diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
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+++ b/doc/Section_commands.txt
@@ -1,1143 +1,1144 @@
"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.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 the
input script commands used to define a LAMMPS simulation.
3.1 "LAMMPS input script"_#cmd_1
3.2 "Parsing rules"_#cmd_2
3.3 "Input script structure"_#cmd_3
3.4 "Commands listed by category"_#cmd_4
3.5 "Commands listed alphabetically"_#cmd_5 :all(b)
:line
:line
3.1 LAMMPS input script :link(cmd_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(cmd_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 last printable character on the line is a "&" character
(with no surrounding quotes), 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. See an exception in (6). Note that a
comment after a trailing "&" character will prevent the command from
continuing on the next line. Also note that for multi-line commands a
single leading "#" will comment out the entire command.
(3) The line is searched repeatedly for $ characters, which indicate
variables that are replaced with a text string. See an exception in
(6).
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 single character immediately following
the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and
"x".
If the $ is followed by parenthesis, then the text inside the
parenthesis is treated as an "immediate" variable and evaluated as an
"equal-style variable"_variable.html. This is a way to use numeric
formulas in an input script without having to assign them to variable
names. For example, these 3 input script lines:
variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete :pre
can be replaced by
region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
The latter produces an identical result, without having to define and
discard a temporary variable X.
See the "variable"_variable.html command for more details of how
strings are assigned to variables and evaluated, and how they can be
used in input script commands.
(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) If you want text with spaces to be treated as a single argument,
it can be enclosed in either double or single quotes. E.g.
print "Volume = $v"
print 'Volume = $v'
if "${steps} > 1000" then quit :pre
The quotes are removed when the single argument is stored internally.
See the "dump modify format"_dump_modify.html or "print"_print.html or
"if"_if.html commands for examples. A "#" or "$" character that is
between quotes will not be treated as a comment indicator in (2) or
substituted for as a variable in (3).
IMPORTANT NOTE: If the argument is itself a command that requires a
quoted argument (e.g. using a "print"_print.html command as part of an
"if"_if.html or "run every"_run.html command), then the double and
single quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.
:line
3.3 Input script structure :h4,link(cmd_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
"Section_example"_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(cmd_4),h4
This section lists all LAMMPS commands, grouped by category. The
"next section"_#cmd_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_dump"_read_dump.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, "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, "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 image"_dump_image.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_data"_write_data.html, "write_restart"_write_restart.html
Actions:
"delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html,
"displace_atoms"_displace_atoms.html, "change_box"_change_box.html,
"minimize"_minimize.html, "neb"_neb.html "prd"_prd.html,
"rerun"_rerun.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(cmd_5),link(comm)
This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The "previous
section"_#cmd_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,
"balance"_balance.html,
"bond_coeff"_bond_coeff.html,
"bond_style"_bond_style.html,
"boundary"_boundary.html,
"box"_box.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,
"displace_atoms"_displace_atoms.html,
"dump"_dump.html,
"dump image"_dump_image.html,
"dump_modify"_dump_modify.html,
"echo"_echo.html,
"fix"_fix.html,
"fix_modify"_fix_modify.html,
"group"_group.html,
"group2ndx"_group2ndx.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,
"neb"_neb.html,
"neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html,
"newton"_newton.html,
"next"_next.html,
"package"_package.html,
"pair_coeff"_pair_coeff.html,
"pair_modify"_pair_modify.html,
"pair_style"_pair_style.html,
"pair_write"_pair_write.html,
"partition"_partition.html,
"prd"_prd.html,
"print"_print.html,
"processors"_processors.html,
"quit"_quit.html,
"read_data"_read_data.html,
"read_dump"_read_dump.html,
"read_restart"_read_restart.html,
"region"_region.html,
"replicate"_replicate.html,
"rerun"_rerun.html,
"reset_timestep"_reset_timestep.html,
"restart"_restart.html,
"run"_run.html,
"run_style"_run_style.html,
"set"_set.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
"suffix"_suffix.html,
"tad"_tad.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_data"_write_data.html,
"write_restart"_write_restart.html :tb(c=6,ea=c)
:line
Fix styles :h4
See the "fix"_fix.html command for one-line descriptions
of each style or click on the style itself for a full description:
"adapt"_fix_adapt.html,
"addforce"_fix_addforce.html,
"append/atoms"_fix_append_atoms.html,
"aveforce"_fix_aveforce.html,
"ave/atom"_fix_ave_atom.html,
"ave/correlate"_fix_ave_correlate.html,
"ave/histo"_fix_ave_histo.html,
"ave/spatial"_fix_ave_spatial.html,
"ave/time"_fix_ave_time.html,
"balance"_fix_balance.html,
"bond/break"_fix_bond_break.html,
"bond/create"_fix_bond_create.html,
"bond/swap"_fix_bond_swap.html,
"box/relax"_fix_box_relax.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,
"evaporate"_fix_evaporate.html,
"external"_fix_external.html,
"freeze"_fix_freeze.html,
"gcmc"_fix_gcmc.html,
"gravity"_fix_gravity.html,
