>The potential energy of the system <I>pe</I> will include contributions
-from fixes if the <A HREF = "fix_modify.html">fix_modify thermo</A> option was set
-for each fix. For example, the <A HREF = "fix_wall_lj93">fix wall/lj93</A> fix will
-contribute the energy of atoms interacting with the wall.
+from fixes if the <A HREF = "fix_modify.html">fix_modify thermo</A> option is set
+for a fix that calculates such a contribution. For example, the <A HREF = "fix_wall_lj93">fix
+wall/lj93</A> fix calculates the energy of atoms
+interacting with the wall. See the doc pages for "individual fixes"
+to see which ones contribute.
</P>
<P>A long-range tail correction <I>etail</I> for the VanderWaal pairwise
energy will be non-zero only if the <A HREF = "pair_modify.html">pair_modify
tail</A> option is turned on. The <I>etail</I> contribution
is included in <I>evdwl</I>, <I>pe</I>, and <I>etotal</I>, and the corresponding tail
correction to the pressure is included in <I>press</I> and <I>pxx</I>, <I>pyy</I>,
etc.
</P>
<HR>
<P>The <I>c_ID</I> and <I>c_ID[N]</I> keywords allow global scalar or vector
quantities calculated by a compute to be output. The ID in the
keyword should be replaced by the actual ID of the compute that has
been defined elsewhere in the input script. See the
<A HREF = "compute.html">compute</A> command for details. Note that only global
scalar or vector quantities calculated by a compute can be output as
thermodynamic data; per-atom quantities calcalated by a compute are
output by the <A HREF = "dump.html">dump custom</A> command. However, there is a
<A HREF = "compute_sum.html">compute sum</A> command which sums per-atom quantities
into a global scalar or vector which can be output by thermo_style
custom.
</P>
<P>Note that some computes calculate "intensive" global quantities like
temperature; others calculate "extensive" global quantities like
kinetic energy that are summed over all atoms in the compute group.
Intensive quantities are printed directly by thermo_style custom.
Extensive quantites may be normalized by the total number of atoms in
the simulation (NOT the number of atoms in the compute group)
depending on the <A HREF = "thermo_modify.html">thermo_modify norm</A> option being
used.
</P>
<P>If <I>c_ID</I> is used as a keyword, then the scalar quantity calculated by
the compute is printed. If <I>c_ID[N]</I> is used, then the compute must
calculate a vector quantity and N must be an index from 1 to M where M
is the length of the vector calculated by the compute. See the doc
pages for individual compute styles for info on what these quantities
are.
</P>
<P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow global scalar or vector
quantities calculated by a fix to be output. The ID in the keyword
should be replaced by the actual ID of the fix that has been defined
elsewhere in the input script. See the doc pages for individual <A HREF = "fix.html">fix
commands</A> for details of which fixes generate global values.
One particularly useful fix to use in this context is the <A HREF = "fix_ave_time.html">fix
ave/time</A> command, which calculates time-averages of
global scalar and vector quantities calculated by other
<A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A>.
</P>
<P>Note that some fixes calculate "intensive" global quantities like
timestep size; others calculate "extensive" global quantities like
energy that are summed over all atoms in the fix group. Intensive
quantities are printed directly by thermo_style custom. Extensive
quantites may be normalized by the total number of atoms in the
simulation (NOT the number of atoms in the fix group) depending on the
<A HREF = "thermo_modify.html">thermo_modify norm</A> option being used.
</P>
<P>If <I>f_ID</I> is used as a keyword, then the scalar quantity calculated by
the fix is printed. If <I>f_ID[N]</I> is used, then the fix must
calculate a vector quantity and N must be an index from 1 to M where M
is the length of the vector calculated by the fix. See the doc pages
for individual fix styles for info on which fixes calculate these
global quantities and what they are. For fixes that compute a
contribution to the potential energy of the system, the scalar
quantity f_ID is typically that quantity.
</P>
<P>The <I>v_name</I> keyword allow the current value of a variable to be
output. The name in the keyword should be replaced by the actual namd
of the variable that has been defined elsewhere in the input script.
