diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
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@@ -1,1196 +1,1197 @@
<"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
so that you do not have to define (or discard) a temporary variable X.
Note that neither the curly-bracket or immediate form of variables can
contain nested $ characters for other variables to substitute for.
Thus you cannot do this:
variable a equal 2
variable b2 equal 4
print "B2 = $\{b$a\}" :pre
Nor can you specify this $($x-1.0) for an immediate variable, but
you could use $(v_x-1.0), since the latter is valid syntax for an
"equal-style variable"_variable.html.
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_dump"_write_dump.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,
+"dump movie"_dump_movie.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,
"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_dump"_write_dump.html,
"write_restart"_write_restart.html :tb(c=6,ea=c)
These are commands contributed by users, which can be used if "LAMMPS
is built with the appropriate package"_Section_start.html#start_3.
"group2ndx"_group2ndx.html :tb(c=1,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,
"gld"_fix_gld.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,
"property/atom"_fix_property_atom.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,
"tune/kspace"_fix_tune_kspace.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/lj1043"_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,
"qmmm"_fix_qmmm.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/rigid"_compute_erotate_rigid.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,
"ke/rigid"_compute_ke_rigid.html,
"msd"_compute_msd.html,
"msd/molecule"_compute_msd_molecule.html,
"msd/nongauss"_compute_msd_nongauss.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,
"basal/atom"_compute_basal_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,
"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/dipole/cut"_pair_dipole.html,
"lj/cut/dipole/long"_pair_dipole.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/dipole/long"_pair_dipole.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,
"nm/cut"_pair_nm.html,
"nm/cut/coul/cut"_pair_nm.html,
"nm/cut/coul/long"_pair_nm.html,
"peri/lps"_pair_peri.html,
"peri/pmb"_pair_peri.html,
"peri/ves"_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/mod"_pair_tersoff_mod.html,
"tersoff/zbl"_pair_tersoff_zbl.html,
"tip4p/cut"_pair_coul.html,
"tip4p/long"_pair_coul.html,
"tri/lj"_pair_tri_lj.html,
"yukawa"_pair_yukawa.html,
"yukawa/colloid"_pair_yukawa_colloid.html,
"zbl"_pair_zbl.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,
"eam/cd"_pair_eam.html,
"edip"_pair_edip.html,
"eff/cut"_pair_eff.html,
"gauss/cut"_pair_gauss.html,
"list"_pair_list.html,
"lj/cut/dipole/sf"_pair_dipole.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,
"nb3b/harmonic"_pair_nb3b_harmonic.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/gpu"_pair_beck.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/dsf/omp"_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,
"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/dsf/omp"_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/gpu"_pair_lj.html,
"lj/cut/coul/msm/opt"_pair_lj.html,
"lj/cut/cuda"_pair_lj.html,
"lj/cut/dipole/cut/gpu"_pair_dipole.html,
"lj/cut/dipole/cut/omp"_pair_dipole.html,
"lj/cut/dipole/sf/gpu"_pair_dipole.html,
"lj/cut/dipole/sf/omp"_pair_dipole.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,
"mie/cut/gpu"_pair_mie.html,
"morse/cuda"_pair_morse.html,
"morse/gpu"_pair_morse.html,
"morse/omp"_pair_morse.html,
"morse/opt"_pair_morse.html,
"nb3b/harmonic/omp"_pair_nb3b_harmonic.html,
"nm/cut/omp"_pair_nm.html,
"nm/cut/coul/cut/omp"_pair_nm.html,
"nm/cut/coul/long/omp"_pair_nm.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/gpu"_pair_soft.html,
"soft/omp"_pair_soft.html,
"sw/cuda"_pair_sw.html,
"sw/gpu"_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/mod/omp"_pair_tersoff_mod.html,
"tersoff/table/omp"_pair_tersoff.html,
"tersoff/zbl/omp"_pair_tersoff_zbl.html,
"tip4p/cut/omp"_pair_coul.html,
"tip4p/long/omp"_pair_coul.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,
"zbl/omp"_pair_zbl.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/dump_image.txt b/doc/dump_image.txt
index 6affa46f2..9260e76da 100644
--- a/doc/dump_image.txt
+++ b/doc/dump_image.txt
@@ -1,463 +1,503 @@
"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
dump image command :h3
dump movie command :h3
[Syntax:]
dump ID group-ID image-or-movie N file color diameter keyword value ... :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be imaged :l
image-or-movie = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
N = dump every this many timesteps :l
file = name of file to write image to :l
color = atom attribute that determines color of each atom :l
diameter = atom attribute that determines size of each atom :l
zero or more keyword/value pairs may be appended :l
keyword = {adiam} or {atom} or {bond} or {size} or {view} or {center} or {up} or {zoom} or {persp} or {box} or {axes} or {shiny} or {ssao} :l
{adiam} value = number = numeric value for atom diameter (distance units)
{atom} = yes/no = do or do not draw atoms
{bond} values = color width = color and width of bonds
color = {atom} or {type} or {none}
width = number or {atom} or {type} or {none}
number = numeric value for bond width (distance units)
{size} values = width height = size of images
width = width of image in # of pixels
height = height of image in # of pixels
{view} values = theta phi = view of simulation box
theta = view angle from +z axis (degrees)
phi = azimuthal view angle (degrees)
theta or phi can be a variable (see below)
{center} values = flag Cx Cy Cz = center point of image
flag = "s" for static, "d" for dynamic
Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
Cx,Cy,Cz can be variables (see below)
{up} values = Ux Uy Uz = direction that is "up" in image
Ux,Uy,Uz = components of up vector
Ux,Uy,Uz can be variables (see below)
{zoom} value = zfactor = size that simulation box appears in image
zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
zfactor can be a variable (see below)
{persp} value = pfactor = amount of "perspective" in image
pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
pfactor can be a variable (see below)
{box} values = yes/no diam = draw outline of simulation box
yes/no = do or do not draw simulation box lines
diam = diameter of box lines as fraction of shortest box length
{axes} values = yes/no length diam = draw xyz axes
yes/no = do or do not draw xyz axes lines next to simulation box
length = length of axes lines as fraction of respective box lengths
diam = diameter of axes lines as fraction of shortest box length
{shiny} value = sfactor = shinyness of spheres and cylinders
sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
{ssao} value = yes/no seed dfactor = SSAO depth shading
yes/no = turn depth shading on/off
seed = random # seed (positive integer)
dfactor = strength of shading from 0.0 to 1.0 :pre
:ule
[Examples:]
dump d0 all image 100 dump.*.jpg type type :pre
dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6 :pre
dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720 :pre
dump m0 all movie 1000 movie.mpg type type size 640 480 :pre
dump m1 all movie 1000 movie.avi type type size 640 480 :pre
-dump m2 all movie 100 movie.mp4 type type zoom 1.8 adiam v_value size 1280 720 :pre
+dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720 :pre
[Description:]
Dump a high-quality rendered image of the atom configuration every N
timesteps and save it either a JPG or PNG, or PPM file or compress it
into a movie. The options for this command as well as the
"dump_modify"_dump_modify.html command control what is included in the
-image or movie and how it appears. A series of such images can easily
+image or movie and how it appears. A series of such images can easily
be manually converted into an animated movie of your simulation or the
-process can be automated using the movie style; see further details below.
+process can be automated without writing the intermediate files using
+the dump movie style; see further details below.
Other dump styles store snapshots of numerical data asociated with atoms
in various formats, as discussed on the "dump"_dump.html doc page.
Here are two sample images, rendered as 1024x1024 JPG files. Click to
see the full-size images:
<DIV ALIGN=center>
:image(JPG/dump1_small.jpg,JPG/dump1.jpg)
:image(JPG/dump2_small.jpg,JPG/dump2.jpg)
</DIV>
Only atoms in the specified group are rendered in the image. The
"dump_modify region and thresh"_dump_modify.html commands can also
alter what atoms are included in the image.\
The filename suffix determines whether a JPEG, PNG, or PPM file is
-created. If the suffix is ".jpg" or ".jpeg", then a JPEG format file
-is created, if the suffix is ".png", then a PNG format is created,
-else a PPM (aka NETPBM) format file is created. The JPG and PNG files
-are binary; PPM has a text mode header followed by binary data.
-JPG images have lossy compression; PNG has lossless compression; and
-PPM files are uncompressed but can be compressed with gzip, if LAMMPS
-has been compiled with -DLAMMPS_GZIP and a ".gz" suffix is used.
-To write out JPEG and PNG format files, you must build LAMMPS with
-support for the corresponding JPEG or PNG library. See "this
-section"_Section_start.html#start_2_4 of the manual for instructions
+created with the {image} dump style. If the suffix is ".jpg" or ".jpeg",
+then a JPEG format file is created, if the suffix is ".png", then a PNG
+format is created, else a PPM (aka NETPBM) format file is created.