"heat"_fix_heat.html,
"indent"_fix_indent.html,
"langevin"_fix_langevin.html,
"lineforce"_fix_lineforce.html,
"momentum"_fix_momentum.html,
"move"_fix_move.html,
"msst"_fix_msst.html,
"neb"_fix_neb.html,
"nph"_fix_nh.html,
"nphug"_fix_nphug.html,
"nph/asphere"_fix_nph_asphere.html,
"nph/sphere"_fix_nph_sphere.html,
"npt"_fix_nh.html,
"npt/asphere"_fix_npt_asphere.html,
"npt/sphere"_fix_npt_sphere.html,
"nve"_fix_nve.html,
"nve/asphere"_fix_nve_asphere.html,
"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
"nve/body"_fix_nve_body.html,
"nve/limit"_fix_nve_limit.html,
"nve/line"_fix_nve_line.html,
"nve/noforce"_fix_nve_noforce.html,
"nve/sphere"_fix_nve_sphere.html,
"nve/tri"_fix_nve_tri.html,
"nvt"_fix_nh.html,
"nvt/asphere"_fix_nvt_asphere.html,
"nvt/sllod"_fix_nvt_sllod.html,
"nvt/sphere"_fix_nvt_sphere.html,
"orient/fcc"_fix_orient_fcc.html,
"planeforce"_fix_planeforce.html,
"poems"_fix_poems.html,
"pour"_fix_pour.html,
"press/berendsen"_fix_press_berendsen.html,
"print"_fix_print.html,
"qeq/comb"_fix_qeq_comb.html,
"reax/bonds"_fix_reax_bonds.html,
"recenter"_fix_recenter.html,
"restrain"_fix_restrain.html,
"rigid"_fix_rigid.html,
"rigid/nph"_fix_rigid.html,
"rigid/npt"_fix_rigid.html,
"rigid/nve"_fix_rigid.html,
"rigid/nvt"_fix_rigid.html,
"rigid/small"_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,
"srd"_fix_srd.html,
"store/force"_fix_store_force.html,
"store/state"_fix_store_state.html,
"temp/berendsen"_fix_temp_berendsen.html,
"temp/rescale"_fix_temp_rescale.html,
"thermal/conductivity"_fix_thermal_conductivity.html,
"tmd"_fix_tmd.html,
"ttm"_fix_ttm.html,
"viscosity"_fix_viscosity.html,
"viscous"_fix_viscous.html,
"wall/colloid"_fix_wall.html,
"wall/gran"_fix_wall_gran.html,
"wall/harmonic"_fix_wall.html,
"wall/lj126"_fix_wall.html,
"wall/lj93"_fix_wall.html,
"wall/piston"_fix_wall_piston.html,
"wall/reflect"_fix_wall_reflect.html,
"wall/region"_fix_wall_region.html,
"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
These are fix styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"addtorque"_fix_addtorque.html,
"atc"_fix_atc.html,
"colvars"_fix_colvars.html,
"imd"_fix_imd.html,
"langevin/eff"_fix_langevin_eff.html,
"meso"_fix_meso.html,
"meso/stationary"_fix_meso_stationary.html,
"nph/eff"_fix_nh_eff.html,
"npt/eff"_fix_nh_eff.html,
"nve/eff"_fix_nve_eff.html,
"nvt/eff"_fix_nh_eff.html,
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
"phonon"_fix_phonon.html,
"qeq/reax"_fix_qeq_reax.html,
"reax/c/bonds"_fix_reax_bonds.html,
"reax/c/species"_fix_reaxc_species.html,
"smd"_fix_smd.html,
"temp/rescale/eff"_fix_temp_rescale_eff.html :tb(c=6,ea=c)
These are accelerated fix styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"freeze/cuda"_fix_freeze.html,
"addforce/cuda"_fix_addforce.html,
"aveforce/cuda"_fix_aveforce.html,
"enforce2d/cuda"_fix_enforce2d.html,
"gravity/cuda"_fix_gravity.html,
"gravity/omp"_fix_gravity.html,
"nph/omp"_fix_nh.html,
"nphug/omp"_fix_nphug.html,
"nph/asphere/omp"_fix_nph_asphere.html,
"nph/sphere/omp"_fix_nph_sphere.html,
"npt/cuda"_fix_nh.html,
"npt/omp"_fix_nh.html,
"npt/asphere/omp"_fix_npt_asphere.html,
"npt/sphere/omp"_fix_npt_sphere.html,
"nve/cuda"_fix_nh.html,
"nve/omp"_fix_nve.html,
"nve/sphere/omp"_fix_nve_sphere.html,
"nvt/cuda"_fix_nh.html,
"nvt/omp"_fix_nh.html,
"nvt/asphere/omp"_fix_nvt_asphere.html,
"nvt/sllod/omp"_fix_nvt_sllod.html,
"nvt/sphere/omp"_fix_nvt_sphere.html,
"qeq/comb/omp"_fix_qeq_comb.html,
"rigid/omp"_fix_rigid.html,
"rigid/nph/omp"_fix_rigid.html,
"rigid/npt/omp"_fix_rigid.html,
"rigid/nve/omp"_fix_rigid.html,
"rigid/nvt/omp"_fix_rigid.html,
"rigid/small/omp"_fix_rigid.html,
"setforce/cuda"_fix_setforce.html,
"shake/cuda"_fix_shake.html,
"temp/berendsen/cuda"_fix_temp_berendsen.html,
"temp/rescale/cuda"_fix_temp_rescale.html,
"temp/rescale/limit/cuda"_fix_temp_rescale.html,
"viscous/cuda"_fix_viscous.html :tb(c=6,ea=c)
:line
Compute styles :h4
See the "compute"_compute.html command for one-line descriptions of
each style or click on the style itself for a full description:
"angle/local"_compute_angle_local.html,
"atom/molecule"_compute_atom_molecule.html,
"body/local"_compute_body_local.html,
"bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html,
"cluster/atom"_compute_cluster_atom.html,
"cna/atom"_compute_cna_atom.html,
"com"_compute_com.html,
"com/molecule"_compute_com_molecule.html,
"contact/atom"_compute_contact_atom.html,
"coord/atom"_compute_coord_atom.html,
"damage/atom"_compute_damage_atom.html,
"dihedral/local"_compute_dihedral_local.html,
"displace/atom"_compute_displace_atom.html,
"erotate/asphere"_compute_erotate_asphere.html,
"erotate/sphere"_compute_erotate_sphere.html,
"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
"event/displace"_compute_event_displace.html,
"group/group"_compute_group_group.html,
"gyration"_compute_gyration.html,
"gyration/molecule"_compute_gyration_molecule.html,
"heat/flux"_compute_heat_flux.html,
"improper/local"_compute_improper_local.html,
"inertia/molecule"_compute_inertia_molecule.html,
"ke"_compute_ke.html,
"ke/atom"_compute_ke_atom.html,
"msd"_compute_msd.html,
"msd/molecule"_compute_msd_molecule.html,
"pair"_compute_pair.html,
"pair/local"_compute_pair_local.html,
"pe"_compute_pe.html,
"pe/atom"_compute_pe_atom.html,
"pressure"_compute_pressure.html,
"property/atom"_compute_property_atom.html,
"property/local"_compute_property_local.html,
"property/molecule"_compute_property_molecule.html,
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
"reduce/region"_compute_reduce.html,
"slice"_compute_slice.html,
"stress/atom"_compute_stress_atom.html,
"temp"_compute_temp.html,
"temp/asphere"_compute_temp_asphere.html,
"temp/com"_compute_temp_com.html,
"temp/deform"_compute_temp_deform.html,
"temp/partial"_compute_temp_partial.html,
"temp/profile"_compute_temp_profile.html,
"temp/ramp"_compute_temp_ramp.html,
"temp/region"_compute_temp_region.html,
"temp/sphere"_compute_temp_sphere.html,
"ti"_compute_ti.html,
"voronoi/atom"_compute_voronoi_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#start_3.