See the <A HREF = "variable.html">variable</A> command for details. Equal-style
variables can calculate complex formulas involving atom and group
properties, mathematical operations, other variables, etc. This
keyword enables them to be evaluated and their value printed
periodically during a simulation.
</P>
<P>See <A HREF = "Section_modify.html">this section</A> for information on how to add
new compute and fix styles as well as variable options to LAMMPS that
calculate quantities that could then be output with these keywords as
part of thermodyanmic information.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This command must come after the simulation box is defined by a
<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
<A HREF = "create_box.html">create_box</A> command.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_modify.html">thermo_modify</A>,
<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "temperature.html">temperature</A>
</P>
<P><B>Default:</B>
</P>
<PRE>thermo_style one
</PRE>
</HTML>
diff --git a/doc/thermo_style.txt b/doc/thermo_style.txt
index fefecdd4e..e131594f6 100644
--- a/doc/thermo_style.txt
+++ b/doc/thermo_style.txt
@@ -1,280 +1,294 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
thermo_style command :h3
[Syntax:]
thermo_style style args :pre
style = {one} or {multi} or {granular} or {custom} :ulb,l
args = list of arguments for a particular style :l
{one} args = none
{multi} args = none
{granular} args = none
{custom} args = list of attributes
possible attributes = step, atoms, cpu, temp, press,
pe, ke, etotal, enthalpy,
evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
emol, elong, etail,
vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
pxx, pyy, pzz, pxy, pxz, pyz
drot, grot,
c_ID, c_ID\[n\], f_ID, f_ID\[n\], v_name
step = timestep
atoms = # of atoms
cpu = elapsed CPU time
temp = temperature
press = pressure
pe = total potential energy
ke = kinetic energy
etotal = total energy (pe + ke)
enthalpy = enthalpy (pe + press*vol)
evdwl = VanderWaal pairwise energy
ecoul = Coulombic pairwise energy
epair = pairwise energy (evdwl + ecoul + elong + etail)
ebond = bond energy
eangle = angle energy
edihed = dihedral energy
eimp = improper energy
emol = molecular energy (ebond + eangle + edihed + eimp)
elong = long-range kspace energy
etail = VanderWaal energy long-range tail correction
vol = volume
lx,ly,lz = box lengths in x,y,z
xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
drot = rotational energy of dipolar atoms
grot = rotational energy of granular atoms
c_ID = scalar quantity calculated by a compute identified by its ID
c_ID\[N\] = Nth vector quantity calculated by a compute identified by its ID
f_ID = scalar quantity calculated by a fix identified by its ID
f_ID\[N\] = Nth vector quantity calculated by a fix identified by its ID
v_name = current value of a variable identified by the variable name :pre
:ule
[Examples:]
thermo_style multi
thermo_style custom step temp pe etotal press vol
thermo_style custom step temp etotal c_myTemp v_abc :pre
[Description:]
Set the style and content for printing thermodynamic data to the
screen and log file.
Style {one} prints a one-line summary of thermodynamic info that is
the equivalent of "thermo_style custom step temp epair emol etotal
press". The line contains only numeric values.
Style {multi} prints a multiple-line listing of thermodynamic info
that is the equivalent of "thermo_style custom etotal ke temp pe ebond
eangle edihed eimp evdwl ecoul elong press". The listing contains
numeric values and a string ID for each quantity.
Style {granular} is used with "atom style"_atom_style.html granular
and prints a one-line numeric summary that is the equivalent of
"thermo_style custom step atoms ke grot".
Style {custom} is the most general setting and allows you to specify
which of the keywords listed above you want printed on each
thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are
references to "computes"_compute.html, "fixes"_fix.html, and
"variables"_variable.html" that have been defined elsewhere in the
input script or can even be new styles which users have added to
LAMMPS (see the "Section_modify"_Section_modify.html section of the
documentation). Thus the {custom} style provides a flexible means of
outputting essentially any desired quantity as a simulation proceeds.
All styles except {custom} have {vol} appended to their list of
outputs if the simulation box volume changes during the simulation.
The values printed by the various keywords are instantaneous values,
calculated on the current timestep. Time-averaged quantities, which
include values from previous timesteps, can be output by using the
f_ID keyword and accessing a fix that does time-averaging such as the
"fix ave/time"_fix_ave_time.html command.