+The JPG and PNG files are binary; PPM has a text mode header followed
+by binary data. JPG images have lossy compression; PNG has lossless
+compression; and PPM files are uncompressed but can be compressed with
+gzip, if LAMMPS has been compiled with -DLAMMPS_GZIP and a ".gz" suffix
+is used.
+
+Similarly, the format of the resulting movie is chosen with the
+{movie} dump style. This is handled by the underlying FFmpeg converter
+and thus details have to be looked up in the FFmpeg documentation.
+Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif
+Additional settings of the movie compression like bitrate and
+framerate can be set using the "dump_modify"_dump_modify.html command.
+
+To write out JPEG and PNG format files, you must build LAMMPS
+with support for the corresponding JPEG or PNG library. To convert images
+into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG flag. See
+"this section"_Section_start.html#start_2_4 of the manual for instructions
on how to do this.
IMPORTANT NOTE: Because periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an
atom in the image may be slightly outside the simulation box.
:line
Dumps are performed on timesteps that are a multiple of N (including
timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
changed via the "dump_modify first"_dump_modify.html command, which
can be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
using the "dump_modify every"_dump_modify.html command.
-Dump image filenames must contain a wildcard character "*", so that
+Dump {image} filenames must contain a wildcard character "*", so that
one image file per snapshot is written. The "*" character is replaced
with the timestep value. For example, tmp.dump.*.jpg becomes
tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note
that the "dump_modify pad"_dump_modify.html command can be used to
insure all timestep numbers are the same length (e.g. 00010), which
can make it easier to convert a series of images into a movie in the
correct ordering.
-Dump movie filenames on the other hand must not have any wildcard
-character but only one file is written by the movie encoder.
+Dump {movie} filenames on the other hand, must not have any wildcard
+character since only one file combining all images into a single
+movie will be written by the movie encoder.
:line
The {color} and {diameter} settings determine the color and size of
atoms rendered in the image. They can be any atom attribute defined
for the "dump custom"_dump.html command, including {type} and
{element}. This includes per-atom quantities calculated by a
"compute"_compute.html, "fix"_fix.html, or "variable"_variable.html,
which are prefixed by "c_", "f_", or "v_" respectively. Note that the
{diameter} setting can be overridden with a numeric value by the
optional {adiam} keyword, in which case you can specify the {diameter}
setting with any valid atom attribute.
If {type} is specified for the {color} setting, then the color of each
atom is determined by its atom type. By default the mapping of types
to colors is as follows:
type 1 = red
type 2 = green
type 3 = blue
type 4 = yellow
type 5 = aqua
type 6 = cyan :ul
and repeats itself for types > 6. This mapping can be changed by the
"dump_modify acolor"_dump_modify.html command.
If {type} is specified for the {diameter} setting then the diameter of
each atom is determined by its atom type. By default all types have
diameter 1.0. This mapping can be changed by the "dump_modify
adiam"_dump_modify.html command.
If {element} is specified for the {color} and/or {diameter} setting,
then the color and/or diameter of each atom is determined by which
element it is, which in turn is specified by the element-to-type
mapping specified by the "dump_modify element" command. By default
every atom type is C (carbon). Every element has a color and diameter
associated with it, which is the same as the colors and sizes used by
the "AtomEye"_atomeye visualization package.
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
If other atom attributes are used for the {color} or {diameter}
settings, they are interpreted in the following way.
If "vx", for example, is used as the {color} setting, then the color
of the atom will depend on the x-component of its velocity. The
association of a per-atom value with a specific color is determined by
a "color map", which can be specified via the
"dump_modify"_dump_modify.html command. The basic idea is that the
atom-attribute will be within a range of values, and every value
within the range is mapped to a specific color. Depending on how the
color map is defined, that mapping can take place via interpolation so
that a value of -3.2 is halfway between "red" and "blue", or
discretely so that the value of -3.2 is "orange".
If "vx", for example, is used as the {diameter} setting, then the atom
will be rendered using the x-component of its velocity as the
diameter. If the per-atom value <= 0.0, them the atom will not be
drawn. Note that finite-size spherical particles, as defined by
"atom_style sphere"_atom_style.html define a per-particle radius or
diameter, which can be used as the {diameter} setting.
:line
The various kewords listed above control how the image is rendered.
As listed below, all of the keywords have defaults, most of which you
will likely not need to change. The "dump modify"_dump_modify.html
also has options specific to the dump image style, particularly for
assigning colors to atoms, bonds, and other image features.
:line
The {adiam} keyword allows you to override the {diameter} setting to a
per-atom attribute with a specified numeric value. All atoms will be
drawn with that diameter, e.g. 1.5, which is in whatever distance
"units"_units.html the input script defines, e.g. Angstroms.
The {atom} keyword allow you to turn off the drawing of all atoms,
if the specified value is {no}.
The {bond} keyword allows to you to alter how bonds are drawn. A bond
is only drawn if both atoms in the bond are being drawn due to being
in the specified group and due to other selection criteria
(e.g. region, threshhold settings of the
"dump_modify"_dump_modify.html command). By default, bonds are drawn
if they are defined in the input data file as read by the
"read_data"_read_data.html command. Using {none} for both the bond
{color} and {width} value will turn off the drawing of all bonds.
If {atom} is specified for the bond {color} value, then each bond is
drawn in 2 halves, with the color of each half being the color of the
atom at that end of the bond.
If {type} is specified for the {color} value, then the color of each
bond is determined by its bond type. By default the mapping of bond
types to colors is as follows:
type 1 = red
type 2 = green
type 3 = blue
type 4 = yellow
type 5 = aqua
type 6 = cyan :ul
and repeats itself for bond types > 6. This mapping can be changed by
the "dump_modify bcolor"_dump_modify.html command.
The bond {width} value can be a numeric value or {atom} or {type} (or
{none} as indicated above).
If a numeric value is specified, then all bonds will be drawn as
cylinders with that diameter, e.g. 1.0, which is in whatever distance
"units"_units.html the input script defines, e.g. Angstroms.
If {atom} is specified for the {width} value, then each bond
will be drawn with a width corresponding to the minimum diameter
of the 2 atoms in the bond.
If {type} is specified for the {width} value then the diameter of each
bond is determined by its bond type. By default all types have
diameter 0.5. This mapping can be changed by the "dump_modify
bdiam"_dump_modify.html command.
:line
The {size} keyword sets the width and height of the created images,
i.e. the number of pixels in each direction.
:line
The {view}, {center}, {up}, {zoom}, and {persp} values determine how
3d simulation space is mapped to the 2d plane of the image. Basically
they control how the simulation box appears in the image.
All of the {view}, {center}, {up}, {zoom}, and {persp} values can be
specified as numeric quantities, whose meaning is explained below.
Any of them can also be specified as an "equal-style
variable"_variable.html, by using v_name as the value, where "name" is
the variable name. In this case the variable will be evaluated on the
timestep each image is created to create a new value. If the
equal-style variable is time-dependent, this is a means of changing
the way the simulation box appears from image to image, effectively
doing a pan or fly-by view of your simulation.
The {view} keyword determines the viewpoint from which the simulation
box is viewed, looking towards the {center} point. The {theta} value
is the vertical angle from the +z axis, and must be an angle from 0 to
180 degrees. The {phi} value is an azimuthal angle around the z axis
and can be positive or negative. A value of 0.0 is a view along the
+x axis, towards the {center} point. If {theta} or {phi} are
specified via variables, then the variable values should be in
degrees.
The {center} keyword determines the point in simulation space that
will be at the center of the image. {Cx}, {Cy}, and {Cz} are
speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is
the center of the simulation box. These values do not have to be
between 0.0 and 1.0, if you want the simulation box to be offset from
the center of the image. Note, however, that if you choose strange
values for {Cx}, {Cy}, or {Cz} you may get a blank image. Internally,
{Cx}, {Cy}, and {Cz} are converted into a point in simulation space.
If {flag} is set to "s" for static, then this conversion is done once,
at the time the dump command is issued. If {flag} is set to "d" for
dynamic then the conversion is performed every time a new image is
created. If the box size or shape is changing, this will adjust the
center point in simulation space.
The {up} keyword determines what direction in simulation space will be
"up" in the image. Internally it is stored as a vector that is in the
plane perpendicular to the view vector implied by the {theta} and
{pni} values, and which is also in the plane defined by the view
vector and user-specified up vector. Thus this internal vector is
computed from the user-specified {up} vector as
up_internal = view cross (up cross view) :pre
This means the only restriction on the specified {up} vector is that
it cannot be parallel to the {view} vector, implied by the {theta} and
{phi} values.
The {zoom} keyword scales the size of the simulation box as it appears
in the image. The default {zfactor} value of 1 should display an
image mostly filled by the atoms in the simulation box. A {zfactor} >
1 will make the simulation box larger; a {zfactor} < 1 will make it
smaller. {Zfactor} must be a value > 0.0.