"ackland/atom"_compute_ackland_atom.html,
"ke/eff"_compute_ke_eff.html,
"ke/atom/eff"_compute_ke_atom_eff.html,
"meso_e/atom"_compute_meso_e_atom.html,
"meso_rho/atom"_compute_meso_rho_atom.html,
"meso_t/atom"_compute_meso_t_atom.html,
"temp/eff"_compute_temp_eff.html,
"temp/deform/eff"_compute_temp_deform_eff.html,
"temp/region/eff"_compute_temp_region_eff.html,
"temp/rotate"_compute_temp_rotate.html :tb(c=6,ea=c)
These are accelerated compute styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"pe/cuda"_compute_pe.html,
"pressure/cuda"_compute_pressure.html,
"temp/cuda"_compute_temp.html,
"temp/partial/cuda"_compute_temp_partial.html :tb(c=6,ea=c)
:line
Pair_style potentials :h4
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,
"adp"_pair_adp.html,
"airebo"_pair_airebo.html,
"beck"_pair_beck.html,
"body"_pair_body.html,
"bop"_pair_bop.html,
"born"_pair_born.html,
"born/coul/long"_pair_born.html,
"born/coul/msm"_pair_born.html,
"born/coul/wolf"_pair_born.html,
"brownian"_pair_brownian.html,
"brownian/poly"_pair_brownian.html,
"buck"_pair_buck.html,
"buck/coul/cut"_pair_buck.html,
"buck/coul/long"_pair_buck.html,
"buck/coul/msm"_pair_buck.html,
"buck/long/coul/long"_pair_buck_long.html,
"colloid"_pair_colloid.html,
"comb"_pair_comb.html,
"coul/cut"_pair_coul.html,
"coul/debye"_pair_coul.html,
"coul/dsf"_pair_coul.html,
"coul/long"_pair_coul.html,
"coul/msm"_pair_coul.html,
"coul/wolf"_pair_coul.html,
"dipole/cut"_pair_dipole.html,
"dpd"_pair_dpd.html,
"dpd/tstat"_pair_dpd.html,
"dsmc"_pair_dsmc.html,
"eam"_pair_eam.html,
"eam/alloy"_pair_eam.html,
"eam/fs"_pair_eam.html,
"eim"_pair_eim.html,
"gauss"_pair_gauss.html,
"gayberne"_pair_gayberne.html,
"gran/hertz/history"_pair_gran.html,
"gran/hooke"_pair_gran.html,
"gran/hooke/history"_pair_gran.html,
"hbond/dreiding/lj"_pair_hbond_dreiding.html,
"hbond/dreiding/morse"_pair_hbond_dreiding.html,
"kim"_pair_kim.html,
"lcbop"_pair_lcbop.html,
"line/lj"_pair_line_lj.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/msm"_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/coul/cut"_pair_lj.html,
"lj/cut/coul/debye"_pair_lj.html,
"lj/cut/coul/dsf"_pair_lj.html,
"lj/cut/coul/long"_pair_lj.html,
"lj/cut/coul/msm"_pair_lj.html,
"lj/cut/tip4p/cut"_pair_lj.html,
"lj/cut/tip4p/long"_pair_lj.html,
"lj/expand"_pair_lj_expand.html,
"lj/gromacs"_pair_gromacs.html,
"lj/gromacs/coul/gromacs"_pair_gromacs.html,
"lj/long/coul/long"_pair_lj_long.html,
"lj/long/tip4p/long"_pair_lj_long.html,
"lj/smooth"_pair_lj_smooth.html,
"lj/smooth/linear"_pair_lj_smooth_linear.html,
"lj96/cut"_pair_lj96.html,
"lubricate"_pair_lubricate.html,
"lubricate/poly"_pair_lubricate.html,
"lubricateU"_pair_lubricateU.html,
"lubricateU/poly"_pair_lubricateU.html,
"meam"_pair_meam.html,
"mie/cut"_pair_mie.html,
"morse"_pair_morse.html,
"peri/lps"_pair_peri.html,
"peri/pmb"_pair_peri.html,
"reax"_pair_reax.html,
"rebo"_pair_airebo.html,
"resquared"_pair_resquared.html,
"soft"_pair_soft.html,
"sw"_pair_sw.html,
"table"_pair_table.html,
"tersoff"_pair_tersoff.html,
"tersoff/zbl"_pair_tersoff_zbl.html,
"tri/lj"_pair_tri_lj.html,
"yukawa"_pair_yukawa.html,
"yukawa/colloid"_pair_yukawa_colloid.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#start_3.