Options invoked by the "thermo_modify"_thermo_modify.html command can
be used to set the one- or multi-line format of the print-out, the
normalization of energy quantities (total or per-atom), and the
numeric precision of each printed value.
IMPORTANT NOTE: When you specify a "thermo_style" command, all
thermodynamic settings are restored to their default values, including
those previously set by a :thermo_modify"_thermo_modify.html command.
Thus if your input script specifies a thermo_style command, you should
use the thermo_modify command after it.
:line
Several of the thermodynamic quantities require a temperature to be
computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc". By
default this is done by using the "thermo_temp" compute which is
-created by LAMMPS as if this command had been issued:
+created when LAMMPS starts up, as if this command had been issued:
compute thermo_temp all temp :pre
See the "compute temp"_compute_temp.html command for details. Note
that the ID of this compute is {thermo_temp} and the group is {all}.
You can change the attributes of this temperature (e.g. its
degrees-of-freedom) via the "compute_modify"_compute_modify.html
command. Alternatively, you can directly assign a new compute (that
calculates temperature) which you have defined, to be used for
calculating any thermodynamic quantity that requires a temperature.
This is done via the "thermo_modify"_thermo_modify.html command.
Several of the thermodynamic quantities require a pressure to be
-computed: "press", "enthalpy", "pxx etc", "pave". By default this is
-done by using the "thermo_pressure" compute which is created by LAMMPS
-as if this command had been issued:
+computed: "press", "enthalpy", "pxx", etc. By default this is done by
+using the "thermo_pressure" compute which is created when LAMMPS
+starts up, as if this command had been issued:
compute thermo_pressure all pressure thermo_temp :pre
See the "compute pressure"_compute_pressure.html command for details.
Note that the ID of this compute is {thermo_pressure} and the group is
{all}. You can change the attributes of this pressure via the
"compute_modify"_compute_modify.html command. Alternatively, you can
directly assign a new compute (that calculates pressure) which you
have defined, to be used for calculating any thermodynamic quantity
that requires a pressure. This is done via the
"thermo_modify"_thermo_modify.html command.
+Several of the thermodynamic quantities require a potential energy to
+be computed: "pe", "etotal", "ebond", etc. This is done by using the
+"thermo_pe" compute which is created when LAMMPS starts up, as if this
+command had been issued:
+
+compute thermo_pe all pe :pre
+
+See the "compute pe"_compute_pe.html command for details. Note that
+the ID of this compute is {thermo_pe} and the group is {all}. You can
+change the attributes of this potential energy via the
+"compute_modify"_compute_modify.html command.
+
The {drot} keyword requires a rotational energy to be computed for
point dipole particles. To do this, a compute of style
"rotate/dipole" is created, as if this command had been issued:
compute thermo_rotate_dipole all rotate/dipole :pre
See the "compute rotate/dipole"_compute_rotate_dipole.html command for
details. Note that the ID of the new compute is
{thermo_rotate_dipole} and the group is {all}. You can change the
attributes of this computation via the
"compute_modify"_compute_modify.html command. Alternatively, you can
directly assign a new compute which you have defined, to be used for
{drot}. This is done via the "thermo_modify"_thermo_modify.html
command. For example, this could be useful if you wish to exclude
certain particles from the compuation.
The {grot} keyword requires a rotational energy to be computed for
granular particles. To do this, a compute of style "rotate/gran" is
created, as if this command had been issued:
compute thermo_rotate_gran all rotate/gran :pre
See the "compute rotate/gran"_compute_rotate_gran.html command for
details. Note that the ID of the new compute is {thermo_rotate_gran}
and the group is {all}. You can change the attributes of this
computation via the "compute_modify"_compute_modify.html command.
Alternatively, you can directly assign a new compute which you have
defined, to be used for {grot}. This is done via the
"thermo_modify"_thermo_modify.html command. For example, this could
be useful if you wish to exclude frozen particles from the compuation.
:line
The potential energy of the system {pe} will include contributions
-from fixes if the "fix_modify thermo"_fix_modify.html option was set
-for each fix. For example, the "fix wall/lj93"_fix_wall_lj93 fix will
-contribute the energy of atoms interacting with the wall.