The {persp} keyword determines how much depth perspective is present
in the image. Depth perspective makes lines that are parallel in
simulation space appear non-parallel in the image. A {pfactor} value
of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
which is an orthographic rendering with no persepctive. A {pfactor}
value between 0.0 and 1.0 will introduce more perspective. A {pfactor}
value > 1 will create a highly skewed image with a large amount of
perspective.
IMPORTANT NOTE: The {persp} keyword is not yet supported as an option.
:line
The {box} keyword determines how the simulation box boundaries are
rendered as thin cylinders in the image. If {no} is set, then the box
boundaries are not drawn and the {diam} setting is ignored. If {yes}
is set, the 12 edges of the box are drawn, with a diameter that is a
fraction of the shortest box length in x,y,z (for 3d) or x,y (for 2d).
The color of the box boundaries can be set with the "dump_modify
boxcolor"_dump_modify.html command.
The {axes} keyword determines how the coordinate axes are rendered as
thin cylinders in the image. If {no} is set, then the axes are not
drawn and the {length} and {diam} settings are ignored. If {yes} is
set, 3 thin cylinders are drawn to represent the x,y,z axes in colors
red,green,blue. The origin of these cylinders will be offset from the
lower left corner of the box by 10%. The {length} setting determines
how long the cylinders will be as a fraction of the respective box
lengths. The {diam} setting determines their thickness as a fraction
of the shortest box length in x,y,z (for 3d) or x,y (for 2d).
:line
The {shiny} keyword determines how shiny the objects rendered in the
image will appear. The {sfactor} value must be a value 0.0 <=
{sfactor} <= 1.0, where {sfactor} = 1 is a highly reflective surface
and {sfactor} = 0 is a rough non-shiny surface.
The {ssao} keyword turns on/off a screen space ambient occlusion
(SSAO) model for depth shading. If {yes} is set, then atoms further
away from the viewer are darkened via a randomized process, which is
perceived as depth. The calculation of this effect can increase the
cost of computing the image by roughly 2x. The strength of the effect
can be scaled by the {dfactor} parameter. If {no} is set, no depth
shading is performed.
:line
A series of JPG, PNG, or PPM images can be converted into a movie file
-and then played as a movie using commonly available tools. Using the
-movie dump style skips this intermediate step, but requires LAMMPS to
-be compiled with -DLAMMPS_FFMPEG and an FFmpeg executable installed.
+and then played as a movie using commonly available tools. Using dump
+style {movie} automates this step and avoids the intermediate step of
+writing (many) image snapshot file. But LAMMPS has to be compiled with
+-DLAMMPS_FFMPEG and an FFmpeg executable have to be installed.
-Convert JPG or PPM files into an animated GIF or MPEG or other movie
-file:
+To manually convert JPG, PNG or PPM files into an animated GIF or MPEG
+or other movie file you can use:
a) Use the ImageMagick convert program. :ulb,l
% convert *.jpg foo.gif
% convert -loop 1 *.ppm foo.mpg :pre
+Animated GIF files from ImageMagick are unoptimized. You can use a
+program like gifsicle to optimize and massively shrink them.
+MPEG files created by ImageMagick are in MPEG-1 format with rather
+inefficient compression and low quality.
+
b) Use QuickTime. :l
Select "Open Image Sequence" under the File menu
Load the images into QuickTime to animate them
Select "Export" under the File menu
-Save the movie as a QuickTime movie (*.mov) or in another format
+Save the movie as a QuickTime movie (*.mov) or in another format.
+QuickTime can generate very high quality and efficiently compressed
+movie files. Some of the supported formats require to buy a license
+and some are not readable on all platforms until specific runtime
+libraries are installed.
c) Use FFmpeg :ule,l
-If someone tells us how to do this via a common Windows-based tool,
-we'll post the instructions here.
+FFmpeg is a command line tool that is available on many platforms
+and allows extremely flexible encoding and decoding of movies.
+
+cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
+cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi :pre
+
+Frontends for FFmpeg exist for multiple platforms. For more
+information see the "FFmpeg homepage"_http://www.ffmpeg.org/
+
+:line
Play the movie:
a) Use your browser to view an animated GIF movie. :ulb,l
Select "Open File" under the File menu
Load the animated GIF file
-b) Use the freely available mplayer tool to view an MPEG movie. :l
+b) Use the freely available mplayer or ffplays tool to view
+a movie. Both are available for multiple OSes and support a
+large variety of file formats and decoders. :l
-% mplayer foo.mpg :pre
+% mplayer foo.mpg
+% ffplay bar.avi :pre
c) Use the "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html
"animate tool"_http://www.sandia.gov/~sjplimp/pizza/doc/animate.html,
which works directly on a series of image files. :l
a = animate("foo*.jpg") :pre
-d) QuickTime and other Windows-based media players can
-obviously play movie files directly. :ule,l
+d) QuickTime and other Windows- or MacOS-based media players can
+obviously play movie files directly. Similarly the corresponding
+tools bundled with Linux desktop environments, however, due to
+licensing issues of some of the file formats, some formats may
+require installing additional libraries, purchasing a license,
+or are not supported. :ule,l
:line
See "Section_modify"_Section_modify.html of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.
:line
[Restrictions:]
To write JPG images, you must use the -DLAMMPS_JPEG switch when building
LAMMPS and link with a JPEG library. To write PNG images, you must
use the -DLAMMPS_PNG switch when building LAMMPS and link with a PNG library.
+
To write {movie} dumps, you must use the -DLAMMPS_FFMPEG switch when
building LAMMPS and have the FFmpeg executable available on the machine
-where LAMMPS is being run. See the
-"Making LAMMPS"_Section_start.html#start_2_4 section of the documentation
-for details.
+where LAMMPS is being run.
+
+See the "Making LAMMPS"_Section_start.html#start_2_4 section of the
+documentation for details on how to configure and compile optional
+in LAMMPS.
[Related commands:]
"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
[Default:]
The defaults for the keywords are as follows:
adiam = not specified (use diameter setting)
atom = yes
bond = none none (if no bonds in system)
bond = atom 0.5 (if bonds in system)
size = 512 512
view = 60 30 (for 3d)
view = 0 0 (for 2d)
center = s 0.5 0.5 0.5
up = 0 0 1 (for 3d)
up = 0 1 0 (for 2d)
zoom = 1.0
persp = 0.0
box = yes 0.02
axes = no 0.0 0.0
shiny = 1.0
ssao = no :ul
diff --git a/doc/dump_modify.txt b/doc/dump_modify.txt
index f354bc5be..e1f65d95d 100644
--- a/doc/dump_modify.txt
+++ b/doc/dump_modify.txt
@@ -1,772 +1,801 @@
"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
dump_modify command :h3
[Syntax:]
dump_modify dump-ID keyword values ... :pre
dump-ID = ID of dump to modify :ulb,l
one or more keyword/value pairs may be appended :l
-keyword = {acolor} or {adiam} or {amap} or {append} or {bcolor} or {bdiam} or {backcolor} or {boxcolor} or {color} or {every} or {flush} or {format} or {image} or {label} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
+keyword = {append} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} or {acolor} or {adiam} or {amap} or {bcolor} or {bdiam} or {backcolor} or {boxcolor} or {color} or {bitrate} or {framerate} :l
+ {append} arg = {yes} or {no}
+ {element} args = E1 E2 ... EN, where N = # of atom types
+ E1,...,EN = element name, e.g. C or Fe or Ga
+ {every} arg = N
+ N = dump every this many timesteps
+ N can be a variable (see below)
+ {fileper} arg = Np
+ Np = write one file for every this many processors
+ {first} arg = {yes} or {no}
+ {format} arg = C-style format string for one line of output
+ {flush} arg = {yes} or {no}
+ {image} arg = {yes} or {no}
+ {label} arg = string
+ string = character string (e.g. BONDS) to use in header of dump local file
+ {nfile} arg = Nf
+ Nf = write this many files, one from each of Nf processors
+ {pad} arg = Nchar = # of characters to convert timestep to
+ {precision} arg = power-of-10 value from 10 to 1000000
+ {region} arg = region-ID or "none"
+ {scale} arg = {yes} or {no}
+ {sort} arg = {off} or {id} or N or -N
+ off = no sorting of per-atom lines within a snapshot
+ id = sort per-atom lines by atom ID
+ N = sort per-atom lines in ascending order by the Nth column
+ -N = sort per-atom lines in descending order by the Nth column
+ {thresh} args = attribute operation value
+ attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
+ operation = "<" or "<=" or ">" or ">=" or "==" or "!="
+ value = numeric value to compare to
+ these 3 args can be replaced by the word "none" to turn off thresholding
+ {unwrap} arg = {yes} or {no}
{acolor} args = type color
type = atom type or range of types (see below)
color = name of color or color1/color2/...