"awpmd/cut"_pair_awpmd.html,
"coul/diel"_pair_coul_diel.html,
"dipole/sf"_pair_dipole.html,
"eam/cd"_pair_eam.html,
"edip"_pair_edip.html,
"eff/cut"_pair_eff.html,
"gauss/cut"_pair_gauss.html,
+"list"_pair_list.html,
"lj/sdk"_pair_sdk.html,
"lj/sdk/coul/long"_pair_sdk.html,
"lj/sdk/coul/msm"_pair_sdk.html,
"lj/sf"_pair_lj_sf.html,
"meam/spline"_pair_meam_spline.html,
"meam/sw/spline"_pair_meam_sw_spline.html,
"reax/c"_pair_reax_c.html,
"sph/heatconduction"_pair_sph_heatconduction.html,
"sph/idealgas"_pair_sph_idealgas.html,
"sph/lj"_pair_sph_lj.html,
"sph/rhosum"_pair_sph_rhosum.html,
"sph/taitwater"_pair_sph_taitwater.html,
"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
"tersoff/table"_pair_tersoff.html :tb(c=4,ea=c)
These are accelerated pair styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"adp/omp"_pair_adp.html,
"airebo/omp"_pair_airebo.html,
"beck/omp"_pair_beck.html,
"born/coul/long/cuda"_pair_born.html,
"born/coul/long/gpu"_pair_born.html,
"born/coul/long/omp"_pair_born.html,
"born/coul/msm/omp"_pair_born.html,
"born/coul/wolf/gpu"_pair_born.html,
"born/coul/wolf/omp"_pair_born.html,
"born/gpu"_pair_born.html,
"born/omp"_pair_born.html,
"brownian/omp"_pair_brownian.html,
"brownian/poly/omp"_pair_brownian.html,
"buck/coul/cut/cuda"_pair_buck.html,
"buck/coul/cut/gpu"_pair_buck.html,
"buck/coul/cut/omp"_pair_buck.html,
"buck/coul/long/cuda"_pair_buck.html,
"buck/coul/long/gpu"_pair_buck.html,
"buck/coul/long/omp"_pair_buck.html,
"buck/coul/msm/omp"_pair_buck.html,
"buck/cuda"_pair_buck.html,
"buck/long/coul/long/omp"_pair_buck_long.html,
"buck/gpu"_pair_buck.html,
"buck/omp"_pair_buck.html,
"colloid/gpu"_pair_colloid.html,
"colloid/omp"_pair_colloid.html,
"comb/omp"_pair_comb.html,
"coul/cut/omp"_pair_coul.html,
"coul/debye/omp"_pair_coul.html,
"coul/dsf/gpu"_pair_coul.html,
"coul/long/gpu"_pair_coul.html,
"coul/long/omp"_pair_coul.html,
"coul/msm/omp"_pair_coul.html,
"coul/wolf"_pair_coul.html,
"dipole/cut/gpu"_pair_dipole.html,
"dipole/cut/omp"_pair_dipole.html,
"dipole/sf/gpu"_pair_dipole.html,
"dipole/sf/omp"_pair_dipole.html,
"dpd/omp"_pair_dpd.html,
"dpd/tstat/omp"_pair_dpd.html,
"eam/alloy/cuda"_pair_eam.html,
"eam/alloy/gpu"_pair_eam.html,
"eam/alloy/omp"_pair_eam.html,
"eam/alloy/opt"_pair_eam.html,
"eam/cd/omp"_pair_eam.html,
"eam/cuda"_pair_eam.html,
"eam/fs/cuda"_pair_eam.html,
"eam/fs/gpu"_pair_eam.html,
"eam/fs/omp"_pair_eam.html,
"eam/fs/opt"_pair_eam.html,
"eam/gpu"_pair_eam.html,
"eam/omp"_pair_eam.html,
"eam/opt"_pair_eam.html,
"edip/omp"_pair_edip.html,
"eim/omp"_pair_eim.html,
"gauss/gpu"_pair_gauss.html,
"gauss/omp"_pair_gauss.html,
"gayberne/gpu"_pair_gayberne.html,
"gayberne/omp"_pair_gayberne.html,
"gran/hertz/history/omp"_pair_gran.html,
"gran/hooke/cuda"_pair_gran.html,
"gran/hooke/history/omp"_pair_gran.html,
"gran/hooke/omp"_pair_gran.html,
"hbond/dreiding/lj/omp"_pair_hbond_dreiding.html,
"hbond/dreiding/morse/omp"_pair_hbond_dreiding.html,
"line/lj/omp"_pair_line_lj.html,
"lj/charmm/coul/charmm/cuda"_pair_charmm.html,
"lj/charmm/coul/charmm/omp"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit/cuda"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit/omp"_pair_charmm.html,
"lj/charmm/coul/long/cuda"_pair_charmm.html,
"lj/charmm/coul/long/gpu"_pair_charmm.html,
"lj/charmm/coul/long/omp"_pair_charmm.html,
"lj/charmm/coul/long/opt"_pair_charmm.html,
"lj/class2/coul/cut/cuda"_pair_class2.html,
"lj/class2/coul/cut/omp"_pair_class2.html,
"lj/class2/coul/long/cuda"_pair_class2.html,
"lj/class2/coul/long/gpu"_pair_class2.html,
"lj/class2/coul/long/omp"_pair_class2.html,
"lj/class2/coul/msm/omp"_pair_class2.html,
"lj/class2/cuda"_pair_class2.html,
"lj/class2/gpu"_pair_class2.html,
"lj/class2/omp"_pair_class2.html,
"lj/long/coul/long/omp"_pair_lj_long.html,
"lj/cut/coul/cut/cuda"_pair_lj.html,
"lj/cut/coul/cut/gpu"_pair_lj.html,
"lj/cut/coul/cut/omp"_pair_lj.html,
"lj/cut/coul/debye/cuda"_pair_lj.html,
"lj/cut/coul/debye/gpu"_pair_lj.html,
"lj/cut/coul/debye/omp"_pair_lj.html,
"lj/cut/coul/dsf/gpu"_pair_lj.html,
"lj/cut/coul/long/cuda"_pair_lj.html,
"lj/cut/coul/long/gpu"_pair_lj.html,
"lj/cut/coul/long/omp"_pair_lj.html,
"lj/cut/coul/long/opt"_pair_lj.html,
"lj/cut/coul/msm/opt"_pair_lj.html,
"lj/cut/cuda"_pair_lj.html,
"lj/cut/experimental/cuda"_pair_lj.html,
"lj/cut/gpu"_pair_lj.html,
"lj/cut/omp"_pair_lj.html,
"lj/cut/opt"_pair_lj.html,
"lj/cut/tip4p/cut/omp"_pair_lj.html,
"lj/cut/tip4p/long/omp"_pair_lj.html,
"lj/cut/tip4p/long/opt"_pair_lj.html,
"lj/expand/cuda"_pair_lj_expand.html,
"lj/expand/gpu"_pair_lj_expand.html,