+from fixes if the "fix_modify thermo"_fix_modify.html option is set
+for a fix that calculates such a contribution. For example, the "fix
+wall/lj93"_fix_wall_lj93 fix calculates the energy of atoms
+interacting with the wall. See the doc pages for "individual fixes"
+to see which ones contribute.
A long-range tail correction {etail} for the VanderWaal pairwise
energy will be non-zero only if the "pair_modify
tail"_pair_modify.html option is turned on. The {etail} contribution
is included in {evdwl}, {pe}, and {etotal}, and the corresponding tail
correction to the pressure is included in {press} and {pxx}, {pyy},
etc.
:line
The {c_ID} and {c_ID\[N\]} keywords allow global scalar or vector
quantities calculated by a compute to be output. The ID in the
keyword should be replaced by the actual ID of the compute that has
been defined elsewhere in the input script. See the
"compute"_compute.html command for details. Note that only global
scalar or vector quantities calculated by a compute can be output as
thermodynamic data; per-atom quantities calcalated by a compute are
output by the "dump custom"_dump.html command. However, there is a
"compute sum"_compute_sum.html command which sums per-atom quantities
into a global scalar or vector which can be output by thermo_style
custom.
Note that some computes calculate "intensive" global quantities like
temperature; others calculate "extensive" global quantities like
kinetic energy that are summed over all atoms in the compute group.
Intensive quantities are printed directly by thermo_style custom.
Extensive quantites may be normalized by the total number of atoms in
the simulation (NOT the number of atoms in the compute group)
depending on the "thermo_modify norm"_thermo_modify.html option being
used.
If {c_ID} is used as a keyword, then the scalar quantity calculated by
the compute is printed. If {c_ID\[N\]} is used, then the compute must
calculate a vector quantity and N must be an index from 1 to M where M
is the length of the vector calculated by the compute. See the doc
pages for individual compute styles for info on what these quantities
are.
The {f_ID} and {f_ID\[N\]} keywords allow global scalar or vector
quantities calculated by a fix to be output. The ID in the keyword
should be replaced by the actual ID of the fix that has been defined
elsewhere in the input script. See the doc pages for individual "fix
commands"_fix.html for details of which fixes generate global values.
One particularly useful fix to use in this context is the "fix
ave/time"_fix_ave_time.html command, which calculates time-averages of
global scalar and vector quantities calculated by other
"computes"_compute.html and "fixes"_fix.html.
Note that some fixes calculate "intensive" global quantities like
timestep size; others calculate "extensive" global quantities like
energy that are summed over all atoms in the fix group. Intensive
quantities are printed directly by thermo_style custom. Extensive
quantites may be normalized by the total number of atoms in the
simulation (NOT the number of atoms in the fix group) depending on the
"thermo_modify norm"_thermo_modify.html option being used.
If {f_ID} is used as a keyword, then the scalar quantity calculated by
the fix is printed. If {f_ID\[N\]} is used, then the fix must
calculate a vector quantity and N must be an index from 1 to M where M
is the length of the vector calculated by the fix. See the doc pages
for individual fix styles for info on which fixes calculate these
global quantities and what they are. For fixes that compute a
contribution to the potential energy of the system, the scalar
quantity f_ID is typically that quantity.
The {v_name} keyword allow the current value of a variable to be
output. The name in the keyword should be replaced by the actual namd
of the variable that has been defined elsewhere in the input script.
See the "variable"_variable.html command for details. Equal-style
variables can calculate complex formulas involving atom and group
properties, mathematical operations, other variables, etc. This
keyword enables them to be evaluated and their value printed
periodically during a simulation.
See "this section"_Section_modify.html for information on how to add
new compute and fix styles as well as variable options to LAMMPS that
calculate quantities that could then be output with these keywords as
part of thermodyanmic information.
:line
[Restrictions:]
This command must come after the simulation box is defined by a
"read_data"_read_data.html, "read_restart"_read_restart.html, or
"create_box"_create_box.html command.
[Related commands:]
"thermo"_thermo.html, "thermo_modify"_thermo_modify.html,
"fix_modify"_fix_modify.html, "temperature"_temperature.html
[Default:]
thermo_style one :pre