{adiam} args = type diam
type = atom type or range of types (see below)
diam = diameter of atoms of that type (distance units)
{amap} args = lo hi style delta N entry1 entry2 ... entryN
lo = number or {min} = lower bound of range of color map
hi = number or {max} = upper bound of range of color map
style = 2 letters = "c" or "d" or "s" plus "a" or "f"
"c" for continuous
"d" for discrete
"s" for sequential
"a" for absolute
"f" for fractional
delta = binsize (only used for style "s", otherwise ignored)
binsize = range is divided into bins of this width
N = # of subsequent entries
entry = value color (for continuous style)
value = number or {min} or {max} = single value within range
color = name of color used for that value
entry = lo hi color (for discrete style)
lo/hi = number or {min} or {max} = lower/upper bound of subset of range
color = name of color used for that subset of values
entry = color (for sequential style)
color = name of color used for a bin of values
- {append} arg = {yes} or {no}
{bcolor} args = type color
type = bond type or range of types (see below)
color = name of color or color1/color2/...
{bdiam} args = type diam
type = bond type or range of types (see below)
diam = diameter of bonds of that type (distance units)
{backcolor} arg = color
color = name of color for background
{boxcolor} arg = color
color = name of color for box lines
{color} args = name R G B
name = name of color
- R,G,B = red/green/blue numeric values from 0.0 to 1.0
- {element} args = E1 E2 ... EN, where N = # of atom types
- E1,...,EN = element name, e.g. C or Fe or Ga
- {every} arg = N
- N = dump every this many timesteps
- N can be a variable (see below)
- {fileper} arg = Np
- Np = write one file for every this many processors
- {first} arg = {yes} or {no}
- {format} arg = C-style format string for one line of output
- {flush} arg = {yes} or {no}
- {image} arg = {yes} or {no}
- {label} arg = string
- string = character string (e.g. BONDS) to use in header of dump local file
- {nfile} arg = Nf
- Nf = write this many files, one from each of Nf processors
- {pad} arg = Nchar = # of characters to convert timestep to
- {precision} arg = power-of-10 value from 10 to 1000000
- {region} arg = region-ID or "none"
- {scale} arg = {yes} or {no}
- {sort} arg = {off} or {id} or N or -N
- off = no sorting of per-atom lines within a snapshot
- id = sort per-atom lines by atom ID
- N = sort per-atom lines in ascending order by the Nth column
- -N = sort per-atom lines in descending order by the Nth column
- {thresh} args = attribute operation value
- attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
- operation = "<" or "<=" or ">" or ">=" or "==" or "!="
- value = numeric value to compare to
- these 3 args can be replaced by the word "none" to turn off thresholding
- {unwrap} arg = {yes} or {no} :pre
+ R,G,B = red/green/blue numeric values from 0.0 to 1.0 :pre
+ {bitrate} rate = Target bitrate for movie from dump movie command in kbps.
+ {framerate} fps = Frames per second of the images to be converted to a movie.
:ule
[Examples:]
dump_modify 1 format "%d %d %20.15g %g %g" scale yes
dump_modify myDump image yes scale no flush yes
dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
dump_modify xtcdump precision 10000
dump_modify 1 every 1000 nfile 20
dump_modify 1 every v_myVar
dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red :pre
[Description:]
Modify the parameters of a previously defined dump command. Not all
parameters are relevant to all dump styles.
:line
-The {acolor} keyword applies only to the dump {image} style. It can
-be used with the "dump image"_dump_image.html command, when its atom
-color setting is {type}, to set the color that atoms of each type will
-be drawn in the image.
-
-The specified {type} should be an integer from 1 to Ntypes = the
-number of atom types. A wildcard asterisk can be used in place of or
-in conjunction with the {type} argument to specify a range of atom
-types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
-number of atom types, then an asterisk with no numeric values means
-all types from 1 to N. A leading asterisk means all types from 1 to n
-(inclusive). A trailing asterisk means all types from n to N
-(inclusive). A middle asterisk means all types from m to n
-(inclusive).
-
-The specified {color} can be a single color which is any of the 140
-pre-defined colors (see below) or a color name defined by the
-dump_modify color option. Or it can be two or more colors separated
-by a "/" character, e.g. red/green/blue. In the former case, that
-color is assigned to all the specified atom types. In the latter
-case, the list of colors are assigned in a round-robin fashion to each
-of the specified atom types.
-
-:line
-
-The {adiam} keyword applies only to the dump {image} style. It can be
-used with the "dump image"_dump_image.html command, when its atom
-diameter setting is {type}, to set the size that atoms of each type
-will be drawn in the image. The specified {type} should be an integer
-from 1 to Ntypes. As with the {acolor} keyword, a wildcard asterisk
-can be used as part of the {type} argument to specify a range of atomt
-types. The specified {diam} is the size in whatever distance
-"units"_units.html the input script is using, e.g. Angstroms.
-
-:line
-
-The {amap} keyword applies only to the dump {image} style. It can be
-used with the "dump image"_dump_image.html command, with its {atom}
-keyword, when its atom setting is an atom-attribute, to setup a color
-map. The color map is used to assign a specific RGB (red/green/blue)
-color value to an individual atom when it is drawn, based on the
-atom's attribute, which is a numeric value, e.g. its x-component of
-velocity if the atom-attribute "vx" was specified.
-
-The basic idea of a color map is that the atom-attribute will be
-within a range of values, and that range is associated with a a series
-of colors (e.g. red, blue, green). An atom's specific value (vx =
--3.2) can then mapped to the series of colors (e.g. halfway between
-red and blue), and a specific color is determined via an interpolation
-procedure.
-
-There are many possible options for the color map, enabled by the
-{amap} keyword. Here are the details.
-
-The {lo} and {hi} settings determine the range of values allowed for
-the atom attribute. If numeric values are used for {lo} and/or {hi},
-then values that are lower/higher than that value are set to the
-value. I.e. the range is static. If {lo} is specified as {min} or
-{hi} as {max} then the range is dynamic, and the lower and/or
-upper bound will be calculated each time an image is drawn, based
-on the set of atoms being visualized.
-
-The {style} setting is two letters, such as "ca". The first letter is
-either "c" for continuous, "d" for discrete, or "s" for sequential.
-The second letter is either "a" for absolute, or "f" for fractional.
-
-A continuous color map is one in which the color changes continuously
-from value to value within the range. A discrete color map is one in
-which discrete colors are assigned to sub-ranges of values within the
-range. A sequential color map is one in which discrete colors are
-assigned to a sequence of sub-ranges of values covering the entire
-range.
-
-An absolute color map is one in which the values to which colors are
-assigned are specified explicitly as values within the range. A
-fractional color map is one in which the values to which colors are
-assigned are specified as a fractional portion of the range. For
-example if the range is from -10.0 to 10.0, and the color red is to be
-assigned to atoms with a value of 5.0, then for an absolute color map
-the number 5.0 would be used. But for a fractional map, the number
-0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0.
-
-The {delta} setting must be specified for all styles, but is only used
-for the sequential style; otherwise the value is ignored. It
-specifies the bin size to use within the range for assigning
-consecutive colors to. For example, if the range is from -10.0 to
-10.0 and a {delta} of 1.0 is used, then 20 colors will be assigned to
-the range. The first will be from -10.0 <= color1 < -9.0, then 2nd
-from -9.0 <= color2 < -8.0, etc.
-
-The {N} setting is how many entries follow. The format of the entries
-depends on whether the color map style is continuous, discrete or
-sequential. In all cases the {color} setting can be any of the 140
-pre-defined colors (see below) or a color name defined by the
-dump_modify color option.
-
-For continuous color maps, each entry has a {value} and a {color}.
-The {value} is either a number within the range of values or {min} or
-{max}. The {value} of the first entry must be {min} and the {value}
-of the last entry must be {max}. Any entries in between must have
-increasing values. Note that numeric values can be specified either
-as absolute numbers or as fractions (0.0 to 1.0) of the range,
-depending on the "a" or "f" in the style setting for the color map.
-
-Here is how the entries are used to determine the color of an
-individual atom, given the value X of its atom attribute. X will fall
-between 2 of the entry values. The color of the atom is linearly
-interpolated (in each of the RGB values) between the 2 colors
-associated with those entries. For example, if X = -5.0 and the 2
-surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
-atom's color will be halfway between "red" and "blue", which happens
-to be "purple".
-
-For discrete color maps, each entry has a {lo} and {hi} value and a
-{color}. The {lo} and {hi} settings are either numbers within the
-range of values or {lo} can be {min} or {hi} can be {max}. The {lo}
-and {hi} settings of the last entry must be {min} and {max}. Other
-entries can have any {lo} and {hi} values and the sub-ranges of
-different values can overlap. Note that numeric {lo} and {hi} values
-can be specified either as absolute numbers or as fractions (0.0 to
-1.0) of the range, depending on the "a" or "f" in the style setting
-for the color map.