"lj/expand/omp"_pair_lj_expand.html,
"lj/gromacs/coul/gromacs/cuda"_pair_gromacs.html,
"lj/gromacs/coul/gromacs/omp"_pair_gromacs.html,
"lj/gromacs/cuda"_pair_gromacs.html,
"lj/gromacs/omp"_pair_gromacs.html,
"lj/long/coul/long/opt"_pair_lj_long.html,
"lj/sdk/gpu"_pair_sdk.html,
"lj/sdk/omp"_pair_sdk.html,
"lj/sdk/coul/long/gpu"_pair_sdk.html,
"lj/sdk/coul/long/omp"_pair_sdk.html,
"lj/sdk/coul/msm/omp"_pair_sdk.html,
"lj/sf/omp"_pair_lj_sf.html,
"lj/smooth/cuda"_pair_lj_smooth.html,
"lj/smooth/omp"_pair_lj_smooth.html,
"lj/smooth/linear/omp"_pair_lj_smooth_linear.html,
"lj96/cut/cuda"_pair_lj96.html,
"lj96/cut/gpu"_pair_lj96.html,
"lj96/cut/omp"_pair_lj96.html,
"lubricate/omp"_pair_lubricate.html,
"lubricate/poly/omp"_pair_lubricate.html,
"meam/spline/omp"_pair_meam_spline.html,
"morse/cuda"_pair_morse.html,
"morse/gpu"_pair_morse.html,
"morse/omp"_pair_morse.html,
"morse/opt"_pair_morse.html,
"peri/lps/omp"_pair_peri.html,
"peri/pmb/omp"_pair_peri.html,
"rebo/omp"_pair_airebo.html,
"resquared/gpu"_pair_resquared.html,
"resquared/omp"_pair_resquared.html,
"soft/omp"_pair_soft.html,
"sw/cuda"_pair_sw.html,
"sw/omp"_pair_sw.html,
"table/gpu"_pair_table.html,
"table/omp"_pair_table.html,
"tersoff/cuda"_pair_tersoff.html,
"tersoff/omp"_pair_tersoff.html,
"tersoff/table/omp"_pair_tersoff.html,
"tersoff/zbl/omp"_pair_tersoff_zbl.html,
"tri/lj/omp"_pair_tri_lj.html,
"yukawa/gpu"_pair_yukawa.html,
"yukawa/omp"_pair_yukawa.html,
"yukawa/colloid/gpu"_pair_yukawa_colloid.html,
"yukawa/colloid/omp"_pair_yukawa_colloid.html :tb(c=4,ea=c)
:line
Bond_style potentials :h4
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,
"table"_bond_table.html :tb(c=4,ea=c,w=100)
These are bond styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"harmonic/shift"_bond_harmonic_shift.html,
"harmonic/shift/cut"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
These are accelerated bond styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"class2/omp"_bond_class2.html,
"fene/omp"_bond_fene.html,
"fene/expand/omp"_bond_fene_expand.html,
"harmonic/omp"_bond_harmonic.html,
"harmonic/shift/omp"_bond_harmonic_shift.html,
"harmonic/shift/cut/omp"_bond_harmonic_shift_cut.html,
"morse/omp"_bond_morse.html,
"nonlinear/omp"_bond_nonlinear.html,
"quartic/omp"_bond_quartic.html,
"table/omp"_bond_table.html :tb(c=4,ea=c,w=100)
:line
Angle_style potentials :h4
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/delta"_angle_cosine_delta.html,
"cosine/periodic"_angle_cosine_periodic.html,
"cosine/squared"_angle_cosine_squared.html,
"harmonic"_angle_harmonic.html,
"table"_angle_table.html :tb(c=4,ea=c,w=100)
These are angle styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"sdk"_angle_sdk.html,
"cosine/shift"_angle_cosine_shift.html,
"cosine/shift/exp"_angle_cosine_shift_exp.html,
"dipole"_angle_dipole.html,
"fourier"_angle_fourier.html,
"fourier/simple"_angle_fourier_simple.html,
"quartic"_angle_quartic.html :tb(c=4,ea=c)
These are accelerated angle styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"charmm/omp"_angle_charmm.html,
"class2/omp"_angle_class2.html,
"cosine/omp"_angle_cosine.html,
"cosine/delta/omp"_angle_cosine_delta.html,
"cosine/periodic/omp"_angle_cosine_periodic.html,
"cosine/shift/omp"_angle_cosine_shift.html,
"cosine/shift/exp/omp"_angle_cosine_shift_exp.html,
"cosine/squared/omp"_angle_cosine_squared.html,
"dipole/omp"_angle_dipole.html
"fourier/omp"_angle_fourier.html,
"fourier/simple/omp"_angle_fourier_simple.html,
"harmonic/omp"_angle_harmonic.html,
"quartic/omp"_angle_quartic.html
"table/omp"_angle_table.html :tb(c=4,ea=c,w=100)
:line
Dihedral_style potentials :h4
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)
These are dihedral styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cosine/shift/exp"_dihedral_cosine_shift_exp.html,
"fourier"_dihedral_fourier.html,
"nharmonic"_dihedral_nharmonic.html,
"quadratic"_dihedral_quadratic.html,
"table"_dihedral_table.html :tb(c=4,ea=c)
These are accelerated dihedral styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"charmm/omp"_dihedral_charmm.html,
"class2/omp"_dihedral_class2.html,
"cosine/shift/exp/omp"_dihedral_cosine_shift_exp.html,
"fourier/omp"_dihedral_fourier.html,
"harmonic/omp"_dihedral_harmonic.html,
"helix/omp"_dihedral_helix.html,
"multi/harmonic/omp"_dihedral_multi_harmonic.html,
"nharmonic/omp"_dihedral_nharmonic.html,
"opls/omp"_dihedral_opls.html
"quadratic/omp"_dihedral_quadratic.html,
"table/omp"_dihedral_table.html :tb(c=4,ea=c,w=100)
:line
Improper_style potentials :h4
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,
"umbrella"_improper_umbrella.html :tb(c=4,ea=c,w=100)
These are improper styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cossq"_improper_cossq.html,
"fourier"_improper_fourier.html,
"ring"_improper_ring.html :tb(c=4,ea=c)
These are accelerated improper styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"class2/omp"_improper_class2.html,
"cossq/omp"_improper_cossq.html,
"cvff/omp"_improper_cvff.html,
"fourier/omp"_improper_fourier.html,
"harmonic/omp"_improper_harmonic.html,
"ring/omp"_improper_ring.html,
"umbrella/omp"_improper_umbrella.html :tb(c=4,ea=c,w=100)
:line
Kspace solvers :h4
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,
"ewald/disp"_kspace_style.html,
"msm"_kspace_style.html,
"msm/cg"_kspace_style.html,
"pppm"_kspace_style.html,
"pppm/cg"_kspace_style.html,
"pppm/disp"_kspace_style.html,
"pppm/disp/tip4p"_kspace_style.html,
"pppm/tip4p"_kspace_style.html :tb(c=4,ea=c,w=100)
These are accelerated Kspace solvers, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"ewald/omp"_kspace_style.html,
"msm/omp"_kspace_style.html,
"msm/cg/omp"_kspace_style.html,
"pppm/cuda"_kspace_style.html,
"pppm/gpu"_kspace_style.html,
"pppm/omp"_kspace_style.html,
"pppm/cg/omp"_kspace_style.html,
"pppm/tip4p/omp"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/pair_list.html b/doc/pair_list.html
new file mode 100644
index 000000000..28abb4133
--- /dev/null
+++ b/doc/pair_list.html
@@ -0,0 +1,152 @@
+<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>pair_style list command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style list listfile cutoff keyword
+</PRE>
+<UL><LI>listfile = name of file with list of pairwise interactions
+<LI>cutoff = global cutoff (distance units)
+<LI>keyword = optional flag <I>nocheck</I> or <I>check</I> (default is <I>check</I>)
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style list restraints.txt 200.0
+</PRE>
+<P>pair_coeff * *
+</P>
+<PRE>pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff 3* 3* list
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Style <I>list</I> computes interactions between explicitly listed pairs of
+atoms with the option to select functional form and parameters different
+for each individual pair. Because the parameters are all set in the
+list file, the pair_coeff statement has to be empty (but it needs to
+be provided). The <I>check</I> and <I>nocheck</I> keyword respectively enables
+or disables a test that checks whether all listed bonds were present
+and computed.
+</P>
+<P>As a consequence, this style is a hybrid between bonded, non-bonded
+and restraint interactions and most likely to be used as an additional
+interaction with the <I>hybrid/overlay</I> pair style. It currently supports
+three interaction styles: a 12-6 Lennard-Jones, a Morse and a Harmonic
+potential.
+</P>
+<P>The format of the list file is as follows:
+</P>
+<UL><LI>one line per pair of atoms
+
+<LI>empty lines will be ignored
+
+<LI>comment text starts with a '#' character
+line syntax: ID1 ID2 style coeffs cutoff
+
+<PRE> ID1 = atom ID of first atom
+ ID2 = atom ID of second atom
+ style = style of interaction
+ coeffs = list of coeffs
+ cutoff = cutoff for interaction (optional)
+</PRE>
+<LI>examples:
+
+<P># this is a comment
+</P>
+<PRE>15 259 lj126 1.0 1.0 50.0
+15 603 morse 10.0 1.2 2.0 10.0 # and another comment
+18 470 harmonic 50.0 1.2 5.0
+</PRE>
+
+</UL>
+<P>The cutoff parameter is optional. If not specified, the global cutoff is used.
+</P>
+<P>The style <I>lj126</I> computes pairwise interactions with the formula
+</P>
+<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
+</CENTER>
+<P>and the coefficients:
+</P>
+<UL><LI>epsilon (energy units)
+<LI>sigma (distance units)
+</UL>
+<P>The style <I>morse</I> computes pairwise interactions with the formula
+</P>
+<CENTER><IMG SRC = "Eqs/pair_morse.jpg">
+</CENTER>
+<P>and the coefficients:
+</P>
+<UL><LI>D0 (energy units)
+<LI>alpha (1/distance units)
+<LI>r0 (distance units)
+</UL>
+<P>The style <I>harmonic</I> computes pairwise interactions with the formula
+</P>
+<CENTER><IMG SRC = "Eqs/bond_harmonic.jpg">
+</CENTER>
+<P>and the coefficients:
+</P>
+<UL><LI>K (energy units)
+<LI>r0 (distance units)
+</UL>
+<P>Note that the usual 1/2 factor is included in K.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair style does not support mixing since all parameters are
+explicit for each pair.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> shift option is supported by this
+pair style.