-
-Here is how the entries are used to determine the color of an
-individual atom, given the value X of its atom attribute. The entries
-are scanned from first to last. The first time that {lo} <= X <=
-{hi}, X is assigned the color associated with that entry. You can
-think of the last entry as assigning a default color (since it will
-always be matched by X), and the earlier entries as colors that
-override the default. Also note that no interpolation of a color RGB
-is done. All atoms will be drawn with one of the colors in the list
-of entries.
-
-For sequential color maps, each entry has only a {color}. Here is how
-the entries are used to determine the color of an individual atom,
-given the value X of its atom attribute. The range is partitioned
-into N bins of width {binsize}. Thus X will fall in a specific bin
-from 1 to N, say the Mth bin. If it falls on a boundary between 2
-bins, it is considered to be in the higher of the 2 bins. Each bin is
-assigned a color from the E entries. If E < N, then the colors are
-repeated. For example if 2 entries with colors red and green are
-specified, then the odd numbered bins will be red and the even bins
-green. The color of the atom is the color of its bin. Note that the
-sequential color map is really a shorthand way of defining a discrete
-color map without having to specify where all the bin boundaries are.
-
-:line
-
The {append} keyword applies to all dump styles except {cfg} and {xtc}
and {dcd}. It also applies only to text output files, not to binary
or gzipped files. If specified as {yes}, then dump snapshots are
appended to the end of an existing dump file. If specified as {no},
then a new dump file will be created which will overwrite an existing
file with the same name. This keyword can only take effect if the
dump_modify command is used after the "dump"_dump.html command, but
before the first command that causes dump snapshots to be output,
e.g. a "run"_run.html or "minimize"_minimize.html command. Once the
dump file has been opened, this keyword has no further effect.
:line
-The {bcolor} keyword applies only to the dump {image} style. It can
-be used with the "dump image"_dump_image.html command, with its {bond}
-keyword, when its color setting is {type}, to set the color that bonds
-of each type will be drawn in the image.
-
-The specified {type} should be an integer from 1 to Nbondtypes = the
-number of bond types. A wildcard asterisk can be used in place of or
-in conjunction with the {type} argument to specify a range of bond
-types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
-number of bond types, then an asterisk with no numeric values means
-all types from 1 to N. A leading asterisk means all types from 1 to n
-(inclusive). A trailing asterisk means all types from n to N
-(inclusive). A middle asterisk means all types from m to n
-(inclusive).
-
-The specified {color} can be a single color which is any of the 140
-pre-defined colors (see below) or a color name defined by the
-dump_modify color option. Or it can be two or more colors separated
-by a "/" character, e.g. red/green/blue. In the former case, that
-color is assigned to all the specified bond types. In the latter
-case, the list of colors are assigned in a round-robin fashion to each
-of the specified bond types.
-
-:line
-
-The {bdiam} keyword applies only to the dump {image} style. It can be
-used with the "dump image"_dump_image.html command, with its {bond}
-keyword, when its diam setting is {type}, to set the diameter that
-bonds of each type will be drawn in the image. The specified {type}
-should be an integer from 1 to Nbondtypes. As with the {bcolor}
-keyword, a wildcard asterisk can be used as part of the {type}
-argument to specify a range of bond types. The specified {diam} is
-the size in whatever distance "units"_units.html you are using,
-e.g. Angstroms.
-
-:line
-
-The {backcolor} keyword applies only to the dump {image} style. It
-sets the background color of the images. The color name can be any of
-the 140 pre-defined colors (see below) or a color name defined by the
-dump_modify color option.
-
-:line
-
-The {boxcolor} keyword applies only to the dump {image} style. It
-sets the color of the simulation box drawn around the atoms in each
-image. See the "dump image box" command for how to specify that a box
-be drawn. The color name can be any of the 140 pre-defined colors
-(see below) or a color name defined by the dump_modify color option.
-
-:line
-
-The {color} keyword applies only to the dump {image} style. It allows
-definition of a new color name, in addition to the 140-predefined
-colors (see below), and associates 3 red/green/blue RGB values with
-that color name. The color name can then be used with any other
-dump_modify keyword that takes a color name as a value. The RGB
-values should each be floating point values between 0.0 and 1.0
-inclusive.
-
-When a color name is converted to RGB values, the user-defined color
-names are searched first, then the 140 pre-defined color names. This
-means you can also use the {color} keyword to overwrite one of the
-pre-defined color names with new RBG values.
-
-:line
-
The {element} keyword applies only to the the dump {cfg}, {xyz}, and
{image} styles. It associates element names (e.g. H, C, Fe) with
LAMMPS atom types. See the list of element names at the bottom of
this page.
In the case of dump {cfg}, this allows the "AtomEye"_atomeye
visualization package to read the dump file and render atoms with the
appropriate size and color.
In the case of dump {image}, the output images will follow the same
"AtomEye"_atomeye convention. An element name is specified for each
atom type (1 to Ntype) in the simulation. The same element name can
be given to multiple atom types.
In the case of {xyz} format dumps, there are no restrictions to what
label can be used as an element name. Any whitespace separated text
will be accepted.
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
:line
The {every} keyword changes the dump frequency originally specified by
the "dump"_dump.html command to a new value. The every keyword can be
specified in one of two ways. It can be a numeric value in which case
it must be > 0. Or it can be an "equal-style variable"_variable.html,
which should be specified as v_name, where name is the variable name.
In this case, the variable is evaluated at the beginning of a run to
determine the next timestep at which a dump snapshot will be written
out. On that timestep the variable will be evaluated again to
determine the next timestep, etc. Thus the variable should return
timestep values. See the stagger() and logfreq() and stride() math
functions for "equal-style variables"_variable.html, as examples of
useful functions to use in this context. Other similar math functions
could easily be added as options for "equal-style
variables"_variable.html. Also see the next() function, which allows
use of a file-style variable which reads successive values from a
file, each time the variable is evaluated. Used with the {every}
keyword, if the file contains a list of ascending timesteps, you can
output snapshots whenever you wish.
Note that when using the variable option with the {every} keyword, you
need to use the {first} option if you want an initial snapshot written
to the dump file. The {every} keyword cannot be used with the dump
{dcd} style.
For example, the following commands will
write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
variable s equal logfreq(10,3,10)
dump 1 all atom 100 tmp.dump
dump_modify 1 every v_s first yes :pre
The following commands would write snapshots at the timesteps listed
in file tmp.times:
variable f file tmp.times
variable s equal next(f)
dump 1 all atom 100 tmp.dump
dump_modify 1 every v_s :pre
IMPORTANT NOTE: When using a file-style variable with the {every}
keyword, the file of timesteps must list a first timestep that is
beyond the current timestep (e.g. it cannot be 0). And it must list
one or more timesteps beyond the length of the run you perform. This
is because the dump command will generate an error if the next
timestep it reads from the file is not a value greater than the
current timestep. Thus if you wanted output on steps 0,15,100 of a
100-timestep run, the file should contain the values 15,100,101 and
you should also use the dump_modify first command. Any final value >
100 could be used in place of 101.
:line
The {first} keyword determines whether a dump snapshot is written on
the very first timestep after the dump command is invoked. This will
always occur if the current timestep is a multiple of N, the frequency
specified in the "dump"_dump.html command, including timestep 0. But
if this is not the case, a dump snapshot will only be written if the
setting of this keyword is {yes}. If it is {no}, which is the
default, then it will not be written.
:line
The {flush} keyword determines whether a flush operation is invoked
after a dump snapshot is written to the dump file. A flush insures
the output in that file is current (no buffering by the OS), even if
LAMMPS halts before the simulation completes. Flushes cannot be
performed with dump style {xtc}.
The text-based dump styles have a default C-style format string which
simply specifies %d for integers and %g for real values. The {format}
keyword can be used to override the default with a new C-style format
string. Do not include a trailing "\n" newline character in the
format string. This option has no effect on the {dcd} and {xtc} dump
styles since they write binary files. Note that for the {cfg} style,
the first two fields (atom id and type) are not actually written into
the CFG file, though you must include formats for them in the format
string.
The {fileper} keyword is documented below with the {nfile} keyword.
:line
The {image} keyword applies only to the dump {atom} style. If the
image value is {yes}, 3 flags are appended to each atom's coords which
are the absolute box image of the atom in each dimension. For
example, an x image flag of -2 with a normalized coord of 0.5 means
the atom is in the center of the box, but has passed thru the box
boundary 2 times and is really 2 box lengths to the left of its
current coordinate. Note that for dump style {custom} these various
values can be printed in the dump file by using the appropriate atom
attributes in the dump command itself.
:line
The {label} keyword applies only to the dump {local} style. When
it writes local informatoin, such as bond or angle topology
to a dump file, it will use the specified {label} to format
the header. By default this includes 2 lines:
ITEM: NUMBER OF ENTRIES
ITEM: ENTRIES ... :pre
The word "ENTRIES" will be replaced with the string specified,
e.g. BONDS or ANGLES.