+</P>
+<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
+relevant for this pair style.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, so pair_style and pair_coeff commands need
+to be specified in an input script that reads a restart file.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style does not use a neighbor list and instead identifies
+atoms by their IDs. This has two consequences: 1) The cutoff has to
+be chosen sufficiently large, so that the second atom of a pair has
+to be a ghost atom on the same node on which the first atom is local;
+otherwise the interaction will be skipped. You can use the <I>check</I>
+option to detect, if interactions are missing. 2) Unlike for the rest
+of LAMMPS, minimum image conventions apply.
+</P>
+<P>The <I>list</I> style is part of the "user-misc" package. It is only
+enabled if LAMMPS is build with that package. See the <A HREF = "Section_start.html#3">Making of
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>,
+<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>,
+<A HREF = "pair_lj.html">pair_style lj/cut</A>,
+<A HREF = "pair_morse.html">pair_style morse</A>,
+<A HREF = "bond_harmonic.html">bond_style harmonic</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/pair_list.txt b/doc/pair_list.txt
new file mode 100644
index 000000000..f160682cc
--- /dev/null
+++ b/doc/pair_list.txt
@@ -0,0 +1,141 @@
+"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
+
+pair_style list command :h3
+
+[Syntax:]
+
+pair_style list listfile cutoff keyword :pre
+
+listfile = name of file with list of pairwise interactions
+cutoff = global cutoff (distance units)
+keyword = optional flag {nocheck} or {check} (default is {check}) :ul
+
+[Examples:]
+
+pair_style list restraints.txt 200.0 :pre
+pair_coeff * *
+
+pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff 3* 3* list :pre
+
+[Description:]
+
+Style {list} computes interactions between explicitly listed pairs of
+atoms with the option to select functional form and parameters different
+for each individual pair. Because the parameters are all set in the
+list file, the pair_coeff statement has to be empty (but it needs to
+be provided). The {check} and {nocheck} keyword respectively enables
+or disables a test that checks whether all listed bonds were present
+and computed.
+
+As a consequence, this style is a hybrid between bonded, non-bonded
+and restraint interactions and most likely to be used as an additional
+interaction with the {hybrid/overlay} pair style. It currently supports
+three interaction styles: a 12-6 Lennard-Jones, a Morse and a Harmonic
+potential.
+
+The format of the list file is as follows:
+
+one line per pair of atoms :ulb,l
+empty lines will be ignored :l
+comment text starts with a '#' character
+line syntax: ID1 ID2 style coeffs cutoff :l
+ ID1 = atom ID of first atom
+ ID2 = atom ID of second atom
+ style = style of interaction
+ coeffs = list of coeffs
+ cutoff = cutoff for interaction (optional) :pre
+examples: :l
+
+# this is a comment
+
+15 259 lj126 1.0 1.0 50.0
+15 603 morse 10.0 1.2 2.0 10.0 # and another comment
+18 470 harmonic 50.0 1.2 5.0 :pre
+:ule
+
+The cutoff parameter is optional. If not specified, the global cutoff is used.
+
+The style {lj126} computes pairwise interactions with the formula
+
+:c,image(Eqs/pair_lj.jpg)
+
+and the coefficients:
+
+epsilon (energy units)
+sigma (distance units) :ul
+
+The style {morse} computes pairwise interactions with the formula
+
+:c,image(Eqs/pair_morse.jpg)
+
+and the coefficients:
+
+D0 (energy units)
+alpha (1/distance units)
+r0 (distance units) :ul
+
+The style {harmonic} computes pairwise interactions with the formula
+
+:c,image(Eqs/bond_harmonic.jpg)
+
+and the coefficients:
+
+K (energy units)
+r0 (distance units) :ul
+
+Note that the usual 1/2 factor is included in K.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This pair style does not support mixing since all parameters are
+explicit for each pair.
+
+The "pair_modify"_pair_modify.html shift option is supported by this
+pair style.
+
+The "pair_modify"_pair_modify.html table and tail options are not
+relevant for this pair style.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands need
+to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command. It does not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+This pair style does not use a neighbor list and instead identifies
+atoms by their IDs. This has two consequences: 1) The cutoff has to
+be chosen sufficiently large, so that the second atom of a pair has
+to be a ghost atom on the same node on which the first atom is local;
+otherwise the interaction will be skipped. You can use the {check}
+option to detect, if interactions are missing. 2) Unlike for the rest
+of LAMMPS, minimum image conventions apply.
+
+The {list} style is part of the "user-misc" package. It is only
+enabled if LAMMPS is build with that package. See the "Making of
+LAMMPS"_Section_start.html#3 section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html,
+"pair_style hybrid/overlay"_pair_hybrid.html,
+"pair_style lj/cut"_pair_lj.html,
+"pair_style morse"_pair_morse.html,
+"bond_style harmonic"_bond_harmonic.html
+
+[Default:] none
diff --git a/src/USER-MISC/Install.sh b/src/USER-MISC/Install.sh
index d375eccbc..635549f96 100644
--- a/src/USER-MISC/Install.sh
+++ b/src/USER-MISC/Install.sh
@@ -1,138 +1,142 @@
# Install/unInstall package files in LAMMPS
if (test $1 = 1) then
if (test -e ../pair_eam_alloy.cpp) then
cp pair_cdeam.cpp ..
cp pair_cdeam.h ..
fi
cp angle_cosine_shift.cpp ..
cp angle_cosine_shift_exp.cpp ..
cp angle_dipole.cpp ..
cp angle_fourier.cpp ..
cp angle_fourier_simple.cpp ..
cp angle_quartic.cpp ..
cp bond_harmonic_shift.cpp ..
cp bond_harmonic_shift_cut.cpp ..
cp compute_ackland_atom.cpp ..
cp compute_temp_rotate.cpp ..
cp dihedral_cosine_shift_exp.cpp ..
cp dihedral_fourier.cpp ..
cp dihedral_nharmonic.cpp ..
cp dihedral_quadratic.cpp ..
cp dihedral_table.cpp ..
cp improper_fourier.cpp ..
cp fix_addtorque.cpp ..
cp fix_imd.cpp ..
cp fix_smd.cpp ..
cp fix_spring_pull.cpp ..
cp improper_cossq.cpp ..
cp improper_ring.cpp ..
cp pair_coul_diel.cpp ..
cp pair_dipole_sf.cpp ..
cp pair_edip.cpp ..
cp pair_gauss_cut.cpp ..
+ cp pair_list.cpp ..
cp pair_lj_sf.cpp ..
cp pair_meam_spline.cpp ..
cp pair_meam_sw_spline.cpp ..
cp pair_tersoff_table.cpp ..
cp angle_cosine_shift.h ..
cp angle_cosine_shift_exp.h ..
cp angle_dipole.h ..
cp angle_fourier.h ..
cp angle_fourier_simple.h ..
cp angle_quartic.h ..
cp bond_harmonic_shift.h ..
cp bond_harmonic_shift_cut.h ..
cp compute_ackland_atom.h ..
cp compute_temp_rotate.h ..
cp dihedral_cosine_shift_exp.h ..
cp dihedral_fourier.h ..
cp dihedral_nharmonic.h ..
cp dihedral_quadratic.h ..
cp dihedral_table.h ..
cp improper_fourier.h ..
cp fix_addtorque.h ..
cp fix_imd.h ..
cp fix_smd.h ..
cp fix_spring_pull.h ..
cp improper_cossq.h ..
cp improper_ring.h ..
cp pair_coul_diel.h ..
cp pair_dipole_sf.h ..
cp pair_edip.h ..
cp pair_gauss_cut.h ..
+ cp pair_list.h ..
cp pair_lj_sf.h ..
cp pair_meam_spline.h ..
cp pair_meam_sw_spline.h ..
cp pair_tersoff_table.h ..
elif (test $1 = 0) then
rm -f ../angle_cosine_shift.cpp
rm -f ../angle_cosine_shift_exp.cpp
rm -f ../angle_fourier.cpp
rm -f ../angle_fourier_simple.cpp
rm -f ../angle_dipole.cpp
rm -f ../angle_quartic.cpp
rm -f ../bond_harmonic_shift.cpp
rm -f ../bond_harmonic_shift_cut.cpp
rm -f ../compute_ackland_atom.cpp
rm -f ../compute_temp_rotate.cpp
rm -f ../dihedral_cosine_shift_exp.cpp
rm -f ../dihedral_fourier.cpp
rm -f ../dihedral_nharmonic.cpp
rm -f ../dihedral_quadratic.cpp
rm -f ../dihedral_table.cpp
rm -f ../improper_fourier.cpp
rm -f ../fix_addtorque.cpp
rm -f ../fix_imd.cpp
rm -f ../fix_smd.cpp
rm -f ../fix_spring_pull.cpp
rm -f ../improper_cossq.cpp
rm -f ../improper_ring.cpp
rm -f ../pair_cdeam.cpp
rm -f ../pair_coul_diel.cpp
rm -f ../pair_dipole_sf.cpp
rm -f ../pair_edip.cpp
rm -f ../pair_gauss_cut.cpp
+ rm -f ../pair_list.cpp
rm -f ../pair_lj_sf.cpp
rm -f ../pair_meam_spline.cpp
rm -f ../pair_meam_sw_spline.cpp
rm -f ../pair_tersoff_table.cpp
rm -f ../angle_cosine_shift.h
rm -f ../angle_cosine_shift_exp.h
rm -f ../angle_dipole.h
rm -f ../angle_fourier.h
rm -f ../angle_fourier_simple.h
rm -f ../angle_quartic.h
rm -f ../bond_harmonic_shift.h
rm -f ../bond_harmonic_shift_cut.h
rm -f ../compute_ackland_atom.h
rm -f ../compute_temp_rotate.h
rm -f ../dihedral_cosine_shift_exp.h
rm -f ../dihedral_fourier.h
rm -f ../dihedral_nharmonic.h
rm -f ../dihedral_quadratic.h
rm -f ../dihedral_table.h
rm -f ../improper_fourier.h
rm -f ../fix_addtorque.h
rm -f ../fix_imd.h
rm -f ../fix_smd.h
rm -f ../fix_spring_pull.h
rm -f ../improper_cossq.h
rm -f ../improper_ring.h
rm -f ../pair_cdeam.h
rm -f ../pair_coul_diel.h
rm -f ../pair_dipole_sf.h
rm -f ../pair_edip.h
rm -f ../pair_gauss_cut.h
+ rm -f ../pair_list.h
rm -f ../pair_lj_sf.h
rm -f ../pair_meam_spline.h
rm -f ../pair_meam_sw_spline.h
rm -f ../pair_tersoff_table.h
fi
diff --git a/src/pair_list.cpp b/src/USER-MISC/pair_list.cpp
similarity index 100%
rename from src/pair_list.cpp
rename to src/USER-MISC/pair_list.cpp
diff --git a/src/pair_list.h b/src/USER-MISC/pair_list.h
similarity index 100%
rename from src/pair_list.h
rename to src/USER-MISC/pair_list.h