:line
The {nfile} or {fileper} keywords can be used in conjunction with the
"%" wildcard character in the specified dump file name, for all dump
styles except the {dcd}, {xtc}, and {xyz} styles (for which "%" is not
allowed). As explained on the "dump"_dump.html command doc page, the
"%" character causes the dump file to be written in pieces, one piece
for each of P processors. By default P = the number of processors the
simulation is running on. The {nfile} or {fileper} keyword can be
used to set P to a smaller value, which can be more efficient when
running on a large number of processors.
The {nfile} keyword sets P to the specified Nf value. For example, if
Nf = 4, and the simulation is running on 100 processors, 4 files will
be written, by processors 0,25,50,75. Each will collect information
from itself and the next 24 processors and write it to a dump file.
For the {fileper} keyword, the specified value of Np means write one
file for every Np processors. For example, if Np = 4, every 4th
processor (0,4,8,12,etc) will collect information from itself and the
next 3 processors and write it to a dump file.
:line
The {pad} keyword only applies when the dump filename is specified
with a wildcard "*" character which becomes the timestep. If {pad} is
0, which is the default, the timestep is converted into a string of
unpadded length, e.g. 100 or 12000 or 2000000. When {pad} is
specified with {Nchar} > 0, the string is padded with leading zeroes
so they are all the same length = {Nchar}. For example, pad 7 would
yield 0000100, 0012000, 2000000. This can be useful so that
post-processing programs can easily read the files in ascending
timestep order.
:line
The {precision} keyword only applies to the dump {xtc} style. A
specified value of N means that coordinates are stored to 1/N
nanometer accuracy, e.g. for N = 1000, the coordinates are written to
1/1000 nanometer accuracy.
:line
The {region} keyword only applies to the dump {custom} and {cfg} and
{image} styles. If specified, only atoms in the region will be
written to the dump file or included in the image. Only one region
can be applied as a filter (the last one specified). See the
"region"_region.html command for more details. Note that a region can
be defined as the "inside" or "outside" of a geometric shape, and it
can be the "union" or "intersection" of a series of simpler regions.
:line
The {scale} keyword applies only to the dump {atom} style. A scale
value of {yes} means atom coords are written in normalized units from
0.0 to 1.0 in each box dimension. If the simluation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0. A
value of {no} means they are written in absolute distance units
(e.g. Angstroms or sigma).
:line
The {sort} keyword determines whether lines of per-atom output in a
snapshot are sorted or not. A sort value of {off} means they will
typically be written in indeterminate order, either in serial or
parallel. This is the case even in serial if the "atom_modify
sort"_atom_modify.html option is turned on, which it is by default, to
improve performance. A sort value of {id} means sort the output by
atom ID. A sort value of N or -N means sort the output by the value
in the Nth column of per-atom info in either ascending or descending
order.
The dump {local} style cannot be sorted by atom ID, since there are
typically multiple lines of output per atom. Some dump styles, such
as {dcd} and {xtc}, require sorting by atom ID to format the output
file correctly. If multiple processors are writing the dump file, via
the "%" wildcard in the dump filename, then sorting cannot be
performed.
IMPORTANT NOTE: Unless it is required by the dump style, sorting dump
file output requires extra overhead in terms of CPU and communication
cost, as well as memory, versus unsorted output.
:line
The {thresh} keyword only applies to the dump {custom} and {cfg} and
{image} styles. Multiple thresholds can be specified. Specifying
"none" turns off all threshold criteria. If thresholds are specified,
only atoms whose attributes meet all the threshold criteria are
written to the dump file or included in the image. The possible
attributes that can be tested for are the same as those that can be
specified in the "dump custom"_dump.html command, with the exception
of the {element} attribute, since it is not a numeric value. Note
that different attributes can be output by the dump custom command
than are used as threshold criteria by the dump_modify command.
E.g. you can output the coordinates and stress of atoms whose energy
is above some threshold.
:line
The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles.
If set to {yes}, coordinates will be written "unwrapped" by the image
flags for each atom. Unwrapped means that if the atom has passed thru
a periodic boundary one or more times, the value is printed for what
the coordinate would be if it had not been wrapped back into the
periodic box. Note that these coordinates may thus be far outside the
box size stored with the snapshot.
:line
+The {acolor} keyword applies only to the dump {image} style. It can
+be used with the "dump image"_dump_image.html command, when its atom
+color setting is {type}, to set the color that atoms of each type will
+be drawn in the image.
+
+The specified {type} should be an integer from 1 to Ntypes = the
+number of atom types. A wildcard asterisk can be used in place of or
+in conjunction with the {type} argument to specify a range of atom
+types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
+number of atom types, then an asterisk with no numeric values means
+all types from 1 to N. A leading asterisk means all types from 1 to n
+(inclusive). A trailing asterisk means all types from n to N
+(inclusive). A middle asterisk means all types from m to n
+(inclusive).
+
+The specified {color} can be a single color which is any of the 140
+pre-defined colors (see below) or a color name defined by the
+dump_modify color option. Or it can be two or more colors separated
+by a "/" character, e.g. red/green/blue. In the former case, that
+color is assigned to all the specified atom types. In the latter
+case, the list of colors are assigned in a round-robin fashion to each
+of the specified atom types.
+
+:line
+
+The {adiam} keyword applies only to the dump {image} style. It can be
+used with the "dump image"_dump_image.html command, when its atom
+diameter setting is {type}, to set the size that atoms of each type
+will be drawn in the image. The specified {type} should be an integer
+from 1 to Ntypes. As with the {acolor} keyword, a wildcard asterisk
+can be used as part of the {type} argument to specify a range of atomt
+types. The specified {diam} is the size in whatever distance
+"units"_units.html the input script is using, e.g. Angstroms.
+
+:line
+
+The {amap} keyword applies only to the dump {image} style. It can be
+used with the "dump image"_dump_image.html command, with its {atom}
+keyword, when its atom setting is an atom-attribute, to setup a color
+map. The color map is used to assign a specific RGB (red/green/blue)
+color value to an individual atom when it is drawn, based on the
+atom's attribute, which is a numeric value, e.g. its x-component of
+velocity if the atom-attribute "vx" was specified.
+
+The basic idea of a color map is that the atom-attribute will be
+within a range of values, and that range is associated with a a series
+of colors (e.g. red, blue, green). An atom's specific value (vx =
+-3.2) can then mapped to the series of colors (e.g. halfway between
+red and blue), and a specific color is determined via an interpolation
+procedure.
+
+There are many possible options for the color map, enabled by the
+{amap} keyword. Here are the details.
+
+The {lo} and {hi} settings determine the range of values allowed for
+the atom attribute. If numeric values are used for {lo} and/or {hi},
+then values that are lower/higher than that value are set to the
+value. I.e. the range is static. If {lo} is specified as {min} or
+{hi} as {max} then the range is dynamic, and the lower and/or
+upper bound will be calculated each time an image is drawn, based
+on the set of atoms being visualized.
+
+The {style} setting is two letters, such as "ca". The first letter is
+either "c" for continuous, "d" for discrete, or "s" for sequential.
+The second letter is either "a" for absolute, or "f" for fractional.
+
+A continuous color map is one in which the color changes continuously
+from value to value within the range. A discrete color map is one in
+which discrete colors are assigned to sub-ranges of values within the
+range. A sequential color map is one in which discrete colors are
+assigned to a sequence of sub-ranges of values covering the entire
+range.
+
+An absolute color map is one in which the values to which colors are
+assigned are specified explicitly as values within the range. A
+fractional color map is one in which the values to which colors are
+assigned are specified as a fractional portion of the range. For
+example if the range is from -10.0 to 10.0, and the color red is to be
+assigned to atoms with a value of 5.0, then for an absolute color map
+the number 5.0 would be used. But for a fractional map, the number
+0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0.
+
+The {delta} setting must be specified for all styles, but is only used
+for the sequential style; otherwise the value is ignored. It
+specifies the bin size to use within the range for assigning
+consecutive colors to. For example, if the range is from -10.0 to
+10.0 and a {delta} of 1.0 is used, then 20 colors will be assigned to
+the range. The first will be from -10.0 <= color1 < -9.0, then 2nd
+from -9.0 <= color2 < -8.0, etc.
+
+The {N} setting is how many entries follow. The format of the entries
+depends on whether the color map style is continuous, discrete or
+sequential. In all cases the {color} setting can be any of the 140
+pre-defined colors (see below) or a color name defined by the
+dump_modify color option.
+
+For continuous color maps, each entry has a {value} and a {color}.
+The {value} is either a number within the range of values or {min} or
+{max}. The {value} of the first entry must be {min} and the {value}
+of the last entry must be {max}. Any entries in between must have
+increasing values. Note that numeric values can be specified either
+as absolute numbers or as fractions (0.0 to 1.0) of the range,
+depending on the "a" or "f" in the style setting for the color map.
+
+Here is how the entries are used to determine the color of an
+individual atom, given the value X of its atom attribute. X will fall
+between 2 of the entry values. The color of the atom is linearly
+interpolated (in each of the RGB values) between the 2 colors
+associated with those entries. For example, if X = -5.0 and the 2
+surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
+atom's color will be halfway between "red" and "blue", which happens
+to be "purple".
+
+For discrete color maps, each entry has a {lo} and {hi} value and a
+{color}. The {lo} and {hi} settings are either numbers within the
+range of values or {lo} can be {min} or {hi} can be {max}. The {lo}
+and {hi} settings of the last entry must be {min} and {max}. Other
+entries can have any {lo} and {hi} values and the sub-ranges of
+different values can overlap. Note that numeric {lo} and {hi} values
+can be specified either as absolute numbers or as fractions (0.0 to
+1.0) of the range, depending on the "a" or "f" in the style setting
+for the color map.
+
+Here is how the entries are used to determine the color of an
+individual atom, given the value X of its atom attribute. The entries
+are scanned from first to last. The first time that {lo} <= X <=
+{hi}, X is assigned the color associated with that entry. You can
+think of the last entry as assigning a default color (since it will
+always be matched by X), and the earlier entries as colors that
+override the default. Also note that no interpolation of a color RGB
+is done. All atoms will be drawn with one of the colors in the list
+of entries.
+
+For sequential color maps, each entry has only a {color}. Here is how
+the entries are used to determine the color of an individual atom,
+given the value X of its atom attribute. The range is partitioned
+into N bins of width {binsize}. Thus X will fall in a specific bin
+from 1 to N, say the Mth bin. If it falls on a boundary between 2
+bins, it is considered to be in the higher of the 2 bins. Each bin is
+assigned a color from the E entries. If E < N, then the colors are
+repeated. For example if 2 entries with colors red and green are
+specified, then the odd numbered bins will be red and the even bins
+green. The color of the atom is the color of its bin. Note that the
+sequential color map is really a shorthand way of defining a discrete
+color map without having to specify where all the bin boundaries are.
+
+:line
+
+The {bcolor} keyword applies only to the dump {image} style. It can
+be used with the "dump image"_dump_image.html command, with its {bond}
+keyword, when its color setting is {type}, to set the color that bonds
+of each type will be drawn in the image.
+
+The specified {type} should be an integer from 1 to Nbondtypes = the
+number of bond types. A wildcard asterisk can be used in place of or
+in conjunction with the {type} argument to specify a range of bond
+types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
+number of bond types, then an asterisk with no numeric values means
+all types from 1 to N. A leading asterisk means all types from 1 to n
+(inclusive). A trailing asterisk means all types from n to N
+(inclusive). A middle asterisk means all types from m to n
+(inclusive).
+
+The specified {color} can be a single color which is any of the 140
+pre-defined colors (see below) or a color name defined by the
+dump_modify color option. Or it can be two or more colors separated
+by a "/" character, e.g. red/green/blue. In the former case, that
+color is assigned to all the specified bond types. In the latter
+case, the list of colors are assigned in a round-robin fashion to each
+of the specified bond types.
+
+:line
+
+The {bdiam} keyword applies only to the dump {image} style. It can be
+used with the "dump image"_dump_image.html command, with its {bond}
+keyword, when its diam setting is {type}, to set the diameter that
+bonds of each type will be drawn in the image. The specified {type}
+should be an integer from 1 to Nbondtypes. As with the {bcolor}
+keyword, a wildcard asterisk can be used as part of the {type}
+argument to specify a range of bond types. The specified {diam} is
+the size in whatever distance "units"_units.html you are using,
+e.g. Angstroms.
+
+:line
+
+The {backcolor} keyword applies only to the dump {image} style. It
+sets the background color of the images. The color name can be any of
+the 140 pre-defined colors (see below) or a color name defined by the
+dump_modify color option.
+
+:line
+
+The {boxcolor} keyword applies only to the dump {image} style. It
+sets the color of the simulation box drawn around the atoms in each
+image. See the "dump image box" command for how to specify that a box
+be drawn. The color name can be any of the 140 pre-defined colors
+(see below) or a color name defined by the dump_modify color option.
+
+:line
+
+The {color} keyword applies only to the dump {image} style. It allows
+definition of a new color name, in addition to the 140-predefined
+colors (see below), and associates 3 red/green/blue RGB values with
+that color name. The color name can then be used with any other
+dump_modify keyword that takes a color name as a value. The RGB
+values should each be floating point values between 0.0 and 1.0
+inclusive.
+
+When a color name is converted to RGB values, the user-defined color
+names are searched first, then the 140 pre-defined color names. This
+means you can also use the {color} keyword to overwrite one of the
+pre-defined color names with new RBG values.
+
+:line
+
+The {bitrate} keyword applies only to the dump {movie} style. It can
+be used with the "dump movie"_dump_movie.html command to define the
+size of the resulting movie file and its quality via setting how many
+kbits per second are to be used for the movie file. Higher bitrates
+require less compression and will result in higher quality movies.
+The quality is also determined by the compression format and encoder.
+The default setting is 2000 kbit/s, which will result in average
+quality with older compression formats. NOTE: not all movie file
+formats supported by dump movie allow to set the bitrate. If not
+the setting is silently ignored.
+
+:line
+
+The {framerate} keyword applies only to the dump {movie} style. It can
+be used with the "dump movie"_dump_movie.html command to define the
+duration of the resulting movie file. Movie files written by the dump
+{movie} command have a fixed frame rate of 24 frames per second and
+the images generated will be converted at that rate. Thus a sequence
+of 1000 dump images will result in a movie of about 42 seconds. To
+make a movie run longer you can either generate images more frequently
+or lower the frame rate. To speed a movie up, you can do the inverse.
+Using a frame rate higher than 24 is not recommended, as it will
+result in simply dropping the rendered images. It is more efficient
+to dump images less frequently.
+
+:line
+
[Restrictions:] none
[Related commands:]
"dump"_dump.html, "dump image"_dump_image.html, "undump"_undump.html
[Default:]
The option defaults are
acolor = * red/green/blue/yellow/aqua/cyan
adiam = * 1.0
amap = min max cf 0.0 2 min blue max red
append = no
bcolor = * red/green/blue/yellow/aqua/cyan
bdiam = * 0.5
backcolor = black
boxcolor = yellow
color = 140 color names are pre-defined as listed below
element = "C" for every atom type
every = whatever it was set to via the "dump"_dump.html command
first = no
flush = yes
format = %d and %g for each integer or floating point value
image = no
label = ENTRIES
pad = 0
precision = 1000
region = none
scale = yes
sort = off for dump styles {atom}, {custom}, {cfg}, and {local}
sort = id for dump styles {dcd}, {xtc}, and {xyz}
thresh = none
unwrap = no :ul
:line
These are the standard 109 element names that LAMMPS pre-defines for
use with the "dump image"_dump_image.html and dump_modify commands.
1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne"
11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca"
21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn"
31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr"
41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn"
51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd"
61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb"
71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg"
81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th"
91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm"
101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt" :ul
:line
These are the 140 colors that LAMMPS pre-defines for use with the
"dump image"_dump_image.html and dump_modify commands. Additional
colors can be defined with the dump_modify color command. The 3
numbers listed for each name are the RGB (red/green/blue) values.
Divide each value by 255 to get the equivalent 0.0 to 1.0 value.
aliceblue = 240, 248, 255 |
antiquewhite = 250, 235, 215 |
aqua = 0, 255, 255 |
aquamarine = 127, 255, 212 |
azure = 240, 255, 255 |
beige = 245, 245, 220 |
bisque = 255, 228, 196 |
black = 0, 0, 0 |
blanchedalmond = 255, 255, 205 |
blue = 0, 0, 255 |
blueviolet = 138, 43, 226 |
brown = 165, 42, 42 |
burlywood = 222, 184, 135 |
cadetblue = 95, 158, 160 |
chartreuse = 127, 255, 0 |
chocolate = 210, 105, 30 |
coral = 255, 127, 80 |
cornflowerblue = 100, 149, 237 |
cornsilk = 255, 248, 220 |
crimson = 220, 20, 60 |
cyan = 0, 255, 255 |
darkblue = 0, 0, 139 |
darkcyan = 0, 139, 139 |
darkgoldenrod = 184, 134, 11 |
darkgray = 169, 169, 169 |
darkgreen = 0, 100, 0 |
darkkhaki = 189, 183, 107 |
darkmagenta = 139, 0, 139 |
darkolivegreen = 85, 107, 47 |
darkorange = 255, 140, 0 |
darkorchid = 153, 50, 204 |
darkred = 139, 0, 0 |
darksalmon = 233, 150, 122 |
darkseagreen = 143, 188, 143 |
darkslateblue = 72, 61, 139 |
darkslategray = 47, 79, 79 |
darkturquoise = 0, 206, 209 |
darkviolet = 148, 0, 211 |
deeppink = 255, 20, 147 |
deepskyblue = 0, 191, 255 |
dimgray = 105, 105, 105 |
dodgerblue = 30, 144, 255 |
firebrick = 178, 34, 34 |
floralwhite = 255, 250, 240 |
forestgreen = 34, 139, 34 |
fuchsia = 255, 0, 255 |
gainsboro = 220, 220, 220 |
ghostwhite = 248, 248, 255 |
gold = 255, 215, 0 |
goldenrod = 218, 165, 32 |
gray = 128, 128, 128 |
green = 0, 128, 0 |
greenyellow = 173, 255, 47 |
honeydew = 240, 255, 240 |
hotpink = 255, 105, 180 |
indianred = 205, 92, 92 |
indigo = 75, 0, 130 |
ivory = 255, 240, 240 |
khaki = 240, 230, 140 |
lavender = 230, 230, 250 |
lavenderblush = 255, 240, 245 |
lawngreen = 124, 252, 0 |
lemonchiffon = 255, 250, 205 |
lightblue = 173, 216, 230 |
lightcoral = 240, 128, 128 |
lightcyan = 224, 255, 255 |
lightgoldenrodyellow = 250, 250, 210 |
lightgreen = 144, 238, 144 |
lightgrey = 211, 211, 211 |
lightpink = 255, 182, 193 |
lightsalmon = 255, 160, 122 |
lightseagreen = 32, 178, 170 |
lightskyblue = 135, 206, 250 |
lightslategray = 119, 136, 153 |
lightsteelblue = 176, 196, 222 |
lightyellow = 255, 255, 224 |
lime = 0, 255, 0 |
limegreen = 50, 205, 50 |
linen = 250, 240, 230 |
magenta = 255, 0, 255 |
maroon = 128, 0, 0 |
mediumaquamarine = 102, 205, 170 |
mediumblue = 0, 0, 205 |
mediumorchid = 186, 85, 211 |
mediumpurple = 147, 112, 219 |
mediumseagreen = 60, 179, 113 |
mediumslateblue = 123, 104, 238 |
mediumspringgreen = 0, 250, 154 |
mediumturquoise = 72, 209, 204 |
mediumvioletred = 199, 21, 133 |
midnightblue = 25, 25, 112 |
mintcream = 245, 255, 250 |
mistyrose = 255, 228, 225 |
moccasin = 255, 228, 181 |
navajowhite = 255, 222, 173 |
navy = 0, 0, 128 |
oldlace = 253, 245, 230 |
olive = 128, 128, 0 |
olivedrab = 107, 142, 35 |
orange = 255, 165, 0 |
orangered = 255, 69, 0 |
orchid = 218, 112, 214 |
palegoldenrod = 238, 232, 170 |
palegreen = 152, 251, 152 |
paleturquoise = 175, 238, 238 |
palevioletred = 219, 112, 147 |
papayawhip = 255, 239, 213 |
peachpuff = 255, 239, 213 |
peru = 205, 133, 63 |
pink = 255, 192, 203 |
plum = 221, 160, 221 |
powderblue = 176, 224, 230 |
purple = 128, 0, 128 |
red = 255, 0, 0 |
rosybrown = 188, 143, 143 |
royalblue = 65, 105, 225 |
saddlebrown = 139, 69, 19 |
salmon = 250, 128, 114 |
sandybrown = 244, 164, 96 |
seagreen = 46, 139, 87 |
seashell = 255, 245, 238 |
sienna = 160, 82, 45 |
silver = 192, 192, 192 |
skyblue = 135, 206, 235 |
slateblue = 106, 90, 205 |
slategray = 112, 128, 144 |
snow = 255, 250, 250 |
springgreen = 0, 255, 127 |
steelblue = 70, 130, 180 |
tan = 210, 180, 140 |
teal = 0, 128, 128 |
thistle = 216, 191, 216 |
tomato = 253, 99, 71 |
turquoise = 64, 224, 208 |
violet = 238, 130, 238 |
wheat = 245, 222, 179 |
white = 255, 255, 255 |
whitesmoke = 245, 245, 245 |
yellow = 255, 255, 0 |
yellowgreen = 154, 205, 50 :tb(c=5,s=|)
diff --git a/lammps.book b/lammps.book
index a47993d2d..77e05a3be 100644
--- a/lammps.book
+++ b/lammps.book
@@ -1,401 +1,401 @@
#HTMLDOC 1.8.27
-t pdf14 -f "lammps.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=1 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont helvetica --bodyfont times --headfootsize 11.0 --headfootfont helvetica --charset iso-8859-1 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow
doc/Manual.html
doc/Section_intro.html
doc/Section_start.html
doc/Section_commands.html
doc/Section_packages.html
doc/Section_accelerate.html
doc/Section_howto.html
doc/Section_example.html
doc/Section_perf.html
doc/Section_tools.html
doc/Section_modify.html
doc/Section_python.html
doc/Section_errors.html
doc/Section_history.html
doc/balance.html
doc/box.html
doc/boundary.html
doc/change_box.html
doc/clear.html
doc/communicate.html
doc/create_atoms.html
doc/create_box.html
doc/delete_atoms.html
doc/delete_bonds.html
doc/dielectric.html
doc/dimension.html
doc/displace_atoms.html
doc/echo.html
doc/group.html
doc/group2ndx.html
doc/if.html
doc/include.html
doc/jump.html
doc/label.html
doc/lattice.html
doc/log.html
doc/mass.html
doc/minimize.html
doc/min_style.html
doc/min_modify.html
doc/neb.html
doc/neighbor.html
doc/neigh_modify.html
doc/newton.html
doc/next.html
doc/package.html
doc/partition.html
doc/prd.html
doc/print.html
doc/processors.html
doc/quit.html
doc/region.html
doc/replicate.html
doc/reset_timestep.html
doc/run.html
doc/run_style.html
doc/set.html
doc/shell.html
doc/special_bonds.html
doc/suffix.html
doc/tad.html
doc/temper.html
doc/thermo.html
doc/thermo_style.html
doc/thermo_modify.html
doc/timestep.html
doc/timers.html
doc/units.html
doc/variable.html
doc/velocity.html
doc/read_data.html
doc/write_data.html
doc/restart.html
doc/read_restart.html
doc/write_restart.html
doc/dump.html
doc/undump.html
doc/dump_modify.html
-doc/dump_image.html
doc/dump_molfile.html
doc/read_dump.html
doc/write_dump.html
doc/rerun.html
+doc/dump_image.html
doc/atom_style.html
doc/body.html
doc/atom_modify.html
doc/bond_style.html
doc/angle_style.html
doc/dihedral_style.html
doc/improper_style.html
doc/kspace_style.html
doc/kspace_modify.html
doc/fix.html
doc/unfix.html
doc/fix_modify.html
doc/fix_adapt.html
doc/fix_addforce.html
doc/fix_addtorque.html
doc/fix_append_atoms.html
doc/fix_atc.html
doc/fix_ave_atom.html
doc/fix_ave_correlate.html
doc/fix_ave_histo.html
doc/fix_ave_spatial.html
doc/fix_ave_time.html
doc/fix_aveforce.html
doc/fix_balance.html
doc/fix_bond_break.html
doc/fix_bond_create.html
doc/fix_bond_swap.html
doc/fix_box_relax.html
doc/fix_colvars.html
doc/fix_countdown.html
doc/fix_deform.html
doc/fix_deposit.html
doc/fix_drag.html
doc/fix_dt_reset.html
doc/fix_efield.html
doc/fix_enforce2d.html
doc/fix_evaporate.html
doc/fix_external.html
doc/fix_freeze.html
doc/fix_gcmc.html
doc/fix_gld.html
doc/fix_gravity.html
doc/fix_heat.html
doc/fix_imd.html
doc/fix_indent.html
doc/fix_langevin.html
doc/fix_langevin_eff.html
doc/fix_lineforce.html
doc/fix_meso.html
doc/fix_meso_stationary.html
doc/fix_momentum.html
doc/fix_move.html
doc/fix_msst.html
doc/fix_neb.html
doc/fix_nh.html
doc/fix_nh_eff.html
doc/fix_nph_asphere.html
doc/fix_nph_sphere.html
doc/fix_nphug.html
doc/fix_npt_asphere.html
doc/fix_npt_sphere.html
doc/fix_nve.html
doc/fix_nve_eff.html
doc/fix_nve_asphere.html
doc/fix_nve_asphere_noforce.html
doc/fix_nve_body.html
doc/fix_nve_limit.html
doc/fix_nve_line.html
doc/fix_nve_noforce.html
doc/fix_nve_sphere.html
doc/fix_nve_tri.html
doc/fix_nvt_asphere.html
doc/fix_nvt_sllod.html
doc/fix_nvt_sllod_eff.html
doc/fix_nvt_sphere.html
doc/fix_orient_fcc.html
doc/fix_phonon.html
doc/fix_planeforce.html
doc/fix_poems.html